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think forward - UC Davis Nuclear Magnetic Resonance Facility

1. TOPSPIN Interface Processes Send the dataset by email Note that the Close button and Tips switch are automatically created You don t need to specify them The TOGGLE button is typically but not necessarily used to call another button panel In this example it calls the panel bproc2d items must be separated with the character button items with a followed by end of line continues an item on the next line tooltips may use html tags for text formatting commands may be specified as single commands like em or as composite commands like em nft npk Note that in the latter case the commands must be separated by n INPUT FILES lt userhome gt lt topspin hostname gt prop userde fined cmdpanel_ lt name gt prop SEE ALSO bnmr P 571 TOPSPIN Interface Processes cmdindex NAME cmdindex Open the command index DESCRIPTION The command cmdindex opens a command index dialog box see Fig ure 13 3 Command Index A B C D E F G H I A abs1 Automatic baseline correction in F1 2D abs2 Automatic baseline correction in F2 2D absd Automatic baseline correction special algorithm 1D absd1 Autom baseline corr in F1 diff algorithm 2D absd2 Autom baseline corr in F2 diff algorithm 2D absf Automatic baseline correction of the plot region 1D absot1 Autom sel basel corr in F1 diff algorithm 2D absot2 Autom sel basel corr i
2. C bio data guest nmr examld_13C 1 pdata 1 C bio data guest nmr examld_13C 2 pdata 1 C bio data guest nmr examld_13C 3 pdata 1 The Next button in the dialog allows you to go to the next dialog see Figure 11 11 where you can specify the command s macro or Python program to be executed The functions of the buttons are described in the dialog The Browse button not only allow you to browse for macros Python pro grams but also to create new ones Clicking the Execute button will actually start the execution Automation Serial Processing Define Command Please define the command to be executed on the datasets Examples 1 efp 2 Ib 0 8 em ftipk 3 cimymacrosimac efp a full path indicates a macro 4 cimypys py efp py a full path with py indicates a Python script Click on gt Browse For Macro locate a TopSpin macro gt Browse For Python locate a TopSpin Python program gt Execute start processing the dataset list gt Back return to list definition gt Show show datsets while processing Figure 11 11 An example of a simple processing sequence is exponential window multi plication Fourier transform and automatic phase correction of a 1D data set A TOPSPIN macro performing this task would be ef apk A Python programs performing the same task would be EF APK Note that Python programs are much more versatile than macros Details on Python
3. USAGE IN AU PROGRAMS XIF2 XIF 1 SEE ALSO genser xtrfp xtrfp2 xtrfp1 P 253 2D processing commands P 254 NAME xtrf xtrf2 xtrf Custom processing of raw data in F2 and F1 2D xtrf2 Custom processing of raw data in F2 2D DESCRIPTION The command xtrf performs customized processing of the raw data in both the F2 and F1 direction It processes data according to the process ing parameters BC_mod WDW ME_mod FT_mod and PH_mod xtrf works like xfb except for the following differences the Fourier transform is performed according to the processing parameter FT_mod whereas the acquisition status parameter AQ_mod is ignored This for example allows you to process the data without Fourier transform FT_mod no Furthermore you can choose a Fourier transform mode different from the one that would be evaluated from the acquisition mode This feature is not used very often because the Fourier transform as evaluated from the acquisition mode is usually the correct one If however you want to manipulate the acquisition mode of the raw data you can Fourier transform the data with one FT_mod inverse Fourier transform them with a different FT_mod Then you can use genser to create pseudo raw data with a different acquisition 2D processing commands mode than the original raw data Table 4 8 shows a list of values of FT_mod FT_mod Fourier transform mode no no Fourier transform fsr f
4. int2d int3d int NAME int2d Calculate integrals 2D int3d Calculate integrals 2D int Open integral dialog box 1D 2D 3D DESCRIPTION The command int2d calculates 2D integrals It opens the following dia log box amp Integration int2d Parameters relative absolute Minimum threshold Ml 0 0040 222784 Setto P Start manual integration Figure 8 4 Here you can set the minimum threshold for integration You can enter Enter the relative intensity value between 0 0 and 1 0 e Enter the absolute intensity value between 0 0 and YMax_p processing status parameter e Click the Set to button and choose from one of the following options lowest contour level value of the lowest contour level see edlev value stored in MI value of the processing parameter MI see edp most recent MI used value used by last int2d command on any dataset If you enter a relative value the absolute value is automatically adjusted and vice versa Setting the most recent MI used allows you to compare P 377 Analysis commands integral value e g of the NOE peak of a series of 2D spectra Obviously this only makes sense for spectra that are measured and processing un der similar conditions The calculated integrals will be marked in the data field and can be listed by clicking the Integrals tab int3d is the same as int2d except that it works on 3D data The int command can be used on 1D
5. 04 P 9 TOPSPIN parameters 0 20 cece eee eee P 15 2 1 About TOPSPIN parameters 00 000 eee eee P 15 2 2 Parameter valueS 0600 08 bebe eed eee eee tees P 17 2 3 Parameter fileS sisira a Ae Ae ee eee eee es P 18 2 4 List of processing parameters 00 ee eee eee P 19 2 5 Processing status parameters 0 0 0 0 e eee eee P 40 2 6 Relaxation parameters 000 0c eee eee eens P 47 1D Processing commands 00 eee eee eee eee P 51 2D processing commands 0 0c e eee eee eee P 143 3D processing commands 00 e cece eee eee eee P 265 nD processing commands eee cece eee e eee eee P 311 Print Export commands 0000 eee eee eee eee P 347 Analysis commands 000 e eee eee eee eee P 371 Dataset handling 6 00 cece ee eee eee P 415 Parameters lists AU programs 0 20e0005 P 461 Automation ossi raris i aa ees ae tee ae eee ee ea P 501 Conversion commands 00 c cece eee eee eens P 533 TOPSPIN Interface ProceSSeS 0 ccc cece eee P 567 TOPSPIN User Management 00 0c cece e eee teens P 597 Index Chapter 1 Introduction 1 1 About this manual This manual is a reference to TOPSPIN processing commands and parame ters Every command is described on a separate page with its syntax and function as well and its main input output files and input output parameters Most of them are processing comma
6. DESCRIPTION The command rser2d reads a plane from 3D raw data a series of FIDs and stores it as a pseudo raw 2D dataset When entered without argu ments it opens the following dialog box amp Rows amp columns rsr Options Interactive row column display Extract a spectrum row D Extract a spectrum column D Extract a row from raw data D Replace a spectrum row D Replace a spectrum column D Replace a row in raw data by a fid D Replace a row in raw data by processed data Required parameters Row column number 1 Source PROCNO 999 Destination PROCNO 999 Source EXPNO 999 Destination EXPNO 999 Cancel Help Figure 5 4 Here you can specify three required parameters Plane orientation F1 F3 or F2 F3 must contain acquisition F3 direc tion P 284 3D processing commands Plane number the maximum plane number is the TD value in the direc tion orthogonal to the plane orientation Destination EXPNO the expno where the output 2D dataset is stored The parameters can also be entered as arguments on the command line In that case the command is executed without opening the dialog box For example rser2d s23 10 999 reads an F3 F2 plane number 10 and stores it in expno 999 In contrast to rser rser2d can only be entered on the source dataset not on the destination dataset INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser 3D
7. Note that the order of the arguments in AU programs is different from the P 207 2D processing commands order on the command line SEE ALSO wserp rser rser2d wsr wsc rsr rsc slice P 208 2D processing commands wserp NAME wserp Replace row of 2D raw data by 1D processed data SYNTAX wserp lt row gt lt expno gt DESCRIPTION The command wserp replaces one row of 2D raw data by processed 1D data It can be entered on the source 1D dataset or on the destination 2D dataset When entered on a 1D dataset wserp opens the following dia log box Please specify destination Fine J NAME EXPNO PROCNO DIR USER igure 4 20 Here you can enter the FID number to be replaced and the destination data path Usage of wserp with arguments on the source 1D dataset wserp lt row gt the specified row of the 2D raw data is replaced by the current 1D processed data The 2D dataset is the one from which the current 1D dataset was extracted wserp lt row gt lt expno gt P 209 2D processing commands the specified row of the 2D raw data under the specified expno is re placed by the current 1D processed data The 2D dataset name user and dir are the same as in the dataset as the current 1D data were ex tracted from Usage of wserp with arguments on the destination 2D dataset wserp lt row gt lt expno gt the specified row of the current 2D raw data is replaced The sour
8. noise Figure 8 13 sino internally performs a peak picking to determine the highest peak in the signal region The result of sino appears on the screen for example ty sino NOISF1 208 699 NOISF2 184 184 SIG F1 173 592 SIG F2 4 119 Signal 22 761 ppm Noise 2762581 64 371167 2 SINO 372 15 Figure 8 14 sino noprint does not show the result on the screen The noprint op tion is automatically set when sino is part of an AU program The result of sino is also stored in the processing status parameter SINO which can be viewed with s sino or dpp sino real skips the magnitude calculation and works on the real data Note that sino without argument first performs a magnitude calculation P 406 Analysis commands and then calculates the signal to noise ratio on the magnitude data The parameter SINO exists as processing parameter edp and as processing status parameter dpp and they have different functions The latter is used to store the result of the command sino as discussed above The former can be used to specify a signal to noise ratio which must be reached in an acquisition see the parameter SINO in chapter 2 4 and the AU program au_zgsino INPUT PARAMETERS setin sino display mode with edp or by typing noisf1 noisef2 etc NOISF1 low field left limit of the noise region NOISF2 high field right limit of the noise region SIGF1 low field left limit of the signal region SIGF2 hi
9. 4 Figure 6 1 absnd subtracts a polynomial the degree of which is determined by the parameter ABSG which has a value between 0 and 5 with a default of 5 It only corrects a certain spectral region which is determined by the pa rameters ABSF1 and ABSF2 absnd actually processes 2D planes of an nD dataset performing a se ries of abs2 or abs1 commands On 3D data the commands absnd 3 absnd 2 and absnd 1 are equivalent to tabs3 tabs2 and tabs1 re spectively INPUT PARAMETERS Acquisition direction set by the user with edp or by typing absg ABSG degree of the polynomial to be subtracted 0 to 5 default of 5 All directions nD processing commands set by the user with edp or by typing absf1 absf2 ABSF 1 low field limit of the correction region ABSF2 high field limit of the correction region INPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr processed 4D data proc F4 processing parameters proc2 F3 processing parameters proc3 F2 processing parameters proc4 F1 processing parameters For 3D data the input data file is 3rrr whereas the proc4 does not ex ist For data of dimension n where n gt 5 input data files are named nr and ni e g 5r 5i 6r 6i etc OUTPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr processed 4D data procs F4 processing status
10. D1 m s 1e 009 Diffusion coefficient Dimin m s 0 Minimum diffusion coefficient D1 max m s 1e 008 Maximum diffusion coefficient Second component W Fit intensity Intensity Figure 10 2 These parameters are used by the command dosy2d and dosy3d on 2D and 3D data respectively The following buttons are available Undo the last modification Can be used repeatedly P 464 Parameters lists AU programs P Switch to processing parameters G Switch to Gifa parameters iq Copy parameters from experiment AU program setdiffparm J Get display limits from dataset Execute Fourier Transform command xf2 Start fitting 4 Search for the parameter specified in the search field For more information on eddosy click Help Manuals Acquisition Application Manuals Dosy INPUT FILES lt tshome gt exp stan nmr form dosy e format file for eddosy INPUT AND OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt dosy DOSY processing parameters SEE ALSO dosy2d dosy3d P 465 Parameters lists AU programs P 466 edlist dellist NAME edlist Edit Parameter lists dellist Deleter Parameter lists DESCRIPTION The command edlist allows you to edit parameter lists like VD Delay lists VP Pulse lists VC Loop Counts lists VA Amplitude lists VT Tem perature lists F1 Frequency lists SP Shape lists DS Data Set
11. Figure 9 2 This option selects the command dels for execution It lists 1D data sets which contain processed data showing a separate entry for each processed data number procno Each entry contains the dataset NAME EXPNO PROCNO PROC DATA and SIZE To delete data mark one or more datasets and click one of the following buttons Delete selected PROCNOs to delete the procno directories Delete processed data files of the selected PROCNOs Dataset handling 2D 3D raw data This option selects the command delser for execution It lists 2D and 3D datasets which contain raw data showing a separate entry for each experiment number expno Each entry shows the dataset NAME EX PNO ACQU DATA and SIZE To delete data mark one or more data sets and click one of the following buttons Delete selected EXPNOs to delete the expno directory Delete raw data files of the selected EXPNOs 2D processed data This option selects the command de12d for execution It lists 2D da tasets which contain processed data showing a separate entry for each processed data number procno Each entry shows the dataset NAME EXPNO PROCNO PROC DATA and SIZE To delete data mark one or more datasets and click one of the following buttons Delete selected PROCNOs to delete the procno directories Delete processed data files of the selected PROCNOs Imaginary processed data This option selects the command deli for execution It lists datas
12. enter set and click the Change button to the right of the item Setup users for internal Write Protection An item e g pulse program in the database is write protected can not be modified or deleted if its owner is Bruker or if its owner is not P 482 Parameters lists AU programs the current TOPSPIN user Owner Each item e g pulse program in the database has an assigned own er Please note the following aspects For all items e g pulse programs delivered by Bruker the owner is Bruker The description of the Edit New and Import functions above shows how an owner is assigned to an item Bruker owned items are write protected cannot be changed deleted They may however be copied to a new name see Edit above Pulse programs names MUST be unique across all owners The database cannot contain two pulse programs with same name even if their assigned owners are different Using Pulse CPD Programs from a User defined Directory When you run an acquisition using commands like zg gs the re quired pulse or CPD program is normally taken from the database You might however want to use pulse programs from an arbitrary user de fined directory e g for development purposes You can do this by setting the operating system environment variables PULPPROG_DIR and CPDPROG_DIR They can be set in two different ways with or without a minus sign determining the item search order Examples PULPPROG
13. fid raw 1D data input if 1r 1i do not exist lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if they exist OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt lr 1i processed 1D data real imaginary auditp txt processing audit trail P 104 1D Processing commands USAGE IN AU PROGRAMS MC SEE ALSO ps pk apk trf trfp P 105 1D Processing commands mul mulc nm div adsu NAME mul Multiply two datasets 1D mulc Multiply data with a constant 1D nm Negate data 1D div Divide two datasets 1D adsu Open add subtract multiply dialog box 1D 2D DESCRIPTION Multiplication commands can be entered on the command line or started from the add subtract multiply dialog box The latter is opened with adsu This dialog box offers several options each of which selects a certain command for execution Multiply with 1D spectrum fid This option selects the command mu1 for execution It multiplies the second dataset with the third dataset The result is stored in the cur rent dataset Multiply with constant This option selects the command mu1c for execution It multiplies the current data with the value of DC Multiply with 1 This option selects the command nm for execution It negates the cur rent data which means all data points are multiplied by 1 Divide by
14. lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1001 2rr deconvolved processed 2D data second individual peak dcon2dpeaks txt deconvolution parameters and peaks procs processing status parameters etc SEE ALSO Idcon gdcon mdcon P 158 2D processing commands dosy2d NAME dosy2d Process DOSY dataset 2D DESCRIPTION The command dosy2d processes a 2D DOSY dataset DOSY is a special representation of diffusion measurements Instead of generating just numbers using the T1 T2 fitting package i e diffusion co efficients and error values the DOSY processing gives pseudo 2D data where the F1 axis displays diffusion constants rather than NMR frequen cies For more information on dosy click Help Manuals Acquisition Application Manuals Dosy INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt difflist list of gradient amplitudes in Gauss cm lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2D data processed in F2 only dosy DOSY processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2D processed data auditp txt processing audit trail SEE ALSO eddosy dosy3d P 159 2D processing commands f2disco f1disco proj NAME f2disco Calculate disco projection in F2 2D f1disco Calculate disco projection in F1 2D proj Open projectio
15. t determines the detection mode real or complex from the acqui sition status parameter AQ_mod not from ME_mod As such ft does not distinguish between ME_mod LPfr and ME_mod LPfc The same counts for backward prediction Note that the command trf does deter mine the detection mode from ME_mod Linear prediction is only per formed for NCOEF gt 0 Furthermore LPBIN and for backward prediction TDoff play a role see these parameters in chapter 2 4 By default ME_mod is set to no which means no linear prediction is done When executed on a 2D or 3D dataset ft takes up to four arguments e g ft lt row gt lt procno gt y n process the specified row and store it under the specified procno The last two arguments are optional y causes a possibly existing data to be overwritten without warning n prevents TOPSPIN from changing to the destination dataset Note that the oder of the last two arguments y and n is irrelevant If you run a command like t from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that The ft command can be used on multidimensional data In that case it automatically recognizes the dimensionality of the data and prompt you for the row to be processed and the output procno It only applies to the acquisition direction The t command can be used on 1D and 2D data It recognizes the data dimensionality and opens a dial
16. wsc can also be started from the dialog box that is opened with the com mand slice INPUT FILES lt dir gt data lt user gt nmr TEMP 1 pdata 1 1r 1i 1D processed data used_from data path of the 2D data input of wsc on a 1D dataset or lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D processed data used_from data path of the 2D data input of wsc on a 1D dataset OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 204 1 However if the current dataname is TEMP wsc lt column gt lt procno gt writes to the specified Procno in the dataset from which the current 1D dataset was extracted 2D processing commands 2rr 2ri processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS WSC column procno expno name user dir SEE ALSO TSC wsr rsr wser wserp rser rser2d slice P 205 2D processing commands wser NAME wser Replace row of 2D raw data by 1D raw data 2D SYNTAX wser lt row gt lt expno gt DESCRIPTION The command wser replaces one row of 2D raw data by 1D raw data It can be entered on the source 1D dataset or on the destination 2D data set When entered on a 1D dataset wser opens the following dialog box Please specify destination Fo J NAME EXPNO PROCNO DIR USER Figure 4 19 Here you can enter the FID number to
17. COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode 3D processing commands PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum F3 parameters set by the acquisition can be viewed with dpa or s aq_mod etc AQ_mod acquisition mode determines the status FT_mod AQSEQ acquisition sequence 3 2 1 or 3 1 2 BYTORDA byteorder or the raw data NC normalization constant F2 and F1 parameters set by the acquisition can be viewed with dpa or by typing s fnmode FnMODE Fourier transform mode OUTPUT PARAMETERS F3 F2 and F1 parameters can be viewed with dpp or by typing s si s stsr etc SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transfor
18. H frequency half width gauss 100 3304 390 4 52 0 0 0 0 0 3289 368 2 26 0 0 1 3262 410 7 91 0 0 0 3216 022 4 52 0 0 0 ORR ror Signal 1 All 3 Parameters are optimized default Signal 2 All three Parameters are not optimized Signal 3 chemical shift and amplitude are optimized half width is not Signal 4 chemical shift and half width are optimized amplitude is not INPUT PARAMETERS set from the deon dialog box with edp or by typing azfw f1p etc AZFW minimum distance in ppm for peaks to be fitted independently F1P low field left limit of the deconvolution region plot region F2P high field right limit of the deconvolution region plot region MI minimum relative intensity cm for peak picking MAXI maximum relative intensity cm for peak picking PC peak picking sensitivity 1D Processing commands INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data dconpeaks txt peak list input of dconp1 peaklist peak list input of mdcon proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data dconpeaks txt peak list output of Ldcon gdcon mdcon peaklist peak list output of ppp and mdcon auto procs processing status parameters USAGE IN AU PROGRAMS LDCON GDCON MDCON PPP USAGE IN AU PROGRAMS dcon2d For furt
19. The Next button in the dialog allows you to go to the next dialog see Figure 11 7 P 517 Automation Intser Processing Data set list full path Number of region to be normalized 0 1 Value of normalizing region Global scaling yes no Figure 11 7 In this dialog you have to specify the following information Number of region to be normalized An integer 0 1 2 Value of normalization region An arbitrary floating number The intrng file contains the integral regions in the order the integrals are displayed on screen from left to right We number them from 0 on For example if you specify Number of region to be normalized 1 Value of normalization region 37 5 then region 1 of the reference spectrum gets assigned the value 37 5 Global scaling Takes the value yes or no For yes all integrals of all spectra in the list will be scaled relative to the normalization region of the reference spectrum For no all integrals of one spectrum will be scaled relative to the nor malization region of the same spectrum The normalization region number and value are same for each spectrum the specified values Clicking the button Process specified data set list will integrate the data in P 518 Automation the specified dataset list The integration result is stored in a text file whose contents is shown on the screen Its format is demonstrated by the following example Lines beginning with a are
20. TopSpin 2 1 does not use the database anymore which has been used in TopSpin 2 0 1 9 2 Examples of use In order to describe the new userspecific handling of Source Directories in TopSpin 2 1 more considerable you can find two examples of use in the following 1 Protection of user defined files With the new userspecific handling of Source Directories all userspe cific files can be protected If e g all user files are stored in the own Home Directory nobody else than the actual user can read or modi fiy any file because this directory is read and write protected This P 9 Introduction protection for example can be important for pulse program develop ment Simple and secure working in laboratories with various spectrome ters All TopSpin installations that provide the basis for spectormeter con trol can be configured in TopSpin 2 1 to be got from the same direc tories With this use of Manage Source Directories for example Pulse Programs can be taken from one common directory so that all modifi cations and improvements can be used from all spectrometer in the laboratory immediately Along this way Source directory handling becomes much more comfortable and much fewer failures will arrive 1 9 3 Source Directories P 10 In TopSpin 2 1 users can specify individual directories for e Pulse Programs e CPD Programs Shape Files e Gradient Files e Parameter Sets e Macros e Python Programs e AU
21. strip size number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 XDIM submatrix size only used for the command x 2 xdim set by the acquisition can be viewed with dpa or by typing s td TD time domain number of raw data points F2 parameters set from the ftf dialog box with edp or by typing be_mod etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum set by the acquisition can be viewed with dpa or by typing s aq_mod AQ_mod acquisition mode determines the Fourier transform mode BYTORDA
22. vconv fdata lt name gt lt expno gt lt dir gt lt user gt Here the destination dataset is specified as command line argu ments The procno is automatically set to 1 If the dataset specification P 539 Conversion commands is incomplete the dialog window shown in Figure 12 2 will appear fconv can convert raw and processed Felix data Note that fconv converts 1D data only INPUT FILES lt fdata_name gt Felix data file OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid TOPSPIN 1D raw data acqu TOPSPIN acquisition parameters acqus TOPSPIN acquisition status parameters audita txt acquisition audit trail lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1 proc TOPSPIN processing parameters procs TOPSPIN processing status parameters SEE ALSO vconvy jconv conv wincony convdta P 540 Conversion commands fromjdx NAME fromjdx Convert a JCAMP DxX datafile to TOPSPIN format 1D 2D SYNTAX fromjdx lt pathname gt lt path variable gt y DESCRIPTION The command fromdjx converts a JCAMP DX data file to a TOPSPIN da taset JCAMP DX is a standard ascii exchange format for spectroscopic data fromdjx supports the conversion of 1D data raw or processed and 2D data raw or processed real f romjdx takes up to three arguments and can be used as follows fromjdx prompts for the pathname of the JCAMP DxX input file converts it
23. 1p mi etc F1P low field left limit of the peak picking region in F3 F2 and F1 F2P high field left limit of the deconvolution region F3 F2 and F1 MI minimum relative intensity cm MAXI maximum relative intensity cm PC peak picking sensitivity PPRESOL peak picking resolution PPMPNUM maximum number of picked peaks PPIPTYP Interpolation type PSIGN peak sign pos neg or both INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 402 Analysis commands 3rrr real processed 3D data proc F3 processing parameters including peak picking parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt procs F3 processing parameters including peak picking parame ters peaklist t xm1 3D peak list in XML format peak txt t 3D peak list in TXT format lt userhome gt lt topspin hostname prop globals SEE ALSO pp2d pps prop peak picking setup ppl pph ppj P 403 Analysis commands P 404 solaguide NAME solaguide Open the solids analysis guide 1D DESCRIPTION The command solaguide opens a dialog box with a workflow for Solids Line Shape Analysis This procedure is completely described in the TOP SPIN Users Guide To open this click Help Manuals Analysis and Simulation Structure Analysis Tools SEE ALSO sola Analysis commands sin
24. 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters Figure 8 5 shows a region of peaks after peak picking Figure 8 6 shows the same region after 2D integration Here you can see the integral labels and areas The area color can be set in the user preferences command set as Color of 3rd ID spectrum Ox Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fia P 378 5 0 F2 ppm Figure 8 5 Analysis commands O x Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fia 5 0 F2 ppm Figure 8 6 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data input of int2d 3rrr real processed 3D data input of int3d OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt integ points txt data points of integral regions integrals txt peaks integral regions and integral values SEE ALSO li P 379 Analysis commands jmol NAME jmol Open the Jmol molecule structure viewer DESCRIPTION The command jmol opens the Jmol molecule structure editor TOPSPIN 1 3 and newer contains Jmol version 10 A description of the Jmol Molecule Viewer can be found under the Jmol Help menu submenu User Guide INPUT PARAMETERS set by the user with
25. 2ri 2ii processed 2D data procs F2 processing status parameters proc2s F1 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS XTRFP XTRFP2 XTRFP1 SEE ALSO xtrf xtrf2 xfb xf2 xfl P 261 2D processing commands zert2 zert1 zert NAME zert2 Zero a trapezoidal region of each row 2D zert1 Zero a trapezoidal region of each column 2D zert Open zero region dialog box 2D DESCRIPTION The zero region commands can be started from the command line or from the zero region dialog box The latter is opened with the command zert p zert Options Zero trapezoidal region Required parameters F2 and F1 Apply to axis F2 F1 Low field limit for zero region in first row ABSF1 ppm 1000 High field limit for zero region in first row ABSF2 ppm 1000 Low field limit of zero region in last row SIGF1 ppr High field limit of zero region in last row SIGF2 ppr Figure 4 31 This dialog box offers only one option which can be used in the F2 or F1 direction Zero trapezoidal region in F2 This option selects the command zert2 for execution The trapezoi dal region to be zeroed is defined as follows e only the rows between F1 ABSF2 and F1 ABSF1 are zeroed P 262 2D processing commands e the part region of each row which is zeroed shifts from row to row The first row is zeroed between F2 ABSF2 and F2 ABSF 1 The last row is zero
26. H help command 583 Hilbert transform 1D 100 2D 231 250 3D 270 291 306 308 hist command 582 history function 582 ht command 100 ift command 96 101 imaginary data 1D 86 100 104 110 116 133 2D 218 221 231 250 3D 270 291 306 308 deleting 425 input parameters 16 int command 377 381 int2d command 377 int3d command 377 integral extension factor 22 regions 1D 22 53 469 scaling 1D 382 sensitivity 27 sensitivity factor 20 values 1D 27 integration interactive 469 menu 469 intensity histogram 387 390 scaling factor 42 231 255 value 5 intrng file 53 469 intser command 517 inverse Fourier transform 1D 96 101 134 2D 170 252 254 259 J JCAMP DX format 387 390 541 551 jconv command 444 548 Jeol data 533 jmol command 380 K KDE konqueror 524 kill command 515 585 L layout Plot Editor 348 Idcon command 91 least significant byte 41 least square fit 23 69 left shift 30 102 111 li command 54 381 line broadening factor 78 linear prediction 1D 87 88 133 135 2D 213 223 227 256 3D 267 288 296 301 number of coefficients 30 number of points 27 lipp command 54 381 lippf command 381 list found data 435 of active commands 585 of AU programs 525 of datasets 419 421 423 427 430 of integrals 381 of miscellaneous files 469 of parameter sets 488 of processing parameters 19 plot layouts 364 little endian 41 232 271 291 lock substance 411 lock table 410 l
27. QF 3iii real imaginary processed data for FNMODE QF procs F3 processing status parameters proc2s F2 processing status parameters proc3s F1 processing status parameters auditp txt processing audit trail 3D processing commands USAGE IN AU PROGRAMS TF3 store_imag partition where store_image can be y or n and partition is the top level data directory SEE ALSO tf2 tfl ft3d P 295 3D processing commands P 296 tf2 NAME tf2 Process data including FT in F2 3D DESCRIPTION The command t f2 processes a 3D dataset in the F2 direction This in volves a Fourier transform which transforms time domain data FID into frequency domain data spectrum Depending on the processing param eters BC_mod WDW ME_mod and PH_mod t f2 also performs base line correction window multiplication linear prediction and spectrum phase correction The processing steps done by t 2 can be described as follows tf2 only works on data which have already been processed with t 3 It performs the following processing steps in the F2 direction 1 Baseline correction of the F2 time domain data Each column is baseline corrected according to BC_mod This parameter takes the value no single quad spol qpol sfil or qfil More details on BC_mod can be found in chapter 2 4 2 Linear prediction of the F2 time domain data Linear prediction is done according to ME_mod This parameter takes the value no LPfr LPfc LPb
28. SEE ALSO em gm tm traf trafs P 124 1D Processing commands NAME rv Reverse spectrum or FID 1D DESCRIPTION The command rvreverses the data with respect to the middle data point i e the leftmost data point becomes the rightmost point and vice versa The real and imaginary parts of the spectrum are thereby interchanged Depending on the value of DATMOD rv works on the raw or on the proc essed data The result is always store as processed data A spectrum can also be reversed as a part of the Fourier transform by setting the processing parameter REVERSE to TRUE INPUT PARAMETERS set by the user with edp or by typing datmod DATMOD data mode work on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if DATMOD proc proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data procs processing status parameters auditp txt processing audit trail P 125 1D Processing commands USAGE IN AU PROGRAMS RV SEE ALSO ft trf P 126 1D Processing commands sab NAME sab Spline baseline correction 1D DESCRIPTION The command sab performs a spline baseline correction This is base
29. SEE ALSO bas bem basl 1D Processing commands tm traf trafs wm NAME tm Trapezoidal window multiplication of the FID 1D traf Traficante window multiplication of the FID 1D trafs Traficante window multiplication of the FID 1D wm Open window function dialog box 1D 2D DESCRIPTION Window multiplication can be executed from the command line or from the window function dialog box The latter is opened with the command wm see Figure 3 27 Window function tm Options Manual window adjustment Fi Required parameters Window function type WD ot KA Left trapezoid limit O lt TM1 lt 1 Right trapezoid limit O lt TM2 1 Figure 3 27 This dialog box offers several window functions each of which selects a certain command for execution Trapezoid This function selects the command tm for execution It performs a trapezoidal window multiplication of the FID The rising and falling P 129 1D Processing commands P 130 edge of this function are defined by the processing parameters TM1 and TM2 These represent a fraction of the acquisition time as dis played below Factor w AQ 0 TM1 TM2 1 Figure 3 28 Traficante and trafic s n This function selects the commands traf and trafs respectively for execution The algorithms used by these commands are described by D D Traficante and G A Nemeth in J Magn Res 71 237 1987 tm traf and trafs implicitl
30. Save the displayed region 1D 2D DESCRIPTION The command dp1 saves the displayed region in the parameters F1P and F2P The command can also be executed by right clicking in the data window and selecting Save Display Region To This will open the dialog box shown in Figure 7 3 Here select Parameters F1 2 and click OK PN Save display region to Options Parameters F1 2 e g used by restore display dpl O Parameters ABSF1 2 e g used by absf apkf Parameters STSR STSI used by strip ft O Parameters SIGF1 2 signal region used by sino Parameters NOISF1 2 noise region used by sino O A text file for use with other programs igure OUTPUT PARAMETERS can be viewed with edp or by typing f1p or f2p F1P low field left limit of the plot region in ppm F2P high field right limit of the plot region in ppm OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc plot title SEE ALSO plot prnt print autoplot P 354 Print Export commands md md no_load md write NAME md displays spectra in multiple display md no_load entering multiple display by ignoring other sessions md write writes the assoc file containing the data set list for multiple display DESCRIPTION The following arguments of md for controlling data sets from command line AU programs or Python programs are available 1 Specifie
31. TD 2 SI LPBIN TD lt LPBIN lt 2 TD lt 2 SI TD LPBIN TD 2 SI LPBIN Table 2 4 Linear forward prediction MAXI maximum relative intensity for peak picking e used in 1D datasets e takes a float value cm e interpreted by pp li lipp only peaks with an intensity smaller than MAXI will appear in the peak list MAXI can also be set from the pp dialog box and interac tively in peak picking mode MC2 Fourier transform mode of the second and third direction the processing parameter MC2 is only interpreted if the acquisition status parameter FnMODE dpa does not exist or has the value undefined Fn MODE must be set with eda according to the experiment type before the acquisition is started As MC2 FnMODE only exists in the second and third direction On datasets acquired with XWIN NMR 2 6 or earlier MC2 is interpreted and must be set before the data are processed The TOPSPIN parameters parameter MC2 is used in 2D datasets in the second direction F1 is used in 3D datasets in the second and third direction F2 and F1 takes one of the values OF OSEOQ TPPI States States TPPI echo antiecho is interpreted by xfb xf2 xf1 xtrf tf ME_mod FID linear prediction mode used in 1D 2D and 3D datasets in all directions takes one of the values no LPfr LPfc LPbr LPbc LPmifr LPmifc interpreted by ft trf xfb xf2 xf1 xtrf tf also interpreted by em gm sin tm tr
32. TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum XDIM submatrix size only used for the command xf b xdim set by the acquisition can be viewed with dpa or by typing s td P 243 2D processing commands TD time domain number of raw data points F2 parameters set from the ftf dialog box with edp or by typing pkn1 PKNL group delay compensation Avance or filter correction A X set by the acquisition can be viewed with dpa or by typing s aq_mod AQ_mod acquisition mode determines the Fourier transform mode BYTORDA byteorder or the raw data NC normalization constant F1 parameters set by the acquisit
33. TOPSPIN User Management User ID User Name Signature Meanings separated by comma Figure 14 10 The uadmin dialog also offer the following buttons Change Meaning change the signature meaning of the marked user Remove User remove the marked user entry Passwd Length change the minimum password length Save save the user administration Save Close save the user administration and close the dialog Cancel Close the dialog discarding any changes The command can also be started as follows click Options Administration Change internal user password INPUT OUTPUT FILES lt tshome gt conf topspin users prop TOPSPIN users properties file SEE ALSO esign logoff chpwd lockgui P 611 TOPSPIN User Management P 612 Index Symbols basl command 469 md command 355 png files 350 tif files 350 wmf files 350 A about 568 abs command 52 86 469 abs1 command 147 abs2 command 144 absd command 52 absd1 command 147 absd2 command 144 absf command 52 absnd command 312 absot1 command 147 absot2 command 144 abst1 command 147 abst2 command 144 accumulate command 60 acquisition dimension 4 23 143 265 288 mode 31 86 87 134 254 411 parameters 15 18 457 458 490 495 status parameters 15 16 18 19 31 36 405 411 490 time 5 39 78 130 add two 1D datasets 56 two 1D fids 56 two 2D datasets 150 two 2D raw datasets 150 add command 56 add increment in
34. The first row is corrected between F2 ABSF2 and F2 ABSF1 The last row is corrected between F2 SIGF2 and F2 SIGF1 For intermediate rows the low field limit is an interpola tion of F2 ABSF2 and F2 SIGF2 and the high field limit is an interpolation of F2 ABSF1 and F2 SIGF1 F2 Auto correct baseline alternate algorithm This option selects the command absd2 for execution It works like abs2 except that it uses a different algorithm It is for example used when a small peak lies on the foot of a large peak In that case absd2 allows you to correct the baseline around the small peak which can then be integrated Usually absd2 is followed by abs2 F2 Auto correct baseline shift correction region alternate algo rithm This option selects the command absot2 for execution It works like abst2 except that it has a different algorithm which applies a larger correction 1 It uses the same algorithm as the command abs in DISNMR P 145 2D processing commands P 146 If you run a command like abs2 from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that The bas command can be used on 1D 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the bas dialog box with edp or by typing absg absf1 etc ABSG degree of the polynomial to be subtracted
35. Turns off the projection display In the lower part of the dialog you can specify the 1D datasets to be used for the first option The checkboxes allow you to display the F2 projec tion F1 projection or both Clicking OK will show the projections accord ing to the chosen option and close the dialog Note that the effect of the second and third option can also be reached by clicking the 4 button of the toolbar or entering pr on the command line INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdatal lt procno gt 1r 1D processed data input for 1st option OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt curdat2 definition of the second and third dataset SEE ALSO f2projn f2sum rhpp P 174 2D processing commands rev2 rev1 NAME rev2 Reverse spectrum in F2 2D rev1 Reverse spectrum in F1 2D DESCRIPTION The command rev2 reverses the spectrum in the F2 direction This means each row is mirrored about the central column The command revi reverses the spectrum in the F1 direction This means each column is mirrored about the central row Note that the spectrum can also be reversed by during x b by setting the F2 and or F1 processing parameter REVERSE to TRUE INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data OUTPUT FILES lt dir gt dat
36. You can check this by P 411 Analysis commands putting the cursor on this peak If no peak was found you will get the message sref no peak found default calibration done The result of the default calibration step 1 is stored without any further correction The three cases below show the calibration of a 1H 13C and 31P spec trum with C6D6 as a solvent Table 8 4 shows the corresponding entry in the edlock table Sol Lock Nucleu DIS Ref Width RShift Jent Field powe tance ppm ppm ppm r ppm C6D6 150 15 0 1H 7 28 0 0 05 0 000 2H 7 28 0 0 05 0 000 13C 128 0 0 0 5 0 0 220 31P 0 00 10 5 5 0 13 356 Table 8 4 case 1 calibration of a 1H spectrum A spectrum was acquired while being locked on C6D6 sref will do a default calibration and look for a signal at 0 0 ppm Ref in a window of 0 25 ppm If a peak is found its chemical shift will be set to 0 ppm case 2 calibration of a 13C spectrum A spectrum was acquired while being locked on C6D6 sref will do a default calibration and look for a signal at 0 0 ppm Ref in a window of 2 5 ppm If a peak is found its chemical shift will be set to 0 ppm case 3 calibration of a 31P spectrum A spectrum was acquired while being locked on C6D6 sref will do a default calibration and look for a signal at 10 5 ppm Ref in a window of 2 5 ppm If a peak is found its chemical
37. i Positive Negative Base level 3413088 0 3413088 0 Level increment 1 800 1 800 8 Number of levels Figure 7 2 Print Export commands Manual setup This allows you to create an arbitrary sequence of levels 1 Enter the level values in the fields 1 2 at the top of the dialog box 2 Click Apply to update the display or OK to store the levels update the display and close the dialog box Calculation This allows you to easily create a geometric or equidistant sequence of levels 1 Click one of the following items Multiply with increment to create a geometric sequence of levels e Add increment to create a equidistant sequence of levels 2 Enter the desired Base level Level increment and Number of levels 3 Click Fill to display and activate the sequence 4 Click Apply to update the display or OK to store the levels update the display and close the dialog box The Contour level sign allows you to select positive or negative levels or both Note that if you change the intensity interactively for example with the buttons 2 2 or the contour levels are automatically adjusted Entering edlev will show the adjusted levels and clicking amp will save them to disk INPUT AND OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt clevels Contour levels SEE ALSO As It P 353 Print Export commands dpl NAME dpl
38. lt name gt lt expno gt pdata lt procno gt 1r 1i current processed data procs processing status parameters auditp txt processing audit trail SEE ALSO duadd P 61 1D Processing commands apkO apk1 apkOf ph NAME apkO Zero order automatic phase correction 1D apk1 First order automatic phase correction 1D apkOf Customized zero order automatic phase correction 1D ph Open phase correction dialog box 1D 2D DESCRIPTION Phase correction commands can be can be entered on the command line or started from the phase correction dialog box see Figure 3 3 This di EN Phase correction apk0 Options Automatic phasing O Automatic phasing alternate algorithm oO Automatic phasing alternate algorithm 2 Manual phasing O Additive phasing using PHCOM Automatic phasing 1st order only O Automatic phasing selected region only Automatic zero order phasing selected region only Magnitude spectrum Power spectrum Required parameters 85 36169 1 32172 219 160903930664 19 160918955445 Figure 3 3 P 62 1D Processing commands alog is opened with the command ph It offers several options each of which selects a certain command for execution Automatic phasing Oth order only This option selects the command apko for execution It works like apk except that it only performs the zero order phase correction Automatic phasing 1st order only Thi
39. processed data input if they exist but are not Fourier trans formed proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters P 83 1D Processing commands P 84 auditp txt processing audit trail USAGE IN AU PROGRAMS FP FMC SEE ALSO ef efp gf gfp 1D Processing commands ft ftf NAME ft Fourier transform 1D ftf Open the Fourier transform dialog box 1D 2D DESCRIPTION The command ft Fourier transforms a 1D dataset or a row of a dataset with dimension 2 It can be started from the command line or from the Fourier transform dialog box The latter is opened with the command ftf Options Sereccesseccnevesccnsenseccensesscecsnesccsacunsencncesscesseenssceeeseed C Advanced Fourier transform Required parameters Size of real spectrum SI pnts a1 92 of fid data points to be used TDeff fo Index of first output point of strip transform STSR booo Total of output points of strip transform STSI 0 Fid linear prediction LP mode ME_mod Norr z of LP coeficients NCOEF booo of fid data points contributing to backward LP LPBIN jo of fid data points to be predicted TDoff booo Reverse spectrum REVERSE No y Yweighting factor for first fid point A x only FCOR 0 5 Apply 5th order phase correction AX o
40. reb prompts the user for three arguments Alternatively these can be entered on the command line Here are some examples rcb Prompt the user for the cube axis orientation the cube number and destination 3D procno and read the cube accordingly rcb 234 10 999 Read F2 F3 F4 cube 10 and store it in procno 999 rcb 324 10 999 Read F2 F3 F4 plane 10 and store it in procno 999 exchanging the F2 and F3 axes rcb 124 64 101 xdim Read F1 F2 F4 plane 64 with subcube sizes according to the re spective XDIM values and store it in procno 101 rcb 124 64 Read F1 F2 F4 plane 64 prompt the user for the destination proc no rcb 214110 n Read an F1 F2 F4 plane number 1 and store it in procno 10 ex changing the F2 and F1 axes Do not display activate the destina tion dataset rcb entered on a destination 3D dataset This is typically done on a 3D dataset which is a cube extracted by a previous reb command which was entered on the source 4D dataset In that case reb requires only one argument the cube number By de P 331 nD processing commands fault the same cube axis orientation and source 4D dataset procno are used as with the previous reb command as defined in the used_from file of the 3D dataset You can however use two or three arguments to specify a different cube axis orientation and or 4D source procno Ona regular 3D dataset not a plane from a 3D reb requires three argu ments Here are some examp
41. rtr Read trace from data gt 2D and store as 1D data DESCRIPTION The command rtr reads a trace from processed data with dimension gt 2D and stores it as a 1D dataset rtr takes up to four arguments As an example we take a trace read from a 3D dataset lt axis orientation gt 1 2o0r3 The digit refers to the F3 F2 and F1 axis of the 3D data lt trace number gt 1 MAX where MAX is the product of the SI value in the directions orthogo nal to the trace orientation lt procno gt destination 1D procno source 3D procno if rtr is entered on the destination 1D dataset n optional argument prevents the destination dataset from being displayed activated Obligatory arguments that are not specified on the command line will be prompted for rtr can be entered on the source 3D dataset or if this already exists on the destination 1D dataset The number of required arguments is differ ent see below rtr entered on a source 3D dataset In this case rtr prompts the user for three arguments Alternatively these can be entered on the command line rtr Prompt the user for the axis orientation trace number and destination P 338 nD processing commands procno and read the trace accordingly rtr 3 10 999 Read F3 trace 10 and store it in procno 999 rtr 1 1 10 n Read F1 trace 1 and store it in procno 10 Do not display activate the destination dataset rtr entered on a destination 1D dataset Thi
42. 0 to 5 default is 5 ABSF 1 low field limit of the region which is baseline corrected ABSF2 high field limit of the region which is baseline corrected SIGF1 low field limit of the correction region in the last row SIGF2 high field limit of the correction region in the last row INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc F2 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data procs F2 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS ABS2 ABST2 ABSD2 ABSOT2 SEE ALSO abs1 abstl1 absd1 absot1 2D processing commands abs1 abst1 absd1 absot1 bas NAME abs1 Automatic baseline correction in the F1 2D abst1 Automatic selective baseline correction in the F1 2D absd1 Automatic baseline correction in F1 diff algorithm 2D absot1 Automatic selective baseline correction in F1 diff algorithm 2D bas Open baseline correction dialog box 1D 2D DESCRIPTION Baseline correction can be started from the command line with abs1 abst1 etc or from the baseline dialog box The latter is opened with the command bas cy Baseline correction abs1 Options Auto correct baseline using polynomial O Auto correct baseline shift correction region Oo Auto correct baseline alternate
43. 1000 Seduce 100 Sinc1 1000 Squa100 1000 Squaramp 20 1 Tanntan 300 50 250 Upaate info Eait Dispiay close Figure 10 5 On the topright of the upcoming window you can find the Sources where the listed Shape Files are stored With pull down menu and click on the respective Source you can change the Shape File Source to let them be listed in this dialog The AU programs are selected from the Source directory as selected at the upper right of the dialog Note that lt tshome gt exp stan nmr lists wave P 471 Parameters lists AU programs contains all Bruker Shape Files lt tshome gt exp stan nmr lists wave user contains all user defined Shape Files The dialog offers the following buttons Edit Edit the selected Shape File Equivalent to double clicking the Shape File name or entering edshape lt name gt on the command line Display Display the selected Shape File The Shape Tool will be opened for dis play the current Shape File The result can be seen in 10 6 1a A mix anjel aE 8 3auss Truncation Levi F 2arameters J 13C fH AV500 Cholesterylacetate a 000 Size of Sh 10 200 150 100 50 ppm av J Ahpiitude a4 o 4 oJ 4 gi o 44 J Phase g4 Wf g3 E 83 z pey ee Se ee a ee oem es ee ee 200 400 600 800 points Figure 10 6 Close Close the dialog P 472 Parameters lists AU programs The Fi
44. 128 998 n calculates the positive F1 F3 projection of the planes 10 to 128 along F2 and stores it under PROCNO 998 Instead of specifying the first and last plane you can also use the argu ment a11 for all cubes For example projplp 23 all 10 calculates the positive F2 F3 projection of all planes along F1 and stores it under PROCNO 10 projplp projpln and sump1 work on data of dimension 23D On 4D and 5D data the dialog shown in Figure 5 1 does not appear Instead the arguments are prompted for one at a time if they are not specified on the command line INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data SEE ALSO rpl wpl rser2d P 276 3D processing commands r12 r13 r23 slice NAME r12 Read F1 F2 plane from 3D data and store as 2D data r13 Read F1 F3 plane from 3D data and store as 2D data r23 Read F2 F3 plane from 3D data and store as 2D data slice Open the read plane dialog box 2D 3D DESCRIPTION The commands r12 r13 and r23 read a plane from 3D processed data and store it as a 2D dataset When entered without arguments they open the dialog box shown in Fig ure 5 2 ie Cross sections r12 Options Extract an orthogonal spectrum plane O Extract a diagonal spectrum plane Extract
45. 1D spectrum fid This option selects the command div for execution It divides the sec ond dataset by the third dataset The result is stored in the current da taset mu1 div perform a complex multiplication division on complex spectra This requires that for both the second and third dataset the status parameter FT_mod fac or fsc e real file 1r and imaginary file 1i data exist P 106 1D Processing commands ie Add subtract mul x Options C Adda spectrum of same size point wise current DC second Add a spectrum of same or different size ppm Hz wise current DC second C Adda FID current DC second C Add a constant C Multiply with constant C Multiply with 1 C Divide by a 1D spectrumifid current second Required parameters Constant DC o NAME 2nd spectrum exami e E i EXPNO h PROCNO h USER guest DIR Ic thio Shift 2nd spectrum by ppr bo SoS i i Apply command to raw processed data DATMOD proc bd Add corresponding ppm or hz values bm J OK Cancel Help Figure 3 11 This is the case for most data that have been acquired in Avance spec trometers If the above requirements are not fulfilled real and imaginary data are multiplied divided pointwise When a complex operation has been performed this is reported in the audit trail output file Please note in addition that deleting the imaginary data enforces a poin twise multiplication for the
46. 225 2D processing commands P 226 proc2 F1 processing parameters Note that if 2rr is input 2ri is also input if x 1 has been done OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr first quadrant real processed data 2ir second quadrant imaginary processed data output if FAMODE QF 2ii second quadrant imaginary processed data output if FAMODE QF procs F2 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS XF2 SEE ALSO xfl xfb xtrf xtrf2 2D processing commands xfb ftf NAME xfb Process data including FT in F2 and F1 2D ftf Open Fourier transform dialog box 1D 2D DESCRIPTION The command xfb processes a 2D dataset or a plane of a dataset with dimension gt 3 It can be started from the command line or from the Fou rier transform dialog box see Figure 4 29 The latter is opened with the command ftf The ftf command recognizes the data dimensionality and opens a dia log box with the appropriate options and parameters For 2D data two options appear both of which select the x b command for execution provided the F2 and F1 direction are both enabled Standard Fourier transform This option only allows you to set the parameter SI the size of the real spectrum Advanced Fourier transform This option allows you to set all Fourier transform related parameters xfb Fourier transforms t
47. 5 Auto correct baseline alternate algorithm 5 Define baseline points for cubic spline correction 5 Correct baseline using cubic spline 5 Correct baseline using base_info file Correct baseline of the FID Required parameters Degree of polynomial ABSG 0 5 5 Left limit for correction region ABSF1 ppm 240 Right limit for correction region ABSF2 ppm 10 Number of averaging points 1 Baseline points file defining cubic spline baslpnts Baseline info file stored by manual correction base_info Fid baseline mode BC_mod quad ok Cancel Help Figure 3 1 1D Processing commands command bas This dialog box offers several options each of which selects a certain command for execution Auto correct baseline using polynomial This option selects the command abs for execution It performs an au tomatic baseline correction of the spectrum by subtracting a polyno mial The degree of the polynomial is determined by the parameter ABSG which has a value between 0 and 5 with a default of 5 abs first determines which parts of the spectrum contain spectral information and stores the result in the file int rng integral regions The remain ing part of the spectrum is considered baseline and used to fit the pol ynomial function abs also interprets the parameters ABSL AZFW AZFE and ISEN Since these parameters apply to integration rather than baseline cor rection they do not ap
48. Automation Chapter 11 Automation This chapter describes all TOPSPIN commands which handle parameters and parameter sets Furthermore you will find commands that are used to read or edit lists like pulse programs gradient programs frequency lists etc and finally commands which are used to read edit or run AU pro grams Note that several commands in this chapter are acquisition related rather than processing related Nevertheless they play a role in the processing part of TOPSPIN P 501 Automation at NAME at schedule a TOPSPIN command for execution SYNTAX at HH mm DD MM YY command DESCRIPTION The command at performs command scheduling When entered without arguments it opens the dialog shown in Figure 11 1 Here you can spec ify the command to be scheduled e g zg and the starting time and date New schedule Schedule Command zal Time 11 33 AM Date November 23 2005 Figure 11 1 The Time and Date fields are initialized with the current time and date respectively By clicking OK the specified is scheduled for execution The time and date as well as the command to be scheduled can also be specified on the command line using the following syntax at HH mm DD MM YY command Here are some examples at 23 30 25 12 07 zg will start an acquisition on the 25th of December 2007 at 23 30 at 13 zg P 502 Automation will start an acquisition today at 13 0
49. Bruker parameter set which defines the experiment you want to do 3 Modify the acquisition parameters with eda to your preference and run the acquisition 4 Modify processing parameters with edp to your preference and process the data 5 Store the parameters with wpar under a new experiment name for general usage son is that is that rpar with two arguments is used in automation INPUT FILES lt dir gt data lt user gt nmr lt 1D data name gt lt expno gt acqu acquisition parameters lt dir gt data lt user gt nmr lt 1D data name gt lt expno gt pdata lt procno gt proc processing parameters outd output device parameters lt dir gt data lt user gt nmr lt 2D data name gt lt expno gt acqu F2 acquisition parameters acqu2 F1 acquisition parameters lt dir gt data lt user gt nmr lt 2D data name gt lt expno gt pdata lt procno gt proc F2 processing parameters proc2 F1 processing parameters outd output device parameters clevels 2D contour levels OUTPUT FILES lt tshome gt exp stan nmr par user lt 1D parameter set gt acqu acquisition parameters P 495 Parameters lists AU programs proc processing parameters outd output device parameters lt tshome gt exp stan nmr par user lt 2D parameter set gt acqu F2 acquisition parameters acqu2 F1 acquisition parameters proc F2 processing parameters proc2 F1 processing parameters outd output device param
50. Editor portfolio input file is it exists lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt layout xwp Plot Editor layout last_plot xwp Last stored Plot Editor layout portfolio por Plot Editor portfolio INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data procs processing status parameters intrng integral regions parm txt ascii file containing parameters which appear on the plot title default title file outd output device parameters For a 2D dataset the files 2rr proc2s and clevels are also input SEE ALSO print prnt autoplot P 362 Print Export commands print NAME print Open print dialog box 1D 2D 3D DESCRIPTION The command print opens the following dialog box PN Print Ctrl P plot Options Print active window prnt Print with layout start Plot Editor plot Print with layout plot directly autoplot Required parameters LAYOUT 1D_H xwp Use plot limits Fill data set list from your default portfolio from Plot Editor Reset Actions as saved in Plot Editor from portfolio saved in data set O Override plotter saved in Plot Editor CURPLOT Wolympus HP LaserJet 4000 PCL 6 Figure 7 5 Here you can choose from three print options Print active window prnt The data window is printed as it is displayed on
51. Figure 6 2 Extract 1D 2D or 3D data from 4D 5D processed data To view the result of 4D processing open the dataset procno where the processed data are stored and read a 3D cube 2D plane or 1D trace This can be done with the commands rcb rpl and rtr respectively These commands automatically switch to the destination dataset show ing the 3D 2D or 1D dataset respectively see the description of these P 315 nD processing commands P 316 commands for more information Furthermore you can extract positive negative or sum cube projections with the commands projecbp pro jcbn and sumcb respectively Similarly you can extract plane projec tions with the commands projplp projpln and sump1 respectively Instead of processing the entire 4D dataset and reading a certain plane or trace you can also process single 2D planes or 1D fids of the 4D raw data To process a plane just enter xfb xf2 or xtrf and specify the requested plane axis orientation plane number and output procno To process a trace just enter a 1D processing command like ft or trf and specify the requested fid number and output procno Obviously 1D 2D processing commands can also be used to further process or reprocess traces planes or processed 4D data For example 1 Open a 4D dataset 2 ftnd 4 Perform 4D processing in the F4 direction 3 rpl 34 1 999 Read F3 F4 plane 1 and store it in procno 999 Note that the plane is stored as a F2 process
52. Gaussian function of width BCFW quadrature Table 2 2 a Marion Ikura Bax J Magn Res 84 425 420 1989 COROFFS correction offset for FID baseline correction P 23 TOPSPIN parameters P 24 e used in 1D 2D and 3D datasets in all directions e takes a double value Hz default is 0 0 e interpreted by be em gm trf xfb xf2 xf1 xtrf tf3 tf2 tf1 e COROFFS is only interpreted for BC_mod qpol or qfil The center of the baseline correction is shifted by COROFFS Hz CURPLOT Default plotter for Plot Editor e used in 1D and 2D datasets e interpreted by plot and autoplot The plotter set by CURPLOT overrides the plotter specified in the Plot Editor Layout It allows you to use the same plotter for all lay outs DATMOD data mode work on raw or proc essed data e used in 1D datasets e takes the value raw or proc e interpreted by add addc and div filt mul mulc 1s or rs Iv xox Zf zp DC multiplication factor or addition constant e used in 1D datasets e takes a float value e interpreted by add addc addfid and mulc For addc DC is an addition constant For add addfid and mulc DC is a multiplication factor DFILT Digital filter filename e used in 1D datasets e takes a character string value e interpreted by filt e The file specified by DFILT must reside in the directory lt tshome gt exp stan nmr filt ld and must be set up from a command shell One standard f
53. Maximum intensity rel MAXI Resolution points PPRESOL Miscellaneous Maximum of peaks PPMPNUM Interpolation type PPIPTYP None v Pick peaks of sign PSIGN Positive v Figure 8 12 peak picking was done i 1 To store displayed region right click in the data window and select Save display region to 1 Only active when peak picking was already done P 400 Analysis commands Sensitivity parameters Here you can set the peak picking parameters MI and MAXI which are also used for 1D peak picking Note that MI can also be set interactively with the button Sef to to the current value of MI or the lowest contour lev el Furthermore the parameter PPRESOL for peak picking resolution can be set Miscellaneous parameters Here you can set the following parameters PPMPNUM Maximum number of picked peaks Note that 0 or no value specified means unlimited PPIPTYP Peak picking interpolation type parabolic or none PSIGN The sign of the picked peaks positive negative or both To start peak picking Click OK The peak picking progress will be shown in the TOPSPIN status line When the peak picking process has finished e The number of found peaks is displayed in the status line Note that if the option Append peaks to list is checked only additional peaks are reported as found e The peaks and parameters are stored in the processing directory To view the peak list click the Peak
54. OK Cancel Help Figure 3 8 Use mixed shape use peaks from file peaklist This option selects the command mdcon for execution It works like mdcon auto except that it uses an existing peaklist file This file must have been created by executing mdcon auto by executing ppp by executing pps and exporting the peak table Peaks tab in data window to the file peaklist Generate peaklist no deconvolution This option selects the command ppp for execution It picks the peaks P 92 1D Processing commands for deconvolution and stores the result in the file peaklist ppp is implicitly executed by mdcon auto Re Display peaklist from last deconvolution This option selects the command dconp1 for execution It shows the peaklist file dconpeaks txt which was created with the last de convolution on the current dataset Display the Lorentz Gauss curves of the last deconvolution This option selects the command dceonp1 v for execution It shows the individually fitted peaks and their sum The deconvolution commands only work on the displayed region as ex pressed by the parameters F1P and F2P Furthermore they select peaks according to the peak picking parameters MI MAXI and PC They also evaluate the parameter AZFW which determines the minimum distance between two peaks for them to be fitted independently Peaks which are less than AZFW ppm apart are considered to be overlapping As a rule of the thumb yo
55. Open other file Required parameters Browser type File Chooser v Figure 9 10 This dialog box has three options each with several file types Each file type selects a certain command for execution Open NMR data stored in standard Bruker format This option allows you to open Bruker format data in the following ways File chooser reb e RE dialog re e PROCNO dialog rep Open NMR data stored in special formats This option allows you to open the following NMR data types for P 443 Dataset handling mats JCAMP DX fromjdx Zipped TOPSPIN fromzip WIN NMR winconv A3000 conv VNMR veconv JNMR jconv Felix fconv Open other file This option allows you to open the following lists and programs Pulse programs edpu1 Au programs edau Gradient programs edgp CPD programs edcpd Miscellaneous files edmisc Parameter lists edlist Python program edpy The corresponding command line commands are specified in square brackets After clicking OK a new dialog box will appear according to the selected option and file type SEE ALSO re rep rew repw reb fromjdx fromzip winconv conv vconv jconv fconv edpul edau edgp edcpd edmisc edlist edmac P 444 Dataset handling paste NAME paste Open the dataset that was last copied nD DESCRIPTION The command paste opens the dataset which was previously copied from the a TOPSPIN data window or
56. PM 9 3 2004 8 32 AM 9 2 2004 5 00 PM 9 3 2004 8 32 AM 9 3 2004 8 32 AM 9 3 2004 8 32 AM 9 2 2004 5 13 PM 9 3 2004 8 32 AM 9 3 2004 8 32 AM 3 16 2004 10 43 AM 16 abject s 279 KB g My Computer 7 Figure 13 10 If no dataset is open in the TOPSPIN data area the users home directory TOPSPIN Interface Processes will be shown exp allows you to access to the current data files as well as the entire data directory tree An alternative way to access the processed data files is to right click in the data window and select Files The command can also be used with one argument expl top shows the contents of the TOPSPIN home directory expl home shows the contents of the User home directory expl spect shows the contents of the directory lt tshome gt conf instr lt curinst lt expl prop shows the contents of the User properties directory expl lt absolute_path gt shows the contents of directory lt absolute_path gt SEE ALSO run P 581 TOPSPIN Interface Processes P 582 hist NAME hist Show the TOPSPIN history and protocol DESCRIPTION The command hist shows the TOPSPIN protocol and history files These files only contain information if the protocol function is active You can switch on this function as follows 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Check the item Record commands in protocol file The protocol file contains TO
57. TABLE XY XY 2 3241 1 58 2 2962 1 18 1 9943 10 00 1 8725 1 36 Table 8 3 last part of the file pp dx looks like The pp command can be used on 1D 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters For compatibility reasons INPUT PARAMETERS set by the user with edp or by typing mi maxi etc MI minimum relative intensity cm MAXI maximum relative intensity cm PC peak picking sensitivity PSIGN peak sign pos neg or both PSCAL determines the region with the reference peak for vertical scaling SREGLST name of the scaling region file used for PSCAL sreg psreg ASSFAC assign the highest or second highest peak as reference for scaling ASSWID region excluded from second highest peak search set by the user with edp or by typing fip 2p etc F1P low field left limit of the plot region in ppm F2P high field right limit of the plot region in ppm P 391 Analysis commands INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data proc processing parameters reg region with the reference peak for PSCAL ireg or pireg lt tshome gt exp stan nmr lists scl lt SREGLST gt regions containing the reference peak if PSCAL sreglpsreg OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt peak
58. TOPSPIN 2 0 and newer acquisition command like zg go rga and atma are automatically queued if auto spooling is enabled in the User Preferences command set Queued commands can be viewed in the command spooler which can be started with the command spooler and is available in the spectrom eter status bar SEE ALSO cron at qumulti atmulti spooler Automation qumulti NAME qumulti queue a TOPSPIN command for execution on multiple expnos SYNTAX qumulti 1 2 3 1 7 1 7 1 7 20 21 DESCRIPTION The command qumulti queues a command for execution on multiple ex pnos of the current dataset When entered without arguments qumul ti opens the dialog shown in Figure 11 8 Job Command EA Experiment IDs O1 02 O3 O4 Os O16 O11 O39 Figure 11 8 Here you can enter the command to be executed and select the experi P 521 Automation ments numbers on which the specified command should work The dia log shows all available expnos with the active dataset selected Clicking OK queues the command for execution The command qumu1ti takes two arguments the command to be exe cuted and the target experiment number s The dialog will open with the specified arguments pselected Expnos can be specified in one of the fol lowing ways n a single experiment number all expnos under the current dataname n m expno n through m n m equivalent to n m n m expno n and m n m equival
59. The latter is shown by the processing status parameter NC_proc type dpp Smaller more negative values of nc_proc are ignored to avoid data overflow The command xfb nc_proc last takes the current value of the processing status parameter NC_proc type dpp as input value PPARMOD dimensionality of the processed data takes one of the values 1D 2D 8D interpreted by TOPSPIN display parameter editor edp and processing commands that access processed data like abs and apk can be set by changing the dimension from the parameter editor edp toolbar The status parameter PPARMOD defines the dimensionality of the processed data Note the following restriction PPARMOD lt PAR MODE PHCO zero order phase correction value frequency independent used in 1D 2D and 3D datasets in all directions takes a float value degrees set by apk apks apkf apk0 apkOf apkmin 1D datasets set interactively in Phase correction mode in 1D and 2D datasets also exists as processing parameter edp PHCO is one of the few examples where a processing parameter is set by a processing command For example apk sets both the processing and processing status parameter PHCO pk reads the processing parameter and updates the processing status parameter After multiple phase corrections the processing status parameter PHCO shows the total zero order phase correction P 43 TOPSPIN parameters PHC 1 first order phase correction val
60. a Python program This option selects the command xpy for execution It prompts you for the pathname of a Python program Just enter this pathname and click OK to execute the Python program Execute a Macro This option selects the command xmac for execution It opens the Macro dialog box showing a list of available macros Here you can se lect macro and click Execute to execute it xmac can also be entered on the command line in which case you can specify the macro as an argument Open a text editor This option selects the command edtext for execution It opens an empty text file with the TOPSPIN editor The file can be stored in any direc tory SEE ALSO expl shell xau xpy xmac edtext P 525 Automation serial NAME serial Serial processing with macro or Python script DESCRIPTION The command serial opens the dialog window shown in Figure 11 10 Serial Processing Define Datasets Please define the full path name of the dataset list to be processed Click on gt Browse For List locate an existing dataset list gt Find Datasets search for datasets and use the selected ones as the list gt Edit List edit the current or a new dataset list gt Next continue with command definition P 526 Figure 11 10 Here you can specify find or edit the list of datasets to be processed The functions of the buttons are described in the dialog A dataset list is a list of full pathnames e g
61. a raw data plane O Extract a row from raw data O Replace a spectrum plane Required parameters Plane orientation Plane number 1 1 999 Destination PROCNO 999 999 Figure 5 2 P 277 3D processing commands P 278 This dialog box offers several options each of which selects a certain command for execution Furthermore you must specify three parame ters Plane orientation F1 F2 F1 F3 or F2 F3 This parameter determines which of the commands r12 r13 or r23 is executed Plane number the maximum plane number is the SI value in the direc tion orthogonal to the plane orientation Destination procno the procno where the output 2D dataset is stored For each option described below a table shows how the processing state of the output 2D data relates to the processing state of the input 3D data This table can be interpreted as follows FID data have not been Fourier transformed time domain data real data have been Fourier transformed but imaginary data do not exist real imag data have been Fourier transformed and imaginary data exist Depending on the processing state an extracted plane can be further processed with 2D processing commands like xf2 xf1 xf2p etc Extract an orthogonal spectrum plane in F1 F2 This option selects the command r12 for execution It reads an F1 F2 plane from a 3D dataset and stores it as a 2D dataset see Table 5 3 Extract an orthogonal spectru
62. additive baseline corrections to re 1D Processing commands move multiple frequency baseline distortions This cannot be done with be or trf because these commands always work on the raw data i e they are not additive Note that the window multiplication commands e g em gm sine etc are additive The same counts for linear prediction part of ft and phase correction pk trf can be used to do a combination of forward and backward predic tion Just run trf with ME_mod LPfc and then trfp or t with ME_mod LPbc When executed on a 2D or 3D dataset trf takes up to four arguments trf lt row gt lt procno gt n y process the specified row and store it under the specified procno The last two arguments are optional n prevents changing the display to the output 1D data y causes a possibly existing data to be overwritten without warning When executed on a dataset with 2D or 3D raw data but 1D processed data trf takes one argument trf lt row gt process the specified row and store it under the current procno trf same process the same row as the previous processing command and store it under the current procno The same option is automatically used by the AU program macro TRF When used on a regular 1D dataset i e with 1D raw data it has no effect INPUT PARAMETERS set by the user with edp or by typing si tdeff etc SI size of the processed data TDeff number of raw data points to be used for process
63. algorithm Auto correct baseline shift correction region altern algo Correct baseline using correction result from 1D row column Required parameters F2 and F1 Apply to axis F2 F1 Degree of polynomial ABSG 0 5 Left limit for correction region ABSF1 ppm Right limit for correction region ABSF2 ppm Figure 4 2 This dialog box offers several options each of which selects a certain command for execution The command further depends on the selected direction Here we describe the commands for the F1 direction P 147 2D processing commands P 148 F1 Auto correct baseline using polynomial This option selects the command abs1 for execution It performs an automatic baseline correction in the F1 direction This means it sub tracts a polynomial from the columns of the processed 2D data The degree of the polynomial is determined by the parameter ABSG which has a value between 0 and 5 with a default of 5 It works like abs in 1D which means it only corrects the spectral region between ABSF 1 and ABSF2 F1 Auto correct baseline shift correction region This option selects the command abst1 for execution It performs an automatic selective baseline correction in the F1 direction This means it corrects the columns of the processed 2D data It works like abs1 except for the following e only the columns between F2 ABSF2 and F2 ABSF1 are cor rected e the part region of each column which is
64. and PHC1 mc magnitude calculation ps power spectrum Table 2 6 The value PH_mod pk is only useful if the phase values are known and the parameters PHCO and PHC1 have been set accordingly In 1D they can be determined with apk or apks or interactively from the Phase correction mode In 2D and 3D they can only be deter mined interactively PKNL group delay compensation Avance or filter correction A X e used in 1D 2D and 3D datasets in the first direction e takes the value true or false interpreted by ft trf xfb xf2 xf1 xtrf tf On A X spectrometers PKNL true causes a non linear 5th order phase correction of the raw data This corrects possible errors caused by non linear behaviour of the analog filters On Avance spectrometers PKNL must always be set to TRUE For digitally fil tered data it causes ft to handle the group delay of the FID For analog data it has no effect PSCAL determines the region with the reference peak for vertical scaling e used in 1D datasets e takes one of the values global preg ireg pireg sreg psreg noise e interpreted by pp li lipp P 33 TOPSPIN parameters the values of PSCAL have the following meaning PSCAL Peak used as reference for vertical scaling global The highest peak of the entire spectrum preg The highest peak within the plot region ireg The highest peak within the regions specified in the r
65. and older and XWIN NmR file peak txt peaklist Mixed Shape Deconvolution format file peaklist ml AUREMOL format file 1r m1 1D masterlist m1 2D peaks XEASY format file xeasy peaks INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt peaklist xml peak list for the Plot Editor in XML format OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt peak txt peak list for the Plot Editor in TXT format SEE ALSO pps pp mdcon P 538 Conversion commands fconv NAME fconv Convert Felix type data to Bruker TOPSPIN type data 1D DESCRIPTION The command fconv converts Felix data to TOPSPIN format It opens a dialog window where you can navigate to the Felix input data file Just se lect the desired file and click convert This will open the dialog box shown in Figure 12 2 EN fconv 01_protonFID The selected FELIX datafile will be converted Define destination dataset NAME 01_protonFID EXPNO 1 PROCNO 1 DIR Clbio USER guest Figure 12 2 Her you can specify the TOPSPIN destination dataset and click OK to start the conversion The fconv source and destination data can also be entered on the com mand line Here are some examples fconv lt path gt fdata When the specified input data are found the dialog window shown in Figure 12 2 will appear Here you can specify the output dataset
66. and the specified expno and then changes the display to this expno 2D processing commands rser lt row gt lt expno gt n stores the specified row under the current data name and the specified expno but does not change the display to this expno After rser has read a row and the display has changed to the destination 1D dataset a subsequent rser command can be entered on this 1D da taset This takes two arguments and can be used as follows rser opens the above dialog box where you can specify the row number and the procno of the 2D dataset from which the current 1D dataset was extracted rser lt row gt reads the specified row from the 2D dataset from which the current 1D dataset was extracted rser lt row gt lt expno gt reads the specified row from the 2D dataset that resides under the cur rent data name 1 the specified expno and procno 1 Note that on 3D data rser does not distinguish between the F2 and F1 direction and treats the 3D dataset as a large 2D dataset This implies that the row number must lie between 1 and F2 TD F1 TD rser can also be started from the dialog box that is opened with the com mand slice INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser 2D or 3D raw data OUTPUT FILES If the output expno is specified lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1DFID audita txt acquisition audit trail 1 However if the current dat
67. apk stores the calculated phase values both as processing parameters edp and as processing status parameters dpp Automatic phasing alternate algorithm This option selects the command apks for execution It works like apk except that it uses a different algorithm which gives better results on certain spectra Automatic phasing alternate algorithm 2 This option selects the command apkm for execution It uses symmet ric isolated peaks regions with positive negative signals and regions of flat baseline for automated phase correction of 1D NMR spectra The automated phasing is performed by means of minimization of cer tain penalty function with four terms The first term is responsible for phases of symmetric isolated peaks the second accounts for regions with positive negative signals the third accounts for baseline regions and the fourth gives additional penalty for large values of first order P 65 1D Processing commands EN Phase correction apk Options oO Automatic phasing alternate algorithm Automatic phasing alternate algorithrn 2 Manual phasing O Additive phasing using PHCOM Automatic phasing Oth order only O Automatic phasing 1st order only Automatic phasing selected region only O Automatic zero order phasing selected region only Magnitude spectrum Power spectrum Required parameters 85 36169 132172 219 160903930664 19 160918955445 Figure 3 4 phase
68. be viewed with dpp or by typing s ymax _p etc YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt acqu3s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr processed 3D data Fourier transformed in F1 3iii real imaginary processed data if MC2 QF proc3 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data 3rir real imaginary data if MC2 QF 3iii real imaginary processed data if MC2 QF proc3s F1 processing status parameters P 304 3D processing commands auditp txt processing audit trail USAGE IN AU PROGRAMS TF1 store_imag where store_image can be y orn SEE ALSO tf3 tf2 ft3d P 305 3D processing commands tf3p tf2p tf1p NAME tf3p Phase correction in F3 3D tf2p Phase correction in F2 3D tf1p Phase correction in F1 3D DESCRIPTION tf3p performs a phase correction in the F3 direction applying the values of PHCO and PHC1 These values must first be determined for example ona 2D plane You can do that by typing xfb on the 3D data to process a 23 or 13 plane do a phase correction on the resulti
69. can be set with the command xdim The actually used subcube sizes whether predefined or calcu lated are stored as the F3 F2 and F1 processing status parameter XDIM and can be viewed with dpp Predefining subcube sizes is for example used to read the processed data with third party software which can not interpret the processing status parameter XDIM big little tf3 stores the data in the data storage order of the computer it runs on e g little endian on Windows PCs Note that TOPSPIN s predeces sor XWIN NMR on SGI UNIX workstations stores data in big endian The storage order is stored in the processing status parameter BYTORDP type s bytordp If however you want to read the processed data with third party software which can not interpret this parameter you can use the big little option to predefine the storage order p lt du gt the option p allows you to store the processed data on a different top level data directory typically a different disk The rest of the data di rectory path is the same as that of the raw data If the specified top level directory does not exist it will be created P 291 3D processing commands P 292 Normally t 3 stores the entire spectral region as determined by the spectral width However you can do a so called strip transform which means that only a certain region of the spectrum is stored This can be done by setting the parameters STSR and STSI which represent the strip start and
70. column from 2D data and store as 1D data SYNTAX rsc lt column gt lt procno gt n DESCRIPTION The command rsc reads a column from a 2D spectrum and stores it as a 1D spectrum When entered on a 2D dataset without arguments rsc opens a dialog box where you can specify the column number and the procno of the output data Please specify column option destination procna COLUMN J PROCNO 999 Figure 4 13 The column must be specified as a number between 1 and F2 SI The latter is the F2 processing status parameter SI that can be viewed with s si The procno can be any number other that the current procno If the procno field is left empty the output dataset is stored under data name TEMP When entered on a 2D dataset rsc takes up to three arguments and can be used as follows rsc opens the above dialog box rsc lt column gt stores the specified column under data name TEMP P 180 2D processing commands rsc lt column gt lt procno gt stores the specified column under the current data name the current expno and the specified procno It changes the display to the output 1D data rsc lt column gt lt procno gt n stores the specified column under the current data name the current expno and the specified procno It does not change the display to the output 1D data After rsc has read a column and the display has changed to the desti nation 1D dataset a subsequent rsc command can be ent
71. command like add2d from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that If the second dataset has not been defined yet add2d opens the add subtract adsu dialog box The adsu command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters P 151 2D processing commands P 152 INPUT PARAMETERS set from the adsu dialog box with edp or by typing alpha gamma etc ALPHA multiplication factor of the current spectrum GAMMA multiplication factor of the second spectrum INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data of the current dataset proc F2 processing parameters lt dir2 gt data lt user2 gt nmr lt name2 gt lt expno2 gt pdata lt procno2 gt 2rr 2ir 2ri 2ii processed data of the second dataset OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data procs F2 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS ADD2D ADDSER MUL2D SEE ALSO add duadd mul 2D processing commands bcm2 bcm1 NAME bcm2 User defined baseline correction in F2 2D bcm1 User defined baseline correction in F1 2D DESCRIPTION Baseline correct
72. commands P 346 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data used_ from data path of the source nD data and the trace number OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data wtr on 2D data 3rrr 3irr 3rir 3rri 3iii processed data wtr on 3D data A4rrrr 4iiii processed data wtr on 4D data auditp txt processing audit trail SEE ALSO rtr rpl wpl rcb rser wser wserp Chapter 7 Print Export commands This chapter describes TOPSPIN print plot and export commands Printing can be done directly from the TOPSPIN interface or from the Plot Editor The data window can be exported into a graphics file Commands are available for setting the plot title and for 2D and 3D data the contour levels Print Export commands autoplot NAME autoplot Plot data according to Plot Editor layout 1D 2D DESCRIPTION The command autopilot plots the current dataset according to a Plot Editor layout The layout must be specified with the processing parame ter LAYOUT This layout can be a standard Plot Editor layout which is de livered with TOPSPIN or a user defined layout which has been set up from the Plot Editor autoplot can take the following arguments s setup prt Use printer setup file setup prt instead of the printer setup that was saved with
73. correction of the F2 frequency domain data Each column is phase corrected according to PH_mod This parameter takes the value no pk mc or ps For PH_mod pk t 2 applies the values of PHCO and PHC1 This is only useful if the phase values are known You can determine them by typing xfb on the 3D data to process a 23 or 12 plane do a phase correction on the resulting the 2D dataset and store the phase values to 3D More details on PH_mod can be found in chapter 2 4 The F2 processing parameter SI determines the size of the processed data in the F2 direction This must however be set before t 3 is done and cannot be changed after t 3 See t 3 for the role of TD TDeff and TDoff tf2 can do a strip transform according to the F2 parameters STSR and STSI see t 3 tf2 evaluates the F2 parameter FCOR The first point of the FIDs is mul tiplied with the value of FCOR which is a value between 0 0 and 2 0 As such FCOR allows you to control the DC offset of the spectrum 1 If FAMODE undefined t 3 sets processing status MC2 to processing MC2 P 297 3D processing commands P 298 tf2 evaluates the F2 parameter REVERSE If REVERSE TRUE the spectrum will be reversed in F2 i e the first data point becomes the last and the last data point becomes the first tf2 evaluates the F2 status parameter MC2 For MC2 OF t 2 uses the file 3rrr as input and the files 3rrr and 3rir as output For MC2 QF t 2 uses the files 3rr
74. correction parameter PHC1 For a full description of apkm en ter the TOPSPIN command help apkm Automatic phasing selected region only This option selects the command apk for execution It works like apk except that it uses only a certain region of the spectrum for the calculation of the phase values This region is determined by the pa rameters ABSF1 and ABSF2 The calculated phase values are then applied to the entire spectrum Note that the parameters ABSF1 and ABSF2 are also used by the command absf If you run a command like apk from the command line you have to P 66 1D Processing commands make sure that the required parameters are already set Click the Procpars tab or enter edp to do that If automatic phase correction does not give satisfactory results you can perform interactive phase correction This can be started with the entry Manual phasing in the ph dialog box by clicking the 4 button in the toolbar or by entering ph on the command line The ph command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the ph dialog box with edp or by typing absf1 absf2 etc ABSF 1 low field left limit of the region used by apk ABSF2 high field right limit of the region used by apkf OUTPUT PARAMETERS can be viewed with edp dpp or by typing phcO s phc0O etc PHCO zero order phase corre
75. data from the default Plot Editor portfolio from port folio saved in dataset the portfolio contains the current TOPSPIN dataset plus the data from the portfolio stored in this dataset Override Plotter saved in Plot Editor If enabled the plotter defined in the Plot Editor layout will be overrid den by the plotter defined by the processing parameter CURPLOT P 364 Print Export commands For each Option Required Parameter combination the corresponding command line command is shown in the title bar of the dialog box In the example above this is the command plot f INPUT FILES see the description of prnt plot and autoplot SEE ALSO prnt plot autoplot P 365 Print Export commands P 366 prnt NAME prnt Print the current dataset 1D 2D 3D DESCRIPTION The command prnt prints the current dataset as it is shown on the screen Before printing starts the operating system print dialog box will appear Here you can for example select the printer and printer proper ties SEE ALSO print plot autoplot Print Export commands savelogs NAME savelogs Save logfiles DESCRIPTION The command savelogs collects important support information about the userspecific TopSpin installation and saves them on user pc or on the Bruker FTP server in a zipped tar file tar gz Please note only to use the automatic ftp upload function if you have been instructed by Bruker to do so If it is insturcted by B
76. data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii 2D processed data P 190 1 However if the current data name is TEMP rsr lt row gt lt procno gt reads from the specified Procno in the dataset from which the current 1D dataset was extracted 2D processing commands OUTPUT FILES If no procno is specified lt dir gt data lt user gt nmr TEMP 1 pdata 1 1r 1i 1D spectrum used_from data path of the source 2D data and the row no auditp txt processing audit trail If the output procno is specified lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D spectrum used_from data path of the source 2D data and the row no auditp txt processing audit trail USAGE IN AU PROGRAMS RSR row procno If procno 1 the row is written to the dataset TEMP SEE ALSO rtr rsc wsr wsc rser rser2d wser wserp slice P 191 2D processing commands sub2 sub1 sub1d12 sub1d1 adsu NAME sub2 Subtract 1D data from 2D data rows keep sign 2D sub1 Subtract 1D data from 2D data columns keep sign 2D sub1d2 Subtract 1D data from 2D data rows 2D sub1d1 Subtract 1D data from 2D data columns 2D adsu Open add subtract multiply dialog box 1D 2D DESCRIPTION Subtracting a 1D data from a 2D data can be started from the command line or from the add subtract dialog box The latter is opened with the comm
77. data window nD DESCRIPTION The command reopen reopens the current dataset in a new data win dow This is for example convenient to view various regions or various objects spectrum fid parameters etc of the same dataset Multiple data windows are indicated with a number in square brackets e g 1 in the title bar Entering reopen on the command line is equivalent to clicking File Re open in the menu SEE ALSO open P 453 Dataset handling smail NAME smail Send the current dataset by Email 1D 2D 3D DESCRIPTION The command smail sends the current dataset by Email It opens a di alog box where you can specify the required information or accept the default values Ey smail The currently displayed data set will be sent as an attachment to this mail in form of a ZIP or JCAMP DX archive file Type of archive kip compress v Include these data types FID RSPEC ISPEC w TO Sas FROM SUBJECT SMTP mail server E MAIL TEXT Figure 9 15 In the dialog box you can select the e Archive type ZIP or JCAMP e Data type s included FID Spectrum and or Parameters P 454 Dataset handling For ZIP format data you can choose between compression and no com pression For JCAMP format you can choose between the following compression modes e FIX 0 table format e PACKED 1 no spaces between the intensity values e SQUEEZED 2 the sign of the intensity v
78. dataset cannot be chosen it is always set to 1 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid Avance type 1D raw data ser Avance type 2D or 3D raw data P 536 Conversion commands acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid AMX type 1D raw data ser AMX type 2D or 3D raw data acqu acquisition parameters acqus acquisition status parameters audita txt acquisition audit trail lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters For 2D data the additional parameter files acqu2 acqu2s proc2 and proc2s will be used For 3D data the additional parameter files acqu2 acqu2s proc2 and proc2s and acqu3 acqu3s proc3 and proc3s will be used USAGE IN AU PROGRAMS CONVDTA expno SEE ALSO conv vcony jconv fconv P 537 Conversion commands convertpeaklist NAME convertpeaklist Convert XML format peaklist to TXT format peaklist DESCRIPTION The command convertpeaklist converts an XML format peaklist to various other formats The output format can be controlled with the ar gument txt text format TOPSPIN 2 0
79. dir and user of the specified alias name dalias prgen lt alias gt print the full pathname of the specified alias name dalias prall print the name expno procno dir and user of all alias names dalias prallgen print the full datapath of all alias names Remove alias names dalias rm lt alias gt remove the specified alias name dalias rmall remove all alias names Note that removing alias names does not remove the corresponding da P 417 Dataset handling ta Entering the command dalias without arguments shows a help mes sage with a summary of the above information SEE ALSO re P 418 Dataset handling del dela delp deldat delete NAME del Delete data nD dela Delete raw data nD delp Delete processed data nD deldat Delete data acquired at certain dates nD delete Open the delete dialog box nD SYNTAX del lt name gt DESCRIPTION Delete commands can be started from the command line or from the de lete dialog box The latter is opened with the command delete see Fig ure 9 1 This dialog box has several options each of which selects a certain com mand for execution The commands del dela delpand deldat allow you to display a list of datasets Such a list includes datasets containing raw and or proc essed data as well as empty datasets which only contain parameter files You can click one or more datasets in the list to mark them for deletion and then clic
80. display the calculated projection with the 2D dataset The cur rent 2D dataset remains the active dataset as 1D to display the calculated projection as a 1D dataset The active dataset changes to the destination procno The required parameters can also be specified as arguments on the com mand line As an example we use the command 2disco here f2disco lt firstrow gt prompts for astrow and refrow and stores the disco projection under data name TEMP f2disco lt firstrow gt lt lastrow gt lt refrow gt stores the specified disco projection under data name TEMP f2disco lt firstrow gt lt lastrow gt lt refrow gt lt procno gt stores the specified disco projection under the specified procno of the current data name f2disco lt firstrow gt lt lastrow gt lt refcol gt lt procno gt n stores the specified disco projection under the specified procno of the current data name but does not change the display to this procno INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 161 2D processing commands P 162 2rr 2ir 2ri 2ii processed data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D spectrum containing the F1 disco projection auditp txt processing audit trail USAGE IN AU PROGRAMS F2DISCO firstrow lastrow refcol procno F1DISCO firstcol lastcol refrow procno for procno 1 the disco
81. distribution of one peak over a series of experiments i e a series of rows in a pseudo 2D dataset First the peak positions are determined on one row for example with ppt1 Then the command pd deter mines the intensity at these positions in each row However peak positions sometimes drifts in the course of the experiment i e they can be slightly different in different rows Therefore pd searches for the maximum intensity in a range around a each peak position This range is determined by the parameter DRIFT P 47 TOPSPIN parameters P 48 EDGUESS table of initial values and step rates of the function variables used in pseudo 2D relaxation datasets interpreted by simfit The EDGUESS table shows all variables of the function specified by FCTTYPE For each variable the initial guess G and step rate S can be set for each component C Table 2 9 shows the EDGUESS table for an inversion recovery experiment with 2 components The initial guess for I 0 must be such that the total value of all compo nents GC110 0 5 SC110 0 05 GC1A 1 0 SC1A 0 1 GC1T1 2 0 SC1T1 0 2 GC2I0 0 5 SC2l0 0 05 GC2A 1 0 SC2A 0 1 GC2T1 2 0 SC2T1 0 2 Table 2 9 does not exceed 1 If there is only one component I 0 is usually set to 1 The step rate is usually set to about one tenth or the initial guess If the step rate of a variable is set to zero then this variable is not changed during the iterations Note that the commands
82. exist e g NC_proc e the corresponding processing parameter is not interpreted e g FT_mod e the value of the corresponding processing parameter is adjusted e g STSI These type of processing status parameters are listed below and described TOPSPIN parameters as output parameters for each processing command They can be viewed with dpp see also chapter 2 1 BYTORDP byte order of the processed data used in 1D 2D and 3D datasets in the first direction takes the value little or big set by the first processing command interpreted by various processing commands Big endian and little endian are terms that describe the order in which a sequence of bytes are stored in a 4 byte integer Big endian means the most significant byte is stored first i e at the lowest storage address Little endian means the least significant byte is stored first TOPSPIN only runs on computers with byte order little endian How ever TOPSPIN S predecessor XWIN NMR also runs on SGI workstations which are big endian The byte order of the raw data is determined by the computer which controls the spectrometer and is stored in the acquisition status parameter BYTORDA type s bytorda This allows raw data to be processed on computers of the same or differ ent storage types The first processing command interprets BYTORDA stores the processed data in the byte order of the com puter on which it runs and sets the processing status parameter BY
83. file Data extension of data file extension of parameter type file EX gxd gxp GX gxd gxp ALPHA nmf txt DELTA bin hdr FX num an integer no parameter file number Table 12 1 jconv converts all JNMR parameters which have a TOPSPIN equivalent First the JNMR parameter EXMOD is interpreted If it is set to a certain name jconv checks the existence of a TOPSPIN parameter set with that name If it exists it is copied to the destination dataset If it does not exist a standard parameter set standard1D for 1D data is copied Then jconv converts all JNMR parameters which have a TOPSPIN equivalent and over writes the values of the parameter set which was previously copied The parameters of the TOPSPIN parameter set which do not have a JNMR equivalent keep their original values If you frequently convert Jnmr data with typical values of EXMOD you might want to create the TOPSPIN pa P 549 Conversion commands rameter sets with the corresponding names This can be done by reading a standard parameter set with rpar modify it with eda and edp and then store it with wpar INPUT FILES lt jdata ext gt Jeol raw data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid TOPSPIN 1D raw data acqu TOPSPIN acquisition parameters acqus TOPSPIN acquisition status parameters audita txt acquisition audit trail lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1
84. found peaks are appended to a possibly existing list When it is unchecked a new list is created pp2d append e Discard new peak s if already in list Check this option to avoid duplicate peaks pp2d noduplicates Export results as XwinNmr peak list In addition to TOPSPIN XML format the result is also stored in XWIN NMR format file peak txt pp2d txt This file is typically used with XWIN NMR AU programs Furthermore you can set the following peak picking parameters Region parameters Here you can set the region limits for both the F2 and F1 direction Only peaks within this region will be picked Note that the limits can be speci fied in the text fields or set with the button Set to The latter allows you to select from Full range full spectrum Displayed range range displayed in the data window Range defined by stored parameters range stored in parameters F1P F2P 1 Analysis commands EJ Peak picking _pp2d append noduplicates Append peaks to list Discard new peak s if already in list d Export results as XVVinNMR peak list Parameters Region From F1P To F2P F2 ppm 9 5699 0 5081 Sensitivity F1 ppm 157 8227 7 8397 Minimum intensity rel MI 0 0000 Maximum intensity rel MAXI 1 0000 Diagonal gap points PPDIAG 0 Resolution points PPRESOL 1 Miscellaneous Maximum of peaks PPMPNUM L Interpolation type PPIPTYP Pick peaks of sign
85. intensity 28 minimum intensity 30 parameters 93 sensitivity 31 94 391 peak txt file 392 538 peaklist file 469 peaklist xml file 392 393 538 peaks file 392 peakw command 118 ph command 62 65 217 220 247 phase correction 1D 75 83 98 100 110 133 135 1D automatic 65 86 2D 213 223 227 231 247 250 3D 267 270 288 291 296 301 306 308 326 automatic 20 first order 32 44 62 63 interactive 2D 230 mode 32 multiple 32 43 44 of 1D raw data 111 of raw AMX data 270 290 of raw data 33 87 zero order 32 43 62 63 phase sensitive spectrum 2D 196 218 221 phase values 1D 20 65 110 2D 230 3D 268 270 289 291 297 302 pk command 75 83 98 110 pknd command 326 plane from 3D data 242 277 282 284 306 326 334 341 plot editor 361 layouts 348 region 1D 34 52 388 389 469 title 359 360 553 plot command 54 361 364 Plot Editor 348 364 polynomial baseline correction 1D spectrum 53 54 72 469 2D spectrum 145 148 154 3D spectrum 286 312 fid 23 69 Postscript 348 power spectrum 1D 116 2D 7 220 mode 33 pp command 28 387 394 399 469 pp2d command 394 pp3d command 399 ppd command 393 ppf command 387 pph command 387 ppj command 387 ppl command 387 ppp command 91 469 pps command 387 prguide command 113 print the active window 363 print command 363 prnt command 359 360 363 366 procid command 115 processed data 6 7 24 processing commands 21 43 Processing Guide 113 pr
86. is typically used after reading a window layout with more than one data window SEE ALSO close newwin nextwin Chapter 14 TOPSPIN User Management This chapter describes commands which are related to TOPSPIN audit trail and user management The audit trail contains a record of all acquisition and processing activities data checksums and electronic signatures The can be included by TOPSPIN internal users which can be set up by the NUR administrator Internal users are required to log in to TOPSPIN before they can use it or exit it TOPSPIN User Management audit auditcheck NAME audit Open audit trail dialog box nD auditcheck Check data consistency nD DESCRIPTION The command audit opens the audit trail dialog box PN Audit trail audit proc Options View audit trail of processed data O View audit trail of acquisition data Verify audit trails O Add a comment to audit trail of processed data O Add a comment to audit trail of acquisition data Figure 14 1 This dialog box has several options each of which selects a certain com mand for execution View audit trail of the processed data This option selects the command audit proc for execution It shows the processing audit trail file auditp txt This file is created by the processing command that creates the processed data e g em Any processing command that modifies updates the processed data e g ft makes an additional entry Furthermor
87. just enter the name on the command line Find Find a character string in the command index INPUT FILES lt tshome gt classes prop cmdindex_main prop command index properties file lt tshome gt prog docu gt english xwinproc html html TOPSPIN command help files OUTPUT FILES lt tshome gt exp stan nmr lists mac Macros created by cmdhist Save as SEE ALSO cmdhist P 573 TOPSPIN Interface Processes cmdhist NAME cmdhist Open command history DESCRIPTION The command cmdhist opens a command history control window see Figure 13 4 amp Command History cmdhist Figure 13 4 It shows all commands that have been entered from the command line since TOPSPIN was started You can select one or more commands Fur thermore the following buttons are available Execute Execute the selected command or commands Append Append the first selected command to the command line The ap pended command can be edited and executed Useful for com mands with many arguments such as re Save Macro P 574 TOPSPIN Interface Processes The selected command s are stored as a macro You will be prompted for the macro name To edit this macro enter edmac lt macro name gt To execute it just enter the name on the command line The command history control window can also be started as follows e Click View Command Line History or e Right click in the command line and select Comman
88. keep sign 2D subid1 Subtract 1D data from 2D data columns 2D sub1d2 Subtract 1D data from 2D data rows 2D sub2 Subtract 1D data from 2D data rows keep sign 2D sumpl Calculate sum projection 3D suspend Suspend a running acquisition swin Swap the position and geometry of two data windows sym Symmetrize spectrum about the diagonal 2D syma Symmetrize spectrum about the diagonal keep sign 2D symj Symmetrize spectrum about central horizontal line 2D symt Open symmetrization and tilt command dialog 2D il t1 guide Open the relaxation analysis guide tabs1 Automatic baseline correction in F1 3D Help Execute J New Macro Figure 13 3 It shows all TOPSPIN commands which can be entered from the command line with a one line description for each command You can select one or more commands for further actions The following actions are available Help Open the HTML Help page of the selected command This is equivalent P 572 TOPSPIN Interface Processes to double clicking the command Execute Execute the selected command or commands Append Append the first selected command to the command line The ap pended command can be edited and executed Useful for com mands with many arguments such as re Save as The selected command s are stored as a macro You will be prompted for the macro name To edit this macro enter edmac lt macro name gt To execute it
89. knowledge base This option activaytes the command ghe1p It allows you to search for the specified item in the NMR Guide knowledge base Search in NMR Guide knowledge base This option activaytes the command cmdindex It opens the command index dialog irrespective of the specified command P 583 TOPSPIN Interface Processes P 584 Entering help on the command line is equivalent to clicking Help Ad vanced Search or hitting the F1 key INPUT FILES lt tshome gt prog docu gt english xwinproc html html TOPSPIN command help files lt tshome gt guide NMR Guide files and directories SEE ALSO docs TOPSPIN Interface Processes kill show NAME kill show Show active TOPSPIN commands and allow to kill them DESCRIPTION The command kill displays a list of all active TOPSPIN commands To kill a command e click a command entry e click the button Kill The command show is equivalent to ki11 A running acquisition should not be stopped with ki11 because this would leave an inconsistent dataset Instead the commands halt or stop should be used for this purpose P 585 TOPSPIN Interface Processes P 586 nbook NAME nbook Open the user notebook DESCRIPTION The command nbook opens a user specific notebook Each user can create and keep his her own notebook for individual notes information settings etc INPUT AND OUTPUT FILES lt userhome gt lt topspin hostname prop noteb
90. large history and protocol files Therefore it is useful to regularly check the size of the files or simply restart TOPSPIN after each automation session OUTPUT FILES lt tshome gt prog curdir lt user gt history TOPSPIN history file history i txt TOPSPIN protocol file history traffic txt network traffic log stdout dataserver lt number gt txt dataserver output file lt userhome gt lt topspin hostname gt prop protocol txt TOPSPIN protocol file if TOPSPIN was started as P 589 TOPSPIN Interface Processes topspin client ptrace TopSpin Log File Tracer File 2 Sain Message 12 13 15 36 16 135 TOPSPINVersion 1 3 12 13 15 36 16 145 history registration started 12 13 15 36 16 145 2256 cprserver is running 12 13 15 36 16 145 2320 java virtual machine started 12 13 15 36 16 145 0 current data exam3d 1 1 C bio guest nmr 12 13 15 36 16 155 browseDataTree C A4f13b13 confinstr FILE 6 items a 12 13 15 36 20 671 browseDataTree C bio data DIRECTORY 2 items 12 13 15 36 26 800 browseDataTree C sbio data guestinmr DIRECTORY 12 items 0112 13 15 36 29 153 cmd browse_dispdata_new 12 13 15 36 29 173 lbrowseDataTree C Jhio data questinmriexam d_13C DIRECTORY 9 items 12 13 15 36 29 173 browseDataTree C dbio data guestinmriexarm d_13CA ipdata DIRECTORY _ 12 13 15 36 29 183_ lbrowseDataTree iC bisa eat ates d_13C 2ipd
91. list will be read rmisc lt type gt lt name gt Reads the list lt name gt of the type lt type gt INPUT OUTPUT DIRECTORIES In TopSpin 2 1 and newer the default directory of user defined lists is P 469 Parameters lists AU programs P 470 lt tshome gt exp stan nmr lists intrng integral range files baslpnts spline baseline points file base_info pol exp or sine baseline function files peaklist peak information files reg plot region files USGAE IN AU PROGRAMS RMISC type file WMISC type file SEE ALSO edlist Parameters lists AU programs edshape NAME edshape Edit Shape Files delshape Delete Shape Files DESCRIPTION When entered without arguments the Shape File commands edshape and delshape all open the AU program dialog box see Figure 10 5 r amp Shape Files File Options Help Source C Bruke SPIN exp stan nmrilists wave Search in names Search CABruker TOPSPIN expistaninmrilists wave user CA Bruken TOPSPINe Bip720 100 10 1 Bip 20 50 20 1 Crp20 1 40 1 Crp32 1 5 20 2 Crp42 1 5 20 2 Crp4a 1 5 20 2 Crp 0 0 5 20 1 Crp o_xfilt 2 Crp 0comp 4 Crp80 0 5 20 1 crpaocomp 4 Eburp2 1000 Eburp2tr 1000 G3 256 4 256 G4tr 256 Gaus1 1000 Gaus1_180i 1000 Gaus1_180r 1000 Gaus1_270 1000 Gaus1_90 1000 Mpf7 Pc9 4 120 1000 Pc9_4 90 1000 3 1000 a3ca_Cac0 1000 Q3_ma_c68c1 1 lasiooo ostr 1000 Reburp 1000 Rsnob
92. list with histogram O Like 1st option but peak list in JCAMP format O Calculate width of currently displayed peak Required parameters Left picking limit F1P 219 1609 Right picking limit F2P 19 1608 Intensity of reference peak CY rel iS Minimum intensity MI rel 0 Maximum intensity MAXI rel 10000 Detection sensitivity PC 1 4 0 5 Pick peaks of sign PSIGN pos Reference peak selection mode PSCAL sreg Region file for PSCAL sreg psreg SREGLST 13C CDCI3 v Figure 8 10 e its absolute intensity is larger than PC noise e it lies within the displayed region as expressed by F2P and F1P where MAXI MI and PC are processing parameters and noise is cal culated from the first 32th part of the spectrum The values of MI and MAXI must be chosen in relation to the plot pa rameter CY the intensity in cm of the reference peak The reference peak is the highest peak in the spectrum or in a certain part of it The spectral region which contains reference peak is determined by the Analysis commands parameter PSCAL For PSCAL global this is entire spectrum Table 8 2 shows all possible values of PSCAL and the corresponding re gions For PSCAL ireg or pireg the reg file is interpreted To create PSCAL Peak used as reference for vertical scaling global The highest peak of the entire spectrum preg The highest peak within the plot region ireg The highest peak within th
93. lists SCL Solvent Region lists and PHASE Phases lists The command edlist opens the following window see Figure 10 3 amp Parameter Lists etSemn Eile Options Help Source C Bruker TOPSPINexpistan nmrilistswd v Search in names v Search List type vd delays preemp tidelay filter Edit Ji Close Figure 10 3 On the topright you can change the Source and specifiy the List type with the pull down menus that should be shown in the table see figure 10 4 All items shown in the table can be edited in the upcoming text editor For detailed information user specific definition of Source Directories and the functionalities of Manage Source Directories please refer to the information given in Chapter 1 9 The dialog Figure 10 3 offers the following buttons Parameters lists AU programs Edit After selecting a list by mouseclick the button edit opens a text window in which you can edit the chosen list Same functionality is available by double click Saving the modifications will overwrite the existing list Close Closes the dialog dellist opens the same dialog box as edlist expect that the Delete option is selected When you select a List Type and click OK the availa ble files of that type appear You can click one or more entries to mark them for deletion Clicking the Delete button deletes all marked entries INPUT OUTPUT DIRECTORIES In TopSpin 2 1 and newer the default d
94. lt procno gt P 165 2D processing commands f2projn ascii file specifying the range of rows and the 1D data path f2projp ascii file specifying the range of rows and the 1D data path c1 projn ascii file specifying the range of columns and the 1D data path c1 projp ascii file specifying the range of columns and the 1D data path lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1D spectrum containing the projection auditp txt processing audit trail If the commands are used with less than three arguments the files are stored in lt dir gt data lt user gt nmr TEMP 1 pdata 1 USAGE IN AU PROGRAMS F2PROJN firstrow lastrow procno F2PROJP firstrow lastrow procno F1PROJN firstcol lastcol procno F1PROJP firstcol lastcol procno For all these macros counts that if procno 1 the projection is written to the dataset TEMP SEE ALSO f2disco f2sum rhpp P 166 2D processing commands f2sum f1sum proj NAME f2sum Calculate partial sum in F2 2D f1sum Calculate partial sum in F1 2D proj Open the projections dialog box 2D 3D DESCRIPTION The projection sum commands open the projections dialog box selecting the corresponding command amp f2sum Options Calculate positive projection O Calculate negative projection Calculate disco sum O Read positive projection O Read negative projection oO Update r
95. multiplication and a Fourier trans form efp is a combination of em ft and pk i e it does the same as ef but in addition performs a phase correction ef and efp automatically perform an FID baseline correction according to BC_mod All composite processing commands can be found under the menu Processing More Transforms Shortcuts INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data input if they exist but are not Fourier trans formed proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail P 75 1D Processing commands USAGE IN AU PROGRAMS EF EFP SEE ALSO gf gfp fp fme P 76 1D Processing commands em gm wm NAME em Exponential window multiplication of the FID 1D gm Gaussian window multiplication of the FID 1D wm Open window function dialog box 1D 2D DESCRIPTION Window multiplication commands can be entered on the command line or started from the window function dialog box The latter is opened with the command wm ie Window func
96. multiplied with the constant DC to the current dataset add performs a point to point addition which is independent of the spectrum calibration The result is stored in the current dataset DC can be set by entering de on the command line or in the Procpars pane If the second dataset has not been defined yet the add subtract dialog box is opened Here you can define the second dataset and start the add command add works on raw or on processed data de pending on the value of DATMOD For DATMOD raw add adds the raw data of the current and second dataset but stores the result as processed data in the current dataset As such the raw data of the current dataset are not overwritten Add a 1D spectrum ppm Hz wise This option selects the command duadd for execution It works like add except that it adds two datasets according to their chemical shift values Each ppm value of one dataset is added to the same ppm val ue of a second dataset duadd is useful when the two input spectra are 1D Processing commands Add subtract add ee Add a spectrum of same or different size ppm Hz wise current DC second C Add a FID current DC second C Add a constant C Multiply with 1D spectrur fid current second Multiply with constant C Multiply with 1 Divide by a 1D spectrumifid current second Required parameters Constant DC jo NAME 2nd spectrum exam e ei EXPNO fi PROCNO fi USER quest DI
97. of the 2D data input of wsr on a 1D dataset or lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D processed data used_ from data path of the 2D data input of wsr on a 1D dataset OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS WSR row procno expno name user dir SEE ALSO WSC rsr rsc wser wserp rser rser2d slice P 212 2D processing commands xf1 NAME xf1 Process data including FT in F1 2D DESCRIPTION The command xf1 processes a 2D dataset in the F1 direction It can be started from the command line or from the Fourier transform dialog box The latter is opened with the command ftf xf1 Fourier transforms time domain data FID into frequency domain data spectrum Depending on the F1 processing parameters BC_mod WDW ME_mod and PH_mod xf1 also performs baseline correction window multiplication linear prediction and phase correction respective ly These steps are described in detail for the command x b Normally 2D data are processed with the command x b which performs a Fourier transform in both directions F2 and F1 In some cases howev er it is useful to process the data in two separate steps using the se quence xf2 xf1 for example to view the data after processing them in F2 only If you run x 1
98. offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum F3 F2 and F1 parameters set by t 3 can be viewed with dpp or by typing s si s stsi etc SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform P 303 3D processing commands TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 F1 parameters set by the t 3 can be viewed with dpp or by typing s mc2 MC2 Fourier transform mode OUTPUT PARAMETERS F1 parameters can be viewed with dpp or by typing s ft_mod FT_mod Fourier transform mode FTSIZE Fourier transform size F3 parameters can
99. on the F2 processing parameters BC_mod WDW ME_mod and PH_mod x 2 also performs baseline correction window multiplication linear prediction and phase correction respective ly These steps are described in detail for the command x b Normally 2D data are processed with the command x b which performs a Fourier transform in both directions F2 and F1 In some cases howev er 2D data must only be processed in the F2 direction Examples are T1 T2 or Dosy data or a 2D dataset which has been created from a series on 1D datasets Even if a 2D dataset must be processed in both directions it is some times useful to do that in two separate steps using the sequence xf2 xf1 The result is exactly the same as with xfb with one exception xfb performs a quad spike correction see xfb and the sequence xf2 xf1 does not xf2 takes the same options as xfb Furthermore x 2 takes the special option nd2d converting an nD dataset n gt 2 to a 2D dataset processing it in the acquisition direction The size in the orthogonal direction F1 S1 of the destination 2D dataset is the product of the TD values of the source nD dataset xf2 can also be used to process one 2D plane of a 3D spectrum see xfb INPUT PARAMETERS F2 and F1 parameters P 223 2D processing commands set from the t dialog box with edp or by typing si stsr etc SI size of the processed data STSR strip start first output point of strip transform STSI
100. options are P 447 Dataset handling Display data in same window Selects the command rep for execution It reads the specified PROC NO in the current data window Display data in new window Selects the command repw for execution It reads the specified PROCNO in a new data window The destination procno can also be specified on the command line e g rep 77 INPUT FILES For re and rew lt dir gt data lt user gt nmr lt name1D gt lt expno gt fid 1D raw data acqu acquisition parameters acqus acquisition status parameters For re rew rep and repw lt dir gt data lt user gt nmr lt name1 D gt lt expno gt pdata lt procno gt 1r 1i processed 1D data proc processing parameters procs processing status parameters Note that these are only the main files of a 1D dataset OUTPUT FILES lt tshome gt prog curdir lt user gt curdat current data definition USAGE IN AU PROGRAMS RE name SEE ALSO reb open new find dir P 448 Dataset handling reb NAME reb Open a data browser at the level of data names nD DESCRIPTION The command reb opens a file browser see Figure 9 13 x Look in nmr clea File name C bio dataiguestinmr Display Files of type all Files Cancel Figure 9 13 Here you see a list of dataset names under the same lt dir gt and lt user gt as the currently selected dataset Note that TOPSPIN data are stored in a dir
101. parameter REVERSE If REVERSE TRUE the spectrum will be reversed i e the first data point becomes the last and the last data point becomes the first t3d can be used with the following command line arguments n t3d will not store the imaginary data Imaginary data are only need ed for phase correction in last processed direction If the phase values are already known and PHCO and PHC1 have been set accordingly t3d will perform phase correction and there is no need to store the imaginary data This will save processing time and disk space If you still need to do a phase correction after ft3d you can create imagi nary data from the real data with a Hilbert transform see tht1 Note that if the n option is omitted imaginary data are only stored in the last processed direction 210r 12 3D processing commands t3d 21 is equivalent to the command sequence tf 3 t 2 tf1 whereas t3d 12 is equivalent to t 3 tf 1 tf2 xdim 3D spectra are stored in the so called subcube format The size of the subcubes is calculated by t3d and depends on the size of the spec trum and the available memory The option xdim allows you to use predefined subcube sizes It causes t3d to interpret the F3 F2 and F1 processing parameter XDIM which can be set by entering xdim on the commandline Note that XDIM 0 is evaluated as XDIM SI The actually used subcube sizes whether predefined or calculated are stored as the F3 F2 a
102. plane accordingly rpl 11 Read plane 11 Use the plane axis orientation and source 3D procno as defined in current 2D dataset rpl 31 11 Read F1 F3 plane 11 exchanging the F1 and F3 axes Use the source 3D procno as defined in current 2D dataset rpl 13 11 2 read F1 F3 plane 11 from the 3D dataset under procno 2 As described above the rp1 argument plane axis orientation determines whether the axes are exchanged This is sometimes required to match nuclei when you compare a 3D plane with a 2D dataset Example you have a 3D NOESYHSQC F3 1H F2 13C F1 1H and want to compare an F2 F1 plane with a 2D HSQC F2 1H F1 13C Now compare the fol lowing actions rpl 12 The plane is stored as a 2D dataset with F2 13C F1 1H which cannot be directly compared with the a HSQC rpl 21 The plane is stored as a 2D dataset with F2 1H F1 13C which can be directly compared with the a HSQC In special cases rp1 results in a 2D dataset which is not Fourier trans formed in F2 This occurs for example if you run rp1 12 on a 3D dataset which has only been transformed in F3 rp1 unshuffles the output data storing the odd and even points in separate data files 2rr and 2ir As a result the size in F2 parameter Sl is only half the size of the corre sponding direction in the 3D dataset If for some reason you want keep the same size you can use rp1 with the option keepsize The output data are then zero filled once in F2 Here is an examp
103. possibly existing data You can use any other combination of arguments as long they are en tered in the correct order The processed data number procuo of the out put dataset is always set to 1 genfid can be used if you want to reprocess a 1D spectrum for exam ple with different processing parameters but the raw data do not exist any more An example of such a procedure is ift if the data are Fourier transformed genfid to create the pseudo raw data edp to set the processing parameters ef to process the pseudo raw data If the input data are processed but not Fourier transformed you can skip the first step INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed time domain data real imaginary OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid pseudo raw data audita txt acquisition audit trail USAGE IN AU PROGRAMS GENFID expno overwrites possibly existing raw data in the specified expno SEE ALSO ift genser P 97 1D Processing commands gf gfp NAME gf Gaussian window multiplication Fourier transform 1D gfp Gaussian window multiplication FT phase correction 1D DESCRIPTION The composite processing command gf is a combination of gm and ft i e it performs a Gaussian window multiplication and a Fourier transform gfp is a combination of gm ft and pk i e it does the same as gf but in
104. programming can be found under Help Manuals Programming Manuals Python programming Note that serial processing also be started as follows e click Processing Serial Processing or P 527 Automation P 528 e click File Run choose Execute Serial script on Data set list and click OK INPUT OUTPUT FILES lt tshome gt exp stan nmr py lt tshome gt exp stan nmr py user ser _ py Python programs for serial processing lt tshome gt exp stan nmr lists mac lt tshome gt exp stan nmr lists mac user ser _ Macros for serial processing SEE ALSO edpy edmac intser Automation spooler NAME spooler display queued scheduled and cron jobs DESCRIPTION The command spooler displays the spooler jobs It opens a dialog showing e Queued jobs jobs started with the command qu or qumulti e Scheduled jobs jobs started with the command at or atmulti e Cron jobs jobs started with the command cron For each job the dialog shows the command to be executed the target data object the owner and depending on the job various other informa tion The Spooler dialog offer the following menus Spooler Allows you to suspend or remove all queued scheduled or cron jobs Queue Allows you to e Create new jobs e Suspend all jobs e Remove all jobs for priority delayed and cron jobs separately Job Allows you to e Create new jobs e Stop restart or
105. projection is written to the dataset TEMP SEE ALSO f2projn f2sum rhpp 2D processing commands f2projn f2projp f1projn f1projp proj NAME f2projn Calculate negative partial projection in F2 2D f2projp Calculate positive partial projection in F2 2D fiprojn Calculate negative partial projection in F1 2D f1projp Calculate positive partial projection in F1 2D proj Open projections dialog box DESCRIPTION The projection commands open the projections dialog box see Figure 4 7 selecting the corresponding command J f2projp Options oO Calculate negative projection O Calculate sum Calculate disco sum Read positive projection O Read negative projection O Update rows cols from display Required parameters Projection sum of Display projection First row col Last row col Destination PROCNO Figure 4 7 P 163 2D processing commands P 164 This dialog box has several options each of which selects a certain com mand for execution Calculate positive projection of rows This option selects the command 2pro 3p for execution It calculates the positive partial 1D projection of the 2D dataset in the F2 direction Calculate positive projection of columns This option selects the command f1pro jp for execution It calculates the positive partial 1D projection of the 2D dataset in the F1 direction Calculate negative projection of rows This option select
106. r13 and r23 can also be entered as arguments on the command line In that case the command is executed without opening the dialog box For example r1210 999 reads an F1 F2 plane number 10 and stores it in procno 999 Note that the Plane orientation is not specified as an argument but part of the com mand name The commands r12 r13 and r23 are equivalent to the commands rp1 12 rpl 13 and rp1 23 respectively see the description of rp1 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr 3irr 3rir 3rri 3iii processed 3D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data auditp txt processing audit trail P 280 3D processing commands USAGE IN AU PROGRAMS R12 plane procno for example R12 64 1 R13 plane procno for example R13 64 1 R23 plane procno for example R23 64 1 SEE ALSO r12d r13d 123d rpl wpl P 281 3D processing commands r12d r13d r23d NAME r12d Read diagonal F1 F2 plane and store as 2D data 3D r13d Read diagonal F1 F3 plane and store as 2D data 3D r23d Read diagonal F2 F3 plane and store as 2D data 3D DESCRIPTION Read plane commands can be started from the command line or from the read plane dialog box The latter is opened with the command slice ty Cross sections r12 Options Extract an orthogonal
107. r4i1 i1r1 i1i1 i2r1 i211 i3r141 i3i1 i4r1 i4i1 r4r2 r1i2 r2r2 r2i2 r3r2 r3i2 r4r2 r4i2 i1r2 i1i2 i2r2 i2i2 i3r2 i3i2 i4r2 i4i2 2ir file Below the F1 input data are simply redisplayed with the first F1 complex input points in bold Input F1 processing F2 i1r1 i1i1 i2r1 i2i1 i3r1 i3i1 i4r1 i4i1 Fl rartertia 121421 r3rA r3i1 r4r1 r4i1 i1r2 i1i2 i2r2 i2i2 i3r2 i3i2 i4r2 i4i2 r4r2 r1i2 r2r2 r2i2 r3r2 r3i2 r4r2 r4i2 r r4 r1id r2r1 r2i1 r3r1 r3i1 r4r1 r4i1 i1r1 i1i1 i2r1 i2i1 i3r1 i3i1 i4r1 i4i1 r4r2 r1i2 r2r2 r2i2 r3r2 r3i2 r4r2 r4i2 i1r2 i1i2 i2r2 i2i2 i3r2 i3i2 i4r2 i4i2 2ir file P 240 2D processing commands Output F1 processing F2 i1r1 i1i11 i2r1 i2i1 i3r1 i3i1 i4r1 i4i1 FI 472 1112 i2r2 i2i2 i3r2 i3i2 i4r2 i4i2 2rr file r r r1i1 r2r1 r2i1 r3r1 r3i1 r4r1 r4i1 r r2 r1i2 r2r2 r2i2 r3r2 r3i2 r4r2 r4i2 2ir file rartertia 121421 Sr 4r3i1 r4r1 r4i1 rir2 r1i2 r2r2 r2i2 r3r2 r3i2 r4r2 r4i2 i1r1 i1i1 i2r1 i2i1 i3r14 i3i1 i4r1 i4i1 i1r24i1i2 i2r2 i2i2 i3r2 i3i2 i4r2 i4i2 2ii file Note that e for FnMODE QF zero filling once in F1 is done when SI TD For FnMODE OF zero filling once in F1 is done when SI 2 TD e FnMODE QF is normally used on magnitude or power data For this purpose the F1 processing parameter PH_mod must be set to MC or
108. raw data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser 2D pseudo raw data audita txt acquisition audit trail lt dir gt data lt user gt nmr lt name gt lt expno2 gt pdata 1 used_from data path of the source 3D data and the plane number USAGE IN AU PROGRAMS RSER2D direction plane expno SEE ALSO rser wser wserp rpl wpl P 285 3D processing commands tabs3 tabs2 tabs1 NAME tabs3 Automatic baseline correction in F3 3D tabs2 Automatic baseline correction in F2 3D tabs1 Automatic baseline correction in F1 3D DESCRIPTION tabs3 performs an automatic baseline correction in the F3 direction by subtracting a polynomial The degree of the polynomial is determined by the F3 parameter ABSG which has a value between 0 and 5 with a de fault of 5 tabs3 works like absfin 1D and abs2 in 2D This means that it only corrects a certain spectral region which is determined by the pa rameters ABSF1 and ABSF2 tabs2 works like tabs3 except that corrects data in the F2 direction us ing the F2 parameters ABSG ABSF2 and ABSF1 tabs1 works like tabs3 except that corrects data in the F1 direction us ing the F1 parameters ABSG ABSF2 and ABSF1 INPUT PARAMETERS F3 parameters set by the user with edp or by typing absg ABSG degree of the polynomial to be subtracted 0 to 5 default of 5 F3 F2 and F1 parameters set by the user with edp or by typing absf1 absf2 AB
109. size of the processed data and the available computer memory xfb stores the data in sequential or submatrix format Sequen tial format is used when the entire dataset fits in memory otherwise sub matrix format is used xfb automatically calculates the submatrix sizes such that one row F2 of submatrices fits in the available memory The calculated submatrix sizes are stored in the processing status parameter XDIM type dpp Table 4 6 and 4 8 show the alignment of the data points for sequential and submatrix format respectively This example shows a dataset with the following sizes F2 SI 16 F1 SI 16 F2 XDIM 8 F1 XDIM 4 The storage handling is completely transparent to the user and is only of interest when the data are interpreted by third party software P 233 2D processing commands Table 4 6 2D data in sequential storage format P 234 2D processing commands Table 4 7 2D data in 8 4 submatrix storage format As can be seen in table 4 5 the acquisition mode in F1 FnMODE deter mines the Fourier transform mode Furthermore FnMODE determines the data storage mode The description below demonstrates the differ ence in data storage between a data set with FnMODE QF and one with FnMODE QF FnMODE QF xfb performs complex two quadrant p
110. son is that entering sino on the command line would execute the command sino Note that the processing parameter SINO edp has a different purpose than the processing status parameter SINO TOPSPIN parameters dpp The latter represents the signal to noise ratio calculated by the processing command sino SREGLST name of the scaling region file used in 1D datasets takes a character string value interpreted by 1i lipp if PSCAL sreg or psreg interpreted by sino scaling region files contain the regions in which the reference peak is searched They are used to exclude the region in which the solvent peak is expected Because this region is nucleus and solvent specific the name of a scaling region file is of the form NUCLEUS SOLVENT e g 1H CDCI3 For all common nucleus solvent combinations a scaling region file is delivered with TOPSPIN They can be viewed or edited with edlist scl SSB sine bell shift SR used in 1D 2D and 3D datasets in all directions takes a positive float value interpreted by sinm qsin sinc qsinc interpreted by trf xfb xf2 xf1 xtrf tf if WDW sine qsine sinc or qsinc spectral reference used in 1D 2D and 3D datasets in all directions takes a float value Hz set by sref or interactive calibration The spectral reference is calculated according to the relation SR SF BF1 STSI strip size number of output points of strip transform used in 1D 2D and 3D datasets in
111. specified on the command line e g edpul cos Conditional List boxes These list boxes are only offered if the selected item has the corre sponding item defined For example most high resolution pulse pro grams have a Class and Dim definition but not Type or SubType definition Class Allows you to show a particular class of items or all items any Dim Allows you to show items of a particular dataset dimension or all items any P 479 Parameters lists AU programs Type Allows you to show a particular type of items or all items any SubType Allows you to show items of a particular subtype of items or all items any Available Buttons All Show items of all classes dimensions types and subtypes Edit Opens the selected item pulse program CPD program in the TOP SPIN text editor or viewer depending on whether the selected item is writable for the current user or not See below Writable items can be modified in the editor They can be saved from the editor as follows Click File Save Ctr1 s Write protected items can be saved under a different name as follows Click File Save as The new item is owned by and writable for the current TOPSPIN user Items can also be created modified with an external non TOPSPIN edi tor They can then be imported in the database as described below Graphical Edit for pulse programs only Opens a symbolic graphical display of the selected pulse program wit
112. spectrum plane oO Extract a diagonal spectrum plane Extract a raw data plane O Extract a row from raw data O Replace a spectrum plane Required parameters Plane orientation Plane number 1 1 999 Destination PROCNO 999 999 Figure 5 3 This dialog box offers several options each of which selects a certain command for execution P 282 3D processing commands Extract a diagonal spectrum plane in F1 F2 This option selects the command r12d for execution It reads the di agonal F1 F2 plane from a 3D dataset and stores it as a 2D dataset Extract a diagonal spectrum plane in F1 F3 This option selects the command r13d for execution It reads the di agonal F1 F3 plane from a 3D dataset and stores it as a 2D dataset Extract a diagonal spectrum plane in F2 F3 This option selects the command r23d for execution It reads the di agonal F2 F3 plane from a 3D dataset and stores it as a 2D dataset For each option you must specify the destination procno r12d r13d and r23d only store the real data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data SEE ALSO r12 r13 r23 rpl wpl P 283 3D processing commands rser2d NAME rser2d Read plane from raw 3D data and store as a 2D 3D
113. strip size respectively They both can take a value between 0 and SI The values which are actually used can be a little different STSI is always rounded to the next higher multiple of 16 Furthermore when the data are stored in subcube format see below STSI is rounded to the next multiple of the subcube size Type dpp to check this if XDIM is smaller than SI then the data are stored in subcube format and STSI is a multiple of XDIM tf 3 stores the data in subcube format It automatically calculates the subcube sizes such that one row F3 of subcubes fits in the available memory Furthermore one column F2 and one tube F1 of subcubes must fit in the available memory The calculated subcube sizes are stored in the processing status parameter XDIM type dpp The alignment of the data points for sequential and subcube format is the extension of the alignment in a 2D dataset as it is shown in table 4 6 and 4 7 The storage handling is completely transparent to the user and is only of interest when the data are interpreted by third party software INPUT PARAMETERS F3 F2 and F1 parameters set by the user with edp or by typing si stsr etc SI size of the processed data STSR strip start first output point of strip transform STSI number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 F3 parameters set by the user
114. takes the value no single quad spol qpol sfil or qfil More details on BC_mod can be found in chapter 2 4 2 Linear prediction of the F3 time domain data Linear prediction is done according to ME_mod This parameter takes the value no LPfr LPfc LPbr LPbc LPmifr or LPmifc Usu ally ME_mod no which means no prediction is done Forward prediction LPfr LPfc LPmifr or LPmifc can for example be used to extend truncated FIDs Backward prediction LPbr or LPbc can be used to improve the initial data points of the FID Linear predic tion is only performed if NCOEF gt 0 Furthermore the parameters LPBIN and for backward prediction TDoff play a role see these parameters in chapter 2 4 3 Window multiplication of the F3 time domain data Each row is multiplied with a window function according to WDW This parameter takes the value em gm sine gsine trap user sinc qsinc traf or trafs More details on WDW can be found in chapter 4 Fourier transform of the F3 time domain data Each row is Fourier transformed according to the acquisition sta 3D processing commands tus parameter AQ_mod as shown in table 5 6 t 3 does not eval AQ_mod Fourier transform mode status FT_mod qf forward single real fsr qsim forward quad complex fqc qseq forward quad real fqr DQD forward quad complex fqc Table 5 6 uate the processing parameter FT_mod However it stores the Fourier tra
115. the F2 and F1 parameter REVERSE If REVERSE TRUE the spectrum will be reversed in the corresponding direction i e the first data point becomes the last and the last data point becomes the first The same effect can be obtained with the commands rev2 and or rev1 after xfb xfb is normally used without options There are however several op tions available n xfb normally stores real and imaginary processed data However the imaginary data are only needed for phase correction If the parame ters PHCO and PHC1 are set correctly then you don t need to store the imaginary data The option n allows you to do that This will save processing time and disk space If you still want to do a phase correc tion you can create imaginary data from the real data with a Hilbert transform see xht2 and xht1 nc_ proc value xfb scales the data such that i e the highest intensity of the spec trum lies between 22 and 22 The intensity scaling factor is stored in the processing status parameter NC_proc and can be viewed with dpp The option nc_proc causes xfbto use a specific scaling factor However you can only scale down the data by entering a greater more positive value than the one xfb would use without this option P 231 2D processing commands P 232 If you enter a smaller more negative value the option will be ignored to prevent data overflow The option nc_proc last causes xfb to use the current value of the status p
116. trfp command 133 183 truncated fid 88 228 267 288 296 301 tube of 3D data 272 292 301 U uadmin command 610 user defined AU programs 508 baseline correction 72 153 parameter sets 490 plot layouts 364 processing 133 tilt angle 200 User Interface 593 V Varian data 533 560 vconv command 444 560 Ww weighting coefficients 81 winconv command 444 564 window multiplication 1D 86 133 135 1D exponential 75 77 78 1D Gaussian 77 98 1D sinc squared 119 1D sine 119 1D square sine 119 1D Traficante 129 1D trapezoidal 129 2D 213 223 227 228 3D 267 288 296 301 exponential 27 Gaussian 26 mode 39 133 wm command 77 119 129 wmisc command 468 wpar command 490 493 550 561 wpl command 341 wra command 457 wraparam command 457 wrp command 457 wrpa command 457 wrpparam command 457 wsc command 203 wser command 206 wserp command 209 wsr command 211 wtr command 344 X xau command 512 XCMD 8 246 xf1 command 213 223 231 250 278 xf1m command 217 xf1p command 247 xf1ps command 220 xf2 command 213 223 231 250 278 xf2m command 217 xf2p command 247 278 xf2ps command 220 xfb command 213 227 254 xfobm command 217 xfbp command 247 xfbps command 220 xht1 command 250 xht2 command 250 xif1 command 170 171 252 xif2 command 170 171 252 xmac 497 xpy 498 xtrf command 232 254 259 xtrf2 command 254 xtrfp command 252 256 259 xtrfp1 command 252 259 xtrfp2 comman
117. ty Pulse Programs File Options Help Search in names v search Owner Any M Avance incl Avance incl nmrsim Daz incl De incl Delay incl Grad incl nmrsim Solids incl Sysconf incl adeqi1etgprdsp adeqn1 etgp adeqnnetgp alldirs txt aring aring2 atocsygpph19 c_can_mq c_can_mq 2 c_canco_3d c_ccflopsy16 c_ccnoesy c_ccnoesy2 c_ccnoesy_ct c_coca_mq c_con_maq c_con_sq c_cosy c_cosy2_ct c_hcaco_3d c_hecflopsy16_3d_ calibgp chcaconhgp3d chcanhgp3d chcanhgpwa3d ccaconhgp2h3d iccaconhgp3d ccanhgp2h3d ccanhgp3d ceenhgpad ccconhgp2h3d colocat cosydclraf Eat Graphical Ect Graphical Edit Set PULPROG Smee oe Figure 10 12 You can delete items as follows 1 Select the items to be deleted P 486 Parameters lists AU programs 2 Click More Delete 3 Confirm the appearing warning by clicking OK INPUT FILES lt tshome gt exp stan nmr lists pp pulse programs lt tshome gt exp stan nmr lists cpd CPD programs lt tshome gt exp stan nmr lists mac TOPSPIN macros lt tshome gt exp stan nmr py Python programs SEE ALSO edpul edcpd edpy xpy edmac xmac P 487 Parameters lists AU programs rpar NAME rpar Read a parameter set 1D 2D 3D DESCRIPTION The command rpar reads a parameter set experiment to the current dataset When it is entered without arguments rpar opens a dialog box with a list of available paramete
118. used by 1D commands like add duadd mul div and addfidand by 2D commands like add2d mu12d and addser The second dataset is however usually set from the add multiply dialog box command adsu The third dataset is used by the 1D command add when entered from the command line and in various AU programs macro DATASETS INPUT AND OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 433 Dataset handling curdat2 definition of the second dataset SEE ALSO add duadd mul div addfid add2d mul2d addser P 434 Dataset handling find search NAME find Find data according to specified criteria nD DESCRIPTION The command find allows you to find TOPSPIN data according to various criteria To start searching do the following 1 Click Edit Find data Ctr1 f find to open the Find data window see Figure 9 6 2 Enter the search items in the upper part of the dialog Note that e There will be searched for items containing the specified string e Exact matching is performed for dataset variables NAME EXPNO PROCNO and USER if the checkboxes at the right are enabled The search is restricted to data created between the specified dates Note that this refers to the acquisition date The Reset mask button allows you to reset the default criteria 3 Select the Data directories to be searched in the lower part of the dialog If no directories are
119. with another 2D spectrum Required parameters Multiplier for current 2D spectrum ALPHA 0 Multiplier for second 2D spectrum GAMMA 1 NAME 2nd spectrum exam2d_HC EXPNO 4 PROCNO 1 USER guest DIR C Bio Figure 4 3 P 150 2D processing commands see Figure 4 3 This dialog box offers several options each of which selects a certain command for execution Add a 2D spectrum This option selects the command add2d for execution It adds the processed data of the second dataset to those of the current 2D data set according to the following formula current ALPHA current GAMMA second where ALPHA and GAMMA are processing parameters Both real and imaginary data are added The result overwrites the current proc essed data For APLHA 1 and GAMMA 1 the spectra are sub tracted Multiply with another 2D spectrum This option selects the command mu12d for execution It multiplies the processed data of the second dataset with those of the current 2D da taset Both real and imaginary data are multipied The result overwrites the current processed data Add 2D fid ser This option selects the command addser for execution It adds the raw data of the second dataset to those of the current 2D dataset The result overwrites the current raw data Note that addser also works on 3D data Caution the two 2D datasets to be added or multiplied must have equal sizes If you run a
120. with edp or by typing be_mod bcfw etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode 3D processing commands NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum PKNL group delay compensation Avance or filter correction A X set by the acquisition can be viewed with dpa or s aq_mod etc AQ_mod acquisition mode determines the status FT_mod AQSEQ acquisition sequence 3 2 1 or 3 1 2 TD time domain number of raw data points BYTORDA byteorder or the raw data NC normalization constant F2 and F1 parameters set by the acquisition can be viewed with dpa or by typing s fnmode etc FnMODE Fourier transform mode OUTPUT PARAMETERS F3 F2 a
121. without running x 2 first a warning that the F2 transform has not been done will appear When the command has finished the data are in the time domain in F2 and in the frequency domain in F1 The op posite case however is more usual i e data which have only been proc essed with xf2 xf1 takes the same options as xfb The F1 Fourier transform mode and data storage mode depends on the F1 acquisition mode see INPUT PARAMETERS below and the descrip tion of x b INPUT PARAMETERS F2 and F1 parameters set by xf 2 can be viewed with dpp or by typing s si s stsr etc SI size of the processed data P 213 2D processing commands STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 If x 2 has not been done xf1 uses the edp parameters set by the us er F1 parameters set from the ftf dialog box with edp or by typing be_mod etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadenin
122. words you can not process mixed single detection hypercomplex data e For data of dimension gt 5D only the natural acquisition order AQSEQ 0 is supported nD processing commands e Simultaneous echo antiecho not supported the acquisition status parameter FNMODE must not be echo antiecho in more than 1 direction Note that the values of parameters which use a predefined list are stored as integers The first value of the list is always stored as 0 the second value as 1 etc Table 6 1 shows the values of the parameter PH_mod as an example Parameter Integer stored in the proc s value file no 0 pk 1 mc 2 ps 3 Table 6 1 INPUT PARAMETERS F4 F3 F2 and F1 parameters set by the user with edp or by typing si stsr etc SI size of the processed data STSR strip start first output point of strip transform STSI number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDo
123. xht2 Hilbert transform in F2 2D xht1 Hilbert transform in F1 2D DESCRIPTION The command xht2 performs a Hilbert transform of 2D data in the F2 di rection The command xht1 performs a Hilbert transform of 2D data in the F1 di rection Hilbert transform creates imaginary data from the real data Imaginary data are required for phase correction They are normally created during Fourier transform with xfb xf2 or x 1 If however if the imaginary data were not stored xfb n or have been deleted de1i you can re create them with xht2 or xht1 Note that Hilbert Transform is only useful when the real data have been created from zero filled raw data with SI gt TD Hilbert transform can also be used if the imaginary data exist but do not match the real data This is the case when the latter have been manipu lated after Fourier transform for example by abs1 abs2 sub symor third party software INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data 2ir second quadrant imaginary data if existing input of xht1 2ri third quadrant imaginary data if existing input of xht2 OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data 2ir second quadrant imaginary data output of xht2 created from 2rr P 250 2D processing commands 2ri third quadrant imaginary data outpu
124. 0 The command at works user specific i e the scheduled command is only executed if TOPSPIN runs at the specified time and the TOPSPIN inter nal user is the user who scheduled the command For more flexible time definition and user independent scheduling you can use the command Scheduled commands can be viewed in the command spooler which can be started with the command spooler and is available in the spec trometer status bar SEE ALSO cron qu qumulti atmulti spooler P 503 Automation atmulti NAME atmulti schedule a TOPSPIN command for execution on multiple expnos SYNTAX atmulti 1 2 3 1 7 1 7 1 7 20 21 DESCRIPTION The command atmuiti schedules a command for execution on multiple experiment numbers It works like at except that it runs on multiple ex pnos of the current dataset When entered without arguments atmul ti opens the dialog shown in Figure 11 2 Here you can enter the command to be executed specify the time and date of execution and select the target experiments numbers Clicking OK will then schedule the command for execution The command atmul1ti takes two arguments the command to be exe cuted and the target experiment number s The dialog will open with the specified arguments preselected Expnos can be specified in one of the following ways n a single experiment number all expnos under the current dataname n m expno n through m n m equivalent to n m n m
125. 0 nmf NAME alpha500 nmf EXPNO 1 DIR CBio USER guest Figure 12 4 Her you can specify the TOPSPIN destination dataset and click OK to start the conversion The jconv source and destination data can also be entered on the com mand line Here are some examples jconv jdata lt ext gt searches for jdata lt ext gt in the directory defined by the environment variable JNMR 1 When the specified input data are found the dialog window shown in Figure 12 4 will appear Here you can specify the output dataset P 548 1 Can be set with the TOPSPIN command env set JNMR lt path gt Conversion commands vconv lt path gt jdata lt ext gt as above except that the source data are searched for in the directory lt path gt veonv jdata lt ext gt lt name gt lt expno gt lt dir gt lt user gt Here the destination dataset is specified as command line argu ments The procno is automatically set to 1 If the dataset specification is incomplete the dialog window shown in Figure 12 4 will appear jconv can handle Jeol EX GX and ALPHA raw data and works on 1D 2D and 3D data Processed data cannot be converted The conversion of FX FID data has been implemented FX data must have a numerical extension like in proton 1 and the name must be specified on the com mand line e g jconv proton 1 No parameter file is needed for the conversion the most relevant parameters are extracted from the header of the data
126. 12 OK Cancel mand like s si allows you to do that This however could make the data set inconsistent which can be checked with the command auditcheck Before any processing has been done the processing status parameters of a dataset do not contain significant values After the first processing com mand they represent the current processing status of the data Any further processing command will update the processing status parameters After processing the relevant processing status parameters are usually set to the same values as the corresponding processing parameters In other words the command has done what you told it to do There are however some exceptions e when a processing command was interrupted the processing status parameters might not have been updated yet some processing parameters are modified by the processing com mand e g STSI is rounded to the next higher multiple of 16 by x b The rounded value is stored as the processing status parameter e the values of some parameters are a result of processing They can not be set by the user they do not appear as processing parameters but they are stored as processing status parameters Examples are NC_ proc S_DEV and TILT 2 2 Parameter values With respect to the type of values they take parameters can be divided into three groups parameters taking integer values e g SI TDeff ABSG NSP e parameters taking float or double valu
127. 2D levels 353 add2d command 150 addc command 56 addfid command 56 addition factor 24 addser 150 adsu command 56 106 150 192 AMX format 39 536 spectrometer 33 536 apk command 65 86 apkO command 62 apkOf command 62 apk1 command 62 apkf command 65 apkm command 65 apks command 65 at command 502 atmulti command 504 AU program binaries 507 508 516 compile 507 508 install 515 kill 516 macros 8 processing 22 setup 512 sources 507 508 AU reference manual 516 audit command 598 audit trail 605 auditcheck command 598 605 auremol command 373 autolink command 372 automatic baseline correction 1D 52 automatic baseline correction 2D 144 147 automatic mode of the Processing Guide 113 automatic shifting baseline correction 2D 144 147 autoplot command 348 359 360 364 Avance data 25 39 231 270 290 535 536 spectrometer 8 33 87 231 B bas command 52 144 147 base_info file 469 baseline correction 1D automatic 20 52 54 86 469 1D fid 22 69 75 86 133 134 1D spline 127 469 1D user defined 72 469 2D automatic 36 144 145 148 213 223 2D automatic shifting 145 148 2D FID 227 255 2D user defined 153 3D automatic 286 3D FID 267 288 296 301 frequency offset 23 mode 23 multiple additive 259 of integrals 26 382 of the FID 24 bas command 154 baslpnts file 469 bc command 69 86 133 bcm command 72 469 bcm1 command 153 bem2 command 153 bias correction 382 big endian 41 232 271 291 bnm
128. 2r i3r1 i4r1 Fl r4r2 r2r2 r3r2 r4r2 i1r2 i2r2 i3r2 i4r2 2rr file 2ir file r14id4 r2i1 r3i1 r4i1 i1i1 i2i1 i3i1 i4i1 r1i2 r2i2 r3i2 r4i2 i1i2 i2i2 i3i2 i4i2 2ri file 2ii file FnMODE Echo Antiecho xfb performs hypercomplex four quadrant processing Both in F2 and F1 the data are acquired phase sensitive In the example below P 238 2D processing commands the following parameters settings are used In F2 TD 8 Sl is 4 InF1 TD 4 Sl 2 Furthermore the following notation is used for individual data points e rnrm point n of FID m This point is real in F2 and F1 inrm point n of FID m This point is imaginary in F2 and real in F1 e rnim point n of FID m This point is real in F2 and imaginary in F1 inim point n of FID m This point is imaginary in F2 and F1 Input F2 processing raw data F2 red ifr4 r2r1i2r4 r3r1i3r4 r4r1 i4r1 r1i1 i1i1 r2i1 i2i1 r3i1 i3i1 r4i1 i4i1 rmr2itr2 r2r2i2r2 r3r2i3r2 r4r2 i4r2 r1i2 i1i2 r2i2i2i2 r3i2i3i2 r4i2 i4i2 F1 ser file For F2 processing rir1 i1r1 is the first hypercomplex input data point r2r1 i2r1 the second etc P 239 2D processing commands Output F2 processing Input F1 processing F2 i1r1 i1i1 i2r1 i2i1 i3r1 i3i1 i4r1 i4i1 Fl p4qrt4rtit r2r1 r2i1 r3r1 r3i1 r4r1 r4i1 i1r2 i1i2 i2r2 i2i2 i3r2 i3i2 i4r2 i4i2 r4r2 r1i2 r2r2 r2i2 r3r2 r3i2 r4r2 r4i2 2rr file rir4 r1i1 r2r1 r2i1 r3r1 r3i1 r4r1
129. 31 MB JVM Free memory MB Configuration Configuration type Datastation Current probe 5 mm Dual 13C 1H 1234 5678 Current instrument spect_av900 Connection local Computer name DRUDNB Domain name DRUDNB Current user drud Internal user Not used NMR administrator NMRSU DRUDNB Administrator Figure 13 1 This command can also be started as follows Click Help Version Info P 568 TOPSPIN Interface Processes bpan NAME bpan Open a user defined button panel nD DESCRIPTION The command bpan opens a user defined button panel It prompts you for the name the desired panel A button panel is a window with user defined buttons for executing TOP SPIN commands AU programs Python programs or macros It appears as an integral part of the active data window and act on that Bruker de livers a few standard button panels like bnmr To create your own button panels you can modify one of these or write them from scratch In this description we will create a very simple button panel with some 1D processing commands and print export buttons see Figure 13 2 1D Processing Panel Close To 2D Tips Figure 13 2 To write this button panel take the following steps 1 Open the File Explorer and navigate to the subdirectory userdefined of the users properties directory t 2 Create a text file with the name buttonpanel_ lt name gt prop 1 To locate this
130. 4 P 229 2D processing commands P 230 5 Phase correction of the 2D spectrum according to PH_mod This parameter takes the value no pk mc or ps For PH_mod pk xfb applies the values of PHCO and PHC1 This is only useful if the phase values are known If they are not you can do an interactive phase correction in Phase correction mode after x b has finished More details on PH_mod can be found in chapter 2 4 The size of the processed data is determined by the processing param eter SI SI real and SI imaginary points are created A typical value for SI is TD 2 in which case all raw data points are used and no zero filling is done In fact several parameters control the number of input and output data points for example 1 2 SI lt TD 2 only the first 2 SI raw data points are used 3 4 0 lt TDoff lt TD the first TDoff raw data points are cut off at the SI gt TD 2 the raw data are zero filled before the Fourier transform 0 lt TDeff lt TD only the first TDeff raw data points are used beginning and TDoff zeroes are appended at the end corre sponds to left shift TDoff lt 0 TDoff zeroes are prepended at the beginning Note that e for SI lt TD TDoff 2 raw data are cut off at the end for DIGMOD digital the zeroes would be prepended to the group delay which does not make sense You can avoid that by converting the raw data with convdta before you process them 0 lt STSR l
131. 8 Display Display In New Window Display 4s 2D Projection Sort This Column Sort Reverse Show Details Save selection in file Add selection to dataset group File Properties Files Process Selected Datasets Figure 9 8 Display Display the selected dataset s in the current data window If multiple da tasets are selected they are displayed in the same data window in multi ple display mode Equivalent to clicking the Display button or pressing Enter Display In New Window Display the selected dataset s in a new window If multiple datasets are selected they are displayed in the one new data window in multiple dis play mode Display As 2D Projection P 437 Dataset handling Display the selected dataset as a projection of the current 2D dataset A dialog will appear allowing you to choose F1 projection F2 projection or both If multiple datasets are selected only the first one is considered If the current dataset is not a 2D dataset nothing happens Sort This Column Sort the selected column in ascending order Sort Reverse Sort the selected column in descending order Show Details Show hide the dataset details Dimension Pulse program and Acquisition date Save Selection to File Save the list of selected datasets in a text file First opens a file dialog where you can select or specify a filename The saved dataset list can for example be used for serial processing command serial see als
132. ALSO uadmin chpwd logoff lockgui TOPSPIN User Management gdcheck NAME gdcheck Generate data checksum DESCRIPTION The command gdcheck generates a data checksum It updates the au dit trail files It takes one argument and can be used as follows gdcheck make the processing audit trail consistent gdcheck raw make the acquisition audit trail consistent gdcheck is for example required if a dataset has been manipulated with third party software In that case the audit trail would be inconsistent i e the command audi tcheck would report an inconsistency error gd check updates the audit trail file with a new data checksum and adds the entry Unknown data manipulation detected After this auditcheck would report Unknown data manipulation For 2D and 3D data gdcheck adds a data checksum For 1D data a data checksum is automatically created by processing commands In 2D and 3D however processing commands do not create a data checksum because this would be too time consuming If it is required gdcheck al lows you to create it INPUT AND OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt audita txt acquisition audit trail x lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt auditp txt processing audit trail P 605 TOPSPIN User Management P 606 USAGE IN AU PROGRAMS GDCHECK GDCHECK_RAW executes the command gdcheck raw AUDI
133. As such you can compare the areas of peaks in a series of experi ments Furthermore the parameter INTBC is evaluated For INTBC yes an automatic baseline correction slope and bias of the integrals is performed This however is only done when the integral regions were determined with abs not if they were determined interactively The int command can be used on 1D 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters Analysis commands INPUT PARAMETERS set with edp from the int dialog box or by typing intscl intbc etc INTSCL scale 1D integrals relative to a reference dataset INTBC automatic baseline correction of integrals created by abs F1P low field left limit of the plot region in ppm input for 1ipp F2P high field right limit of the plot region in ppm input for Zipp INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data intrng 1D integral regions created by abs or interactive integra tion OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt integrals txt ascii file containing the output of li integrals lipp txt ascii file containing the output of Lipp integrals lippf txt ascii file containing the output of lippf USAGE IN AU PROGRAMS LI LIPP LIPPF SEE ALSO int2d P 383 Analysis comman
134. D datasets in the F2 direction TOPSPIN parameters takes the value no sym syma or symj set by sym syma and symj only exists as processing status parameter dpp SYMM shows the last kind of symmetrization that was done STSI strip size the number of output points of a strip transform used in 1D 2D and 3D datasets in all directions takes an integer value between 0 and SI default 0 also exists as processing parameter edp rounded by ft trf xfb xf2 xf1 xtrf xtrf2 tf3 tf2 tf1 During strip transform only the region determined by STSI and STSR is stored Processing commands round the value of the processing parameter STSI in 1D to the next lower multiple of 4 in 2D and 3D to the next higher multiple of 16 see processing com mand STSI Furthermore when the 2D 3D data are stored in sub matrix subcube format STSI is rounded to the next multiple of the submatrix subcube size The rounded value is stored as the processing status parameter STSI If no strip transform is done STSI 0 the status STSI is set to the value of SI TDeff number of raw data points that were used for processing used in 1D 2D and 3D datasets in all directions set by ft xfb xf2 xf1 trf xtrf also exists as processing parameter edp Normally all raw data points are used as input However the number of input points can be decreased with the processing parameter TDeff or increased by doing linear forward or back
135. DIR c mydir will cause zg gs to search for the pulse program in the data base and then if it did not find it there in c mydir So the data base is searched first then the defined directory PULPPROG DIR c mydir will cause zg gs to search for the pulse program in c mydir and then if it did not find it there in the database So the directory is searched first then the database Each time a pulse or CPD program is taken from a directory rather than from the database a message is written into the history file to be viewed with command hist P 483 Parameters lists AU programs P 484 Please note the commands edpul and edepd do not evaluate the above envi ronment variables e When ToPsPIN is running as a client that controls a remote spectrometer the remote environment variables are evaluated About Macros Macros are text files which contain a sequence of TOPSPIN commands and or Python commands A simple macro for processing and plotting the current dataset is 1D processing macro em Et apk sref autoplot plot according to Plot Editor layout TOPSPIN commands can be inserted in lower or uppercase letters Python commands must be entered as follows xpy lt name gt All text behind a character is treated as comment About Python programs Python programming is extensively described in a separate document available under click Help Manuals P
136. Display data in same window Selects the command re for execution It reads the specified dataset in the current data window Display data in new window Selects the command rew for execution It reads the specified dataset P 446 Dataset handling in a new data window specify the data path variables A full data path is lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt re replaces the dataset in the current data window if it exists The data path variables can also be specified on the command line In this case the dialog box is not opened and the missing data path varia bles are taken from the current dataset Examples re lt name gt re lt expno gt re lt name gt lt expno gt re lt expno gt lt procno gt re lt name gt lt expno gt lt procno gt re lt name gt lt expno gt lt procno gt lt dir gt lt user gt Alternatively re and rew can be entered with an alias name as argu ment i e re lt aliasname gt Note that the first alphanumeric argument is always interpreted as the name or alias name and the first numeric argument as experiment number The commands rep and repw allow you to read and display a new proc essed data number procno of the current dataset They open a dialog box with the corresponding option selected see Figure 9 12 Options Display data in same window O Display data in new window PROCNO J Figure 9 12 These
137. ED 1 no spaces between the intensity values e SQUEEZED 2 the sign of the intensity values is encoded in the first digit e DIFF DUP 3 the difference between successive values is encoded suppressing repetition of successive equal values The default value is DIFF DUP Include these data types For the included data types you have the following choices FID 0 raw data e RSPEC 1 real processed data e RSPEC ISPEC 2 real and imaginary processed data e PARAMS 3 parameter files FID RSPEC ISPEC 4 raw data real and imaginary processed data FID ALL_PROCNOS 5 Raw data real and imaginary processed data of all PROCNO s under the current EXPNO e ALL_EXPNOS_DIM_1_2 6 Raw data real and imaginary processed data of all EXPNO s under the current NAME The default value is RSPEC ISPEC 2 The above information can be entered as arguments of tojdx as fol lows tojdx lt path gt lt data gt lt file gt lt title gt lt origin gt lt owner gt Note that in this case three extra arguments are required The arguments have the following meaning Conversion commands e lt path gt name and directory of the archive file e lt data gt data types included e lt file gt type of archive file e lt title gt the title as it appears in the output file enter a character string e lt origin gt the origin as it appears in the output file enter a charac ter string lt owner gt the
138. Each row and or column is multiplied with a window function according to WDW This parameter takes the value em gm sine qsine trap user sinc qsinc traf or trafs More details on WDW can be found in chapter 2 4 Fourier transform of the 2D time domain data Each row is Fourier transformed according to the acquisition sta tus parameter AQ_mod as shown in table 4 4 Each column F1 F2 Fourier transform mode F2 status FT_mod AQ_mod qf forward single real fsr qsim forward quad complex fqc qseq forward quad real fqr DQD forward quad complex fqc Table 4 4 F1 FnMODE Fourier transform mode F1 status FT_mod QF forward quad complex fqc QSEQ forward quad real fqr TPPI forward single real fsr States forward quad complex fqc States TPPI forward single complex fsc Echo AntiEcho forward quad complex fqc Table 4 5 is Fourier transformed according to the acquisition status parame ter FRMODE as shown in table 4 5 x b does not evaluate the processing parameter FT_mod However it stores the Fourier transform mode as it was evaluated from AQ_mod F2 or FnMODE F1 in the processing status parameter FT_mod If for some reason you want to Fourier transform a spectrum with a dif ferent mode you can set the processing parameter FT_mod with edp and use the command xtrf see xtrf More details on FT_mod can be found in chapter 2
139. Export commands exportfile NAME exportfile Export data window to graphics file 1D 2D 3D DESCRIPTION The command exportfile saves the contents of a data window ina graphics file of selectable type e g png tif wmf etc It opens an Explorer window xi Look in Bruker E P TOPSPIN File name Export Files of type Legar File Extensions png jpg jpeg bmp emf wmf Cancel Figure 7 1 Here you can e Click or type the output file e Click Export The resolution of such a screen dump equals the resolution of your screen When you import a graphics file into an other program you may loose in formation when resizing the graphics Entering exportfile on the command line is equivalent to clicking File gt Expott In TOPSPIN 2 1 and newer the pathname of the destination graphics file is available in the Windows clipboard OUTPUT FILES lt outputdir gt P 350 outputfile png jpg jpeg bmp emf wmf graphics file SEE ALSO plot autoplot prnt print Print Export commands P 352 edlev NAME edlev Edit contour levels 2D 3D DESCRIPTION The command edlev opens a dialog box in which you can set the con tour levels of a 2D dataset see Figure 7 2 PN exam2d_HC 1 1 C Bio guest 136523520 24574233 8 44233620 5 79620516 9 Required parameters Calculation method Multiply with increment Add increment Contour level sign O Negative
140. FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt title plot title SEE ALSO edtix plot prnt print autoplot P 359 Print Export commands edtix NAME edtix Set the dataset title 1D 2D 3D DESCRIPTION The command edtix allows you to define the dataset title with an exter nal editor It uses the editor that is defined in the User Preferences To set this editor 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Select the Preferred text editor or click the respective Change button to add a new editor The title will appear in the data window and on plots created with prnt or autoplot INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt title plot title OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt title plot title SEE ALSO edti plot prnt print autoplot P 360 Print Export commands plot NAME plot Open the Plot Editor 1D 2D DESCRIPTION The command pilot starts the Plot Editor with the current dataset and the layout defined by the processing parameter LAYOUT The plot limits of all data objects will be the same as in TOPSPIN The command plot can take various ar guments and can be used as follows The command plot can be used with the following arguments no option Force all data objects to use limi
141. FSET depends on the acquisition mode When the acquisition status parameter AQ_mod is qsim gseq or DOD which is usually the case the above relation count When AQ_mod is gf the relation OFFSET SFO1 SF 1 1 0e6 is used sref then calculates which data point between 0 and SI in your spec trum corresponds to the ppm value Ref from the edlock table This data point will be used in the second step The first step is independent of a reference substance During the second step sref scans a region around the data point found in the first step for a peak It will normally find the signal of the reference substance The width of the scanned region is defined by the parameter Width in edlock table so this region is Ref 0 5 Width ppm This step is necessary because the lock substance solvent will not always reso nate at exactly the same position relative to the reference shift The ab solute chemical shift of the lock substance solvent differs because of differences in susceptibility temperature concentration or pH for in stance The third step depends on whether or not a peak was found in the second step Ifa peak was found sref determines the interpolated peak top and shifts its ppm value to the ref value from the edlock table The process ing parameters OFFSET SF and SR are changed accordingly As such the result of the default step 1 is slightly corrected in order to set the peak of the reference substance exactly to 0
142. ID Note that the parameter TDoff only plays a role for linear prediction and in 2D and 3D Fourier transform You can also perform a so called strip transform which means that only a certain region of the spectrum is stored This can be done by setting the parameters STSR and STSI which represent the strip start and strip size respectively They can take values between 0 and SI The processing status parameters STSI and SI are both set to this value You can check this by entering dpp or clicking the Procpars tab The Fourier transform mode depends on the acquisition mode single se quential or simultaneous For this purpose t evaluates the acquisition 1D Processing commands status parameter AQ_mod as shown in table 3 2 Note that ft does not AQ_mod FT_mod Fourier transform mode qf fsr forward single channel real qsim fqc forward quadrature complex qseq fqr forward quadrature real DQD fqc forward quadrature complex Table 3 2 evaluate the processing parameter FT_mod but it does store the Fourier transform mode as evaluated from the acquisition mode in the process ing status parameter FT_mod However the command trf determines the Fourier transform mode from the processing parameter FT_mod and not from the acquisition mode see trf ft evaluates the parameter FCOR The first point of the FID is multiplied with FCOR which is a value between 0 0 and 2 0 However on Avance spectrometers
143. IN AU PROGRAMS TF2 store_imag where store_image can be yorn SEE ALSO tf3 tfl ft3d 3D processing commands tf1 NAME tf1 Process data including FT in F2 3D DESCRIPTION The command tf1 processes a 3D dataset in the F1 direction This in volves a Fourier transform which transforms time domain data FID into frequency domain data spectrum Depending on the processing param eters BC_mod WDW ME_mod and PH_mod tf1 also performs base line correction window multiplication linear prediction and spectrum phase correction The processing steps done by t f1 can be described as follows tf1 only works on data which have already been processed with t 3 and possibly with t 2 It performs the following processing steps 1 Baseline correction of the F1 time domain data Each tube is baseline corrected according to BC_mod This parameter takes the value no single quad spol qpol sfil or qfil More details on BC_mod can be found in chapter 2 4 2 Linear prediction of the F1 time domain data Linear prediction is done according to ME_mod This parameter takes the value no LPfr LPfc LPbr LPbc LPmifr LPmifc Usually ME_mod no which means no prediction is done Forward pre diction in F1 LPfr LPfc LPmifr or LPmifc can for example be used to extend truncated FIDs Backward prediction LPbr or LPbc is not used very often in F1 Linear prediction is only per formed for NCOEF gt 0 Furthermore LPBIN and fo
144. N datapath USER is the lt USER gt value of the current TOPSPIN datapath E conv C bio1 bruknet ac200 eng ag 10f 804 The selected DISNMR data will be converted Define destination dataset NAME ag210f EXPNO 804 1 DIR C Bio guest Figure 12 1 P 534 Conversion commands The command conv executes the AU program disconv This means the command expinsta1l1 must have been executed once installing the Bruker AU programs before you can use conv The dialog box in Figure 12 1 shows the button xau disinfo Clicking this button executes the corresponding AU program showing the relevant da taset parameters Please note that the TOPSPIN command conv does not need the disn mr conf or disms1 conf files which were needed by TOPSPIN s pred ecessor XWIN NMR Therefore the XWIN NMR command convsys does not exist in TOPSPIN INPUT FILES lt input directory gt A2000 3000 data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid Avance type 1D raw data ser Avance type 2D or 3D raw data acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i converted processed 1D data 2rr 2ir 2ri 2ii converted processed 2D data proc processing parameters procs processing status parameters For 2D data the additional parameter files acqu2 acqu2s proc2 and proc2s will b
145. O is one of the few examples where a processing parameter is set by a processing command For example apk sets both the processing and processing status parameter PHCO pk reads the processing parameter and updates the processing status parameter For multiple phase corrections the total zero order phase value is stored as the processing status parameter PHCO PHC 1 first order phase correction value frequency dependent used in 1D 2D and 3D datasets in all directions takes a float value degrees set by apk apks apkf apk1 on 1D datasets set interactively in Phase correction mode on 1D and 2D datasets interpreted by pk xfbp xf2p xflp tf p interpreted by trf xfb xf2 xf1 xtrf t 3 tf2 t 1 when PH_mod pk PHC1 is one of the few examples where a processing parameter is set by a processing command For example apk sets both the processing and processing status parameter PHC1 pk reads the processing parameter and updates the processing status parameter For multiple phase corrections the total first order phase value is stored as the processing status parameter PHC1 PH_mod phase correction mode P 32 used in 1D 2D and 3D datasets in all directions TOPSPIN parameters e takes one of the value no pk mc ps e interpreted by trf xfb xf2 xf1 xtrf tf The values of PH_mod are described in table 2 6 PH_mod mode no no phase correction pk phase correction according to PHCO
146. OPSPIN was not running These commands are ex ecuted after TOPSPIN startup Note that commands that were sched uled to run multiple times during TOPSPIN downtime are only executed once Direct execution P 509 Automation The option direct execution allows you to run commands directly i e by passing the default queue mechanism Usually an expired cron job is moved into the priority queue i e the job would wait for any other queued jobs to finish Setting this flag by passes this mechanism i e the job is executed directly when its shedule is due Please note that however processing commands can be ran in parallel This is a useful tool to execute for example nmr_ save and another processing com mand at the same time amp New periodical Job Command Description Execution scope User a Options Cl Off schedule execution E Direct execution Rules Minute of the hour 7 z Add new rule Hour of the day fro Remove rule t Ignore i b Day of the month ee canes Hourly z l Daily Month of the year from gt to Monthly i Weekly Day of the week from t0 Ignore OK Cancel Figure 11 3 P 510 Automation The following time scheduling rules exist Minute of the hour 00 through 59 Hour of the day 00 through 23 Day of the month 00 through 31 Month of the year January through december Day of the week Sunday throu
147. P 263 2D processing commands P 264 OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc2s F1 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS ZERT2 ZERT1 SEE ALSO abst2 abst Chapter 5 3D processing commands This chapter describes all TOPSPIN 3D processing commands They only work on 3D data and store their output in processed data files 3D raw data are never overwritten We will often refer to the three directions of a 3D dataset as the F3 F2 and F1 direction F3 is always the acquisition direction For processed data F2 and F1 are always the second and third direction respectively For raw data this order can be the same or reversed as expressed by the acquisi tion status parameter AQSEQ 3D processing commands which work on raw data automatically determine their storage order from AQSEQ The name of a 3D processing command expresses the direction in which it works e g t 3 works in F3 t 2 in F2 and t 1 in the F1 direction The command r12 reads an F1 F2 plane r13 reads an F1 F3 plane etc For each command the relevant input and output parameters are men tioned Furthermore the relevant input and output files and their location are men tioned Although file handling is completely transparent it is sometimes useful to know which files are involved and where they reside For exam pl
148. PIN parameters REVERSE flag indicating to reverse the spectrum during Fourier trans form e used in 1D 2D and 3D datasets in all directions e takes the value true or false default is false e interpreted by ft trf xfb xf2 xf1 xtrf tf e Reversing the spectrum can also be done after Fourier transform with the commands rv 1D or rev2 rev1 2D SF spectral reference frequency e used in 1D 2D and 3D datasets in the first direction e takes a positive float value e set by sref or interactive calibration e sref calculates SF according to the relation SF BF1 1 0 RShift 1e 6 where RShift is taken from the edlock table and BF1 is an acquisition status parameter SF is interpreted by display and plot routines for generating the axis scale calibration SI size of the processed data e used in 1D 2D and 3D datasets in all directions e takes an integer value e interpreted by processing commands which work on the raw data commands working on processed interpret the processing status parameter Sl The total size of the processed data realt imaginary is 2 SI In Bruker standard parameter sets see rpar SI is set to TD 2 where TD is an acquisition status parameter specifying the number of raw data points SIGF 1 low field left limit of the signal region e used in 1D and 2D datasets e takes a float value ppm must be greater than SIGF2 e interpreted by sino P 35 TOPSPIN parameters P 36 If SIGF1
149. PS respectively Note that in these cases no imaginary data are stored after F1 processing e FnMODE Echo Antiecho is equivalent to FnMODE States except that two consecutive FIDs rows of the 2D raw data are linearly combined according to the following rules re0 im1 im0 imO re1 reO re1 re1 re0 im1 im1 im0O P 241 2D processing commands the command xfb n does not store imaginary data after F1 processing 2D PROCESSING OF 3D DATA xfb can also be used to process one 2D plane of a 3D spectrum This can be a plane in the F3 F2 or in the F3 F1 direction The output 2D data are stored in a separate procno When the current dataset is a 3D xfb will prompt you for the plane axis direction the plane number the output procno and if applicable for the permission to overwrite ex isting data Alternatively you can enter this information as arguments on the command line for example xfb s23 17 2 y will read the F3 F2 plane number 17 and store it under procno 2 over writing possibly existing data Furthermore you can use the nodisp argument to prevent opening displaying the destination dataset e g xfb s23 17 2 y nodisp For 2D processing of 3D echo antiecho EA data the option eao is available This option ensures EA calculation when e the 3D raw data are EA in either F2 or F1 the acquisition status parameter FnMODE Echo Antiecho in F2 or F1 respectively e the processed plane does not inc
150. PSIGN Positive Reset allto gt Start manual picker Figure 8 11 Most recent range stored in peak list range on which last automatic 1 To store displayed region right click in the data window and select Save display region to P 395 Analysis commands peak picking was done 1 Sensitivity parameters Here you can set the peak picking parameters MI and MAXI which are also used for 1D peak picking Note that MI can also be set interactively with the button Set to to the lowest contour level the current value of MI or the most recent value stored in the peak list Furthermore you can set the pa rameters PPDIAG diagonal gap minimum distance between picked peaks and diagonal signals Mainly used for homonuclear spectra PPRESOL peak picking resolution Miscellaneous parameters Here you can set the following parameters PPMPNUM Maximum number of picked peaks Note that 0 or no value specified means unlimited PPIPTYP Peak picking interpolation type parabolic or none PSIGN The sign of the picked peaks positive negative or both To start peak picking Click OK The peak picking progress will be shown in the TOPSPIN status line When the peak picking process has finished e The number of found peaks is displayed in the status line Note that if the option Append peaks to list is checked only additional peaks are reported as found e The peaks and parameters are stored in the processing dir
151. PSPIN startup information and command in formation on interface level The history file contains command informa tion on the level of the command interpreter and application modules It also contains error messages Note that the files history and protocol are emptied when you restart TOPSPIN which means the history of the previous TOPSPIN session is lost In case of problems you should first make a copy of these files before you restart TOPSPIN Note that a long TOPSPIN session especially with au tomation can create very large history and protocol files Therefore it is useful to regularly check the size of the files or simply restart TOPSPIN after each automation session OUTPUT FILES lt tshome gt prog curdir lt user gt history TOPSPIN history file history i txt TOPSPIN protocol file SEE ALSO ptrace TOPSPIN Interface Processes help ghelp NAME help Search for keywords in command help ghelp Search for keywords in command in NMR Guide DESCRIPTION The command help opens a search dialog see Figure 13 11 PY help Options Search in NMR Guide knowledge base Display Command Index Command or Search tern Figure 13 11 This dialog box has several options each of which selects a certain com mand for execution Search in command documentation This option activates the command he1p It allows you to search for the specified item in the command help documents Search in NMR Guide
152. PUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data acqus F2 acquisition status parameters P 257 2D processing commands P 258 acqu2s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc F2 processing parameters proc2 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data procs processing status parameters proc2s processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS XTRF XTRF2 SEE ALSO xtrfp xtrfp2 xtrfp1 xfb xf2 xfl 2D processing commands xtrfp xtrfp2 xtrfp1 NAME xtrfp Custom processing of processed data in F2 and F1 2D xtrfp2 Custom processing of processed data in F2 2D xtrfp1 Custom processing of processed data in F1 2D DESCRIPTION The command xtrfp performs customized processing of processed data both the F2 and F1 direction It works like xtr except that it only works on processed data If processed data do not exist an error mes sage is displayed If processed data do exist they are further processed according to the parameters BC_mod WDW ME_mod FT_mod and PH_mod as described for xtrf xtrfp2 works like xtrfp except that it only works in the F2 direction xtrfp1 works like xt rfp except that it only works in the F1 directio
153. Phase 84 0 f 2007 10 23 10 31 50 Type GaussCascadeG3 Universal180 Refocussing 2007 10 23 10 31 50 Type GaussCascadeG4 Excitation Excitation 2007 10 23 10 31 50 Excitation Excitation 2007 10 23 10 31 50 Type Gauss Universal Excitation 2007 10 23 10 31 50 Inversion Inversion 2007 10 23 10 31 50 Type GaussCascadeQ3 Universal180 Refocussing 2007 10 23 10 31 50 Type GaussCascadeQs Excitation Excitation 2007 10 23 10 31 50 Excitation Excitation 2007 10 23 10 31 50 Excitation Excitation 2007 10 23 10 31 50 Type Sinc Universal Excitation 2007 10 23 10 31 50 Type Rectangle Excitation Excitation 2007 10 23 10 31 50 Type Trapezoid Excitation Excitation X Eoit Display close Figure 10 7 Manage Source Directories Add modify Shape Files source directories Shape Files will be searched for in the order of the directories specified Detailed information about Manage Source Directories are described in Chapter 1 9 INPUT OUTPUT FILES In TopSpin 2 1 and newer the default directory for user defined files is lt tshome gt exp stan nmr lists files SEE ALSO edlist Parameters lists AU programs edp NAME edp Edit processing parameters 1D 2D 3D DESCRIPTION The command edp opens a dialog box in which you can set all process ing parameters examid_1H 1 1 C ibio guest Spectrum ProcPars AcquPa
154. Programs e VD Delay lists e VP Loup Cont lists e VC lists e VA Amplitude lists e VT Temperature lists e F1 Frequency lists e SP Shape lists e DS Data Set lists Solvent Region Files e Phase Program lists Introduction intrng files e peakrng files e baslpnts files e base_info files e peaklist files e clevels files e reg files e int2drng files e Structure files 1 9 4 Default directories The default paths for directories e g Pulse Programs are Bruker files in exp stan nmr lists pp User files in exp stan nmr lists pp user The default path for lists e g VD lists is Bruker User files in exp stan nmr lists vd 1 9 5 How to define userspecific directories With TopSpin 2 1 and newer the directory file structure enables all users to define individual directories The userspecific path definition of Source Directories can be reached from the menu bar by Options Preferences Directories gt Manage Source Directories Change This way leads to a list of all Source Directories where the userspecific paths can be specified see Figure 1 1 With this structure each user can define his own directories in an unlimited number This window enables the user to define the individual directories for all files as Pulse Programs AU Programs etc for the complete list of Source Directories see paragraphe 1 9 3 The order of the directories defines the p
155. R Ic thio Shift 2nd spectrum by ppm bo o S Apply command to raw processed data DATMOD proc bd Add corresponding ppm or hz values bm y OK Cancel Help Figure 3 2 e of different size e referenced differently e acquired with different frequencies i e on different spectrome ters For data with equal size reference and spectrometer frequency add and duadd give the same result Furthermore duadd allows you to shift the second spectrum by a user defined number of ppm The parameter ppm or hz is only relevant if the P 57 1D Processing commands P 58 input data were acquired with different basic frequencies i e when they come from different spectrometers duadd only works on proc essed data independent of the value of DATMOD Add an FID This option selects the command addfid for execution It adds two 1D raw datasets multiplying one of them with the factor DC The result is stored in the current dataset It works like add with DATMOD raw except that it overwrites the raw data Add a constant This option selects the command addc for execution It adds the value of DC to the current dataset It works on raw or processed data de pending on the value of DATMOD The result is stored as processed data in the current dataset If you run a command like add from the command line it behaves slightly different It adds the second and the third dataset as specified with edc2 and stores the
156. SF 1 low field limit of the correction region ABSF2 high field limit of the correction region INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data proc F3 processing parameters proc2 F2 processing parameters P 286 3D processing commands proc3 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data procs F3 processing status parameters proc2s F2 processing status parameters proc3s F1 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS TABS3 TABS2 TABS 1 SEE ALSO abs2 absl absf P 287 3D processing commands P 288 tf3 NAME tf3 Process data including FT in F3 3D DESCRIPTION The command t 3 processes a 3D dataset in the F3 direction F3 is the first direction of a 3D dataset i e the acquisition direction t 3 always performs a Fourier transform which transforms time domain data FID into frequency domain data spectrum Depending on the processing parameters BC_mod WDW ME_mod and PH_mod it also performs baseline correction window multiplication linear prediction and spec trum phase correction The processing steps done by t 3 can be described as follows 1 Baseline correction of the F3 time domain data Each row is baseline corrected according to BC_mod This param eter
157. SIGF2 the signal region is defined by the entire spectrum minus the first 16th part or if the scaling region file exists by the regions in this file The name of the scaling region file is NUC1 SOL VENT where NUC1 and SOLVENT are acquisition status parame ters SIGF1 is also used in 2D datasets as the low field limit for 2D base line correction by abst2 abst1 absot2 absot1 zert1 and zert2 SIGF2 high field right limit of the signal region used in 1D and 2D datasets takes a float value ppm must be smaller than SIGF1 interpreted by sino If SIGF1 SIGF2 the signal region is defined by the entire spectrum minus the first 16th part or if the scaling region file exists by the regions in this file The scaling region file is defined as NUC1 SOL VENT where NUC1 and SOLVENT are acquisition status parame ters SIGF2 is also used in 2D datasets as the high field limit for 2D base line correction by abst2 abst1 absot2 absot1 zert1 and zert2 SINO signal to noise ratio used in 1D datasets takes a float value used in AU as an acquisition criterion not used by processing com mands the processing parameter SINO set with edp can be used in an AU program to specify a signal noise ratio which must be reached in an acquisition The acquisition runs until the value of SINO is reached and then it stops An example of such an AU program is au_zgsino SINO can be set with edp but not from the command line The rea
158. TCOMMENTA user comment adds a user comment to the audita txt file AUDITCOMMENTP user comment adds a user comment to the auditp txt file SEE ALSO audit auditcheck TOPSPIN User Management lockgui NAME lockgui Lock the TOPSPIN interface DESCRIPTION The command lockgui allows you to logoff the internal user It opens the dialog shown in Figure 14 6 Topspin locked by user jos at Thu Jul 07 11 55 40 BST 2005 Please press a button to unlock jos to unlock NMR administrator to unlock Figure 14 6 This indicates the locked status and offers buttons to unlock Note that only the current internal user and the NMR Administrator can unlock the interface The command can also be started as follows click Options Administration Lock TopSpin user interface INPUT FILES lt tshome gt conf topspin users prop TOPSPIN users properties file SEE ALSO uadmin esign chpwd login logoff P 607 TOPSPIN User Management login NAME login Exit TOPSPIN DESCRIPTION The command login allows you to login as a different TOPSPIN internal user It opens the following dialog Please identify yourself UserID jos Password Figure 14 7 Enter the user name of the internal user and enter the password The command can also be started as follows click Options Administration Login As Internal User INPUT FILES lt tshome gt conf topspin users prop TOPSPIN user
159. TMOD raw new processed data are created according to the cur rent processing parameters The result is different when the data have been Fourier transformed with STSI lt SI z with DATMOD proc cre ates STSI zeroes whereas zf with DATMOD raw creates SI zeroes The reason is that zf with DATMOD raw reprocesses the raw data but does not interpret STSI since no Fourier transform is done INPUT PARAMETERS set by the user with edp or by typing datmod si etc DATMOD data mode work on raw or proc essed data SI size of the processed data STSI strip size input if DATMOD proc INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if DATMOD proc proc processing parameters P 138 1D Processing commands OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS ZF SEE ALSO Zp P 139 1D Processing commands zp NAME zp Zero the first NZP data points 1D DESCRIPTION The command zp sets the intensity of the first NZP points of the dataset to zero It works on raw or processed data depending on the value of the parameter DATMOD The parameter NZP can
160. TOPSPIN 3 If ICON NMR runs actively at the exit moment TopSpin cannot be closed see Figure 13 9 v x This command has been disabled by the lcon NMR run Stop the run to enable it again Disabled command exit Close Details Figure 13 9 Entering exit on the command line is equivalent to clicking File Exit SEE ALSO close P 579 TOPSPIN Interface Processes NAME expl expl Open File Explorer show current processing folder DESCRIPTION The command exp1 opens the Explorer Windows or Konqueror Nau tilus Linux showing the processed data files the files in the procno di rectory of the active dataset see Figure 13 10 amp C bio data gquest nmr examid_1H 1 pdata File Edit View Favorites Tools Help Back A Search Gy Folders Address __ C bio data guest nmriexam1d_1H 1 pdata 1 gt Go ge a x fa 1i ja tr a curdat2 intrng El last_plot xwp 5 layout xwp a a peakrng a peaks portfolio por proc a procs title 128 KB 128 KB 2 KB 1KB 1KB 2 KB 2 KB 1 KB 2 KB 8 KB 1 KB 7 KB 1 KB 2 KB 2 KB 1 KB File File Text Document File File XWP File XWP File File Text Document Text Document File File POR File File File File 8 19 2004 10 41 AM 8 30 2004 1 28 PM 8 30 2004 1 28 PM 8 30 2004 12 58 PM 8 30 2004 1 28 PM 8 30 2004 1 08 PM 9 2 2004 5 13
161. TORDP accordingly type s bytordp All further processing commands interpret this status parameter and store the data accord ingly As such the byte order of the computer is handled automati cally and is user transparent 2D and 3D processing commands however allow you to store the processed data with a byte order dif ferent from the computer on which they run For example the com mands xfb big and t 3 big on a Windows or Linux PC store the data in big endian although the computer is little endian The processing status parameter BYTORDP is set accordingly FT_mod Fourier transform mode used in 1D 2D and 3D datasets in all directions takes one of the values no fsr far fsc fac isr igr igc isc set by all Fourier transform commands e g ft trf xfb xf2 xf1 trf xtrf tf3 tf2 tf1 interpreted by trf and xtrf P 41 TOPSPIN parameters P 42 also exists as processing edp parameter interpreted by trf and xtrf The values of FT_mod are described in chapter 2 4 MC2 Fourier transform mode of the second and third direction is used in 2D datasets in the second direction F1 is used in 3D datasets in the second and third direction F2 and F1 takes one of the values OF OSEOQ TPPI States States TPPI echo antiecho is set by xfb xf2 xf1 xtrf tf is interpreted by xf1 xtrf1 tf2 tf1 The processing status parameter MC2 is set according to the acquisi tion status parameter FnMODE If how
162. UT FILES lt tshome gt conf globals spoolerprotocol xml system spooler report lt userhome gt topspin lt hostname gt prop spoolerprotocol xml SEE ALSO cron qu qumulti at atmulti user spooler report Automation P 532 Conversion commands Chapter 12 Conversion commands This chapter describes all TOPSPIN conversion commands These are com mands which convert one data format to another Described are the con version of Bruker Aspect 2000 3000 WINNMR Varian Jeol and Felix data to TOPSPIN Furthermore the conversion to and from JCAMP DxX ZIP and TXT format P 533 Conversion commands conv NAME conv Convert Aspect 2000 3000 data to TOPSPIN format 1D 2D 3D DESCRIPTION The command conv converts DISNMR DISMSL data data from an As pect 2000 3000 to the TOPSPIN format It opens a file browser where you can 1 Navigate to the input directory where the DISNMR DISMSL data reside 2 Select the datafile to be converted and click convert 3 In the appearing dialog box see Figure 12 1 Specify the output TOPSPIN dataset Note that the datapath varia bles are initialized as follows e NAME is the filename of the DISNMR input data e EXPNO is the extension of the DISNMR input dataset If the extension is not numeric or if it is missing EXPNO is initialized with 1 PROCNO is set to 1 and cannot be changed DIR is the lt DIR gt value of the current TOPSPI
163. Varian data which were measured with the VNMR program to TOPSPIN format It opens a browser where you can navigate to the Varian input data file Just select the desired file and click VNMR data conversion This will open the dialog box shown in Figure 12 7 The selected Varian data will be converted Define destination dataset VNMR name C ibiol Warianiaewcosy 001 fid NAME aewcosy 001 fid EXPNO DIR C Bio USER guest Figure 12 7 Here you can specify the TOPSPIN destination dataset and click OK to start the conversion The vconv source and destination data can also be entered on the com mand line Here are some examples vconv vdata fid searches for vdata fid in the directory defined by the environment var iable VNMR 1 When the specified input data are found the dialog win dow shown in Figure 12 7 will appear Here you can specify the 1 Can be set with the TOPSPIN command env set VNMR lt path gt P 561 Conversion commands P 562 output dataset veonv lt path gt vdata fid as above except that the source data are searched for in the directory lt path gt veonv vdata fid lt name gt lt expno gt lt dir gt lt user gt Here the destination dataset is specified as command line argu ments The procno is automatically set to 1 If the dataset specification is incomplete the dialog window shown in Figure 12 7 will appear Note that the extension fid of the Vnmr dataset is not obl
164. W 0 In place operation Normally ftnd can perform an in place operation which means the processed data are stored in the current procno In special cases howev er in place operation is not possible and the processed data must be stored in a different procno ftnd will prompt the user for the output proc no When processing is finished the display will automatically change to the destination PROCNO Whether or not in place operation is possible depends on the direction being processed and the zero filling conditions In place operation is done e In the first direction always e Inthe second direction always as long as all directions are proc essed with one command e g with ftnd 0 Inthe third fourth etc directions if at least single zero filling SI gt TD and STSI 0 or STSI gt TD Note that if a procno is specified on the command line it is used i e the processed data of the last two directions are stored there Restrictions nD processing The command tnd has the following two restrictions e Raw and processed data have the same dimensionality i e the values of the status parameters PARMODE and PPARMOD must be the same Note that 2D processing commands like x b also work on datasets with different raw and processed data dimen sionality e g 3D raw and 2D processed data If the acquisition mode acquisition status parameter FnMODE is QF in one direction it must be QF in all directions In other
165. WDW trap FT_mod Fourier transform mode PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum set by a previous processing command e g xtrf can be viewed with dpp SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 F1 parameters set by a previous processing command e g xtrf can be viewed with dpp MC2 Fourier transform mode OUTPUT PARAMETERS F2 parameters can be viewed with dpp or by typing s ymax_p s ymin_p etc P 260 2D processing commands YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data proc F2 processing parameters proc2 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir
166. Window New Window The command nextwin activates the next open data window It is equiv alent to clicking Window Next Window or hitting the F6 key The command close closes the current data window It is equivalent to clicking File Close or hitting Ctr1 w The command closea11 closes the current data window It is equivalent to clicking File Closeall SEE ALSO newtop P 588 TOPSPIN Interface Processes ptrace NAME ptrace Display messages from various log files time sorted DESCRIPTION The command ptrace shows the TOPSPIN protocol and history files time sorted see Figure 13 12 These files only contain valuable information if the protocol function is active You can switch on this function as fol lows 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Check the item Record commands in protocol file The protocol file contains TOPSPIN startup information and command in formation on interface level The history file contains command informa tion on the level of the command interpreter and application modules It also contains error messages Note that the files history and protocol are emptied when you restart TOPSPIN which means the history of the previous TOPSPIN session is lost In case of problems you should first make a copy of these files before you restart TOPSPIN Note that a long TOPSPIN session especially with au tomation can create very
167. _getlid au_getlcosy au_getliny au_getlinvxref au_getkxhco au_Icid au_lIc2d au_lIconflow au_mult au_noemult au_profid au_prof2d au_gqcpmg lau_noediff jau_qcpmgadd jal_uynmer au_watersc au au zg au jau z915 35 jau au_zgcosy au_water seca cabin ee P 512 Figure 11 4 The dialog offers the following buttons Automation Edit Edit the selected AU program Equivalent to double clicking the AU pro gram name or entering edau lt name gt on the command line Compile Compile the selected AU program Equivalent to entering cplbruk lt name gt on the command line Execute Execute the selected AU program Equivalent to entering lt name gt or xau lt name gt on the command line Close Close the dialog The AU programs are selected from the Source directory as selected at the upper right of the dialog Note that lt tshome gt exp stan nmr au sre contains all Bruker AU programs lt tshome gt exp stan nmr au srce user contains all user defined AU programs The File menu The File menu offers the following functions New Create a new AU program Note that new AU programs can only be stored in user defined directories Save as Save the selected AU program under a new name A dialog will ap pear where you can specify the AU program name and destination di rectory Delete Delete the selected AU program Note that bot
168. a Example accumulate start 0 0 1 0 ppm 3 P 60 1D Processing commands Note that here the arguments offset and ppm hz do not affect the data but do affect the status parameter OFFSET In the examples above the accumulated dataset has the same data path as the original data except for the procno To accumulate data with a different datapath you can specify other parts of the datapath as arguments Parts that are not specified are taken from the current dataset Examples accumulate lt offset gt lt scale gt ppm hz lt procno gt lt expno gt accumulate start lt offset gt lt scale gt ppm hz lt procno gt lt expno gt lt user gt lt dir gt accumulate works like the command duadd except that all information is specified on the command line accumulate is typically used repeat edly to accumulate a series of 1D processed data The first instance of accumulate overwrites the current data with the specified data defining the accumulation start All further instances add the specified data to the current data OUTPUT PARAMETERS OFFSET the ppm value of the first data point of the spectrum INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i current processed data proc processing parameters lt dir2 gt data lt user2 gt nmr lt name2 gt lt expno2 gt pdata lt procno2 gt 1r 1i second processed data OUTPUT FILES lt dir gt data lt user gt nmr
169. a interpreted by pd pseudo 2D data Note that the default value 1 is not the first but the second point of a 1D dataset It is however the first row of a pseudo 2D dataset The point or row used is START n INC Chapter 3 1D Processing commands This chapter describes all TOPSPIN 1D processing commands Several of them can also be used to process one row of 2D or 3D data They store their output in processed data files and do not change the raw data For each command the relevant input and output parameters are men tioned Furthermore the relevant input and output files and their location are mentioned Although file handling is completely transparent it is some times useful to know which files are involved and where they reside For example if you have permission problems or if you want to process or interpret your data with third party software 1D Processing commands P 52 abs absf absd bas NAME abs Automatic baseline correction 1D absf Automatic baseline correction of the plot region 1D absd Automatic baseline correction special algorithm 1D bas Open baseline correction dialog box 1D DESCRIPTION Baseline correction commands can be started on the command line or from the baseline correction dialog box The latter is opened with the F amp Baseline correction abs Options 5 Correct baseline manually g polynomia Auto correct spectral range ABSF1 ABSF2 only
170. a lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data auditp txt processing audit trail USAGE IN AU PROGRAMS REV2 REV 1 SEE ALSO I v P 175 2D processing commands rhpp rhnp rvpp rvnp proj NAME rhpp Calculate horizontal F2 positive projection 2D rhnp Calculate horizontal F2 negative projection 2D rvpp Calculate vertical F1 positive projection 2D rvnp Calculate vertical F1 negative projection 2D proj Open the projections dialog box 2D 3D DESCRIPTION The projection commands can be started from the command line or from the projection dialog box selecting the corresponding command Options Calculate positive projection oO Calculate negative projection O Calculate sum Calculate disco sum O Read negative projection oO Update rows cols from display Required parameters Projection sum of Destination PROCNO Figure 4 11 P 176 2D processing commands This dialog box has several options each of which selects a certain com mand for execution Read positive projection on rows This option selects the command rhpp for execution It calculates the full positive projection of a 2D spectrum in the F2 direction and stores itas a 1D dataset Read positive projection on columns This option selects the command rvpp for execution It calculates the full positive projection of a 2D spectrum in t
171. a comment to one of the audit trail files raw or processed Each audit trail file entry contains the following elements Number the entry number 1 2 3 When starting date and time of the command Who user who starts the command the user that started TOPSPIN Where location where the command started the computer host name Version the TopSpin version which performed the acquisition or processing What command and associated parameters e g lt em LB 0 3 SI 16384 gt The last line of the file is a checksum which looks like 24 EB 5D 82 76 AD F2 2B 7E D2 A1 35 7B B5 C4 D5 The command auditcheck uses this line for the consistency check INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt P 600 TOPSPIN User Management audita t x t acquisition audit trail lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt x auditp txt processing audit trail Note that these are also the output files for audit com SEE ALSO gdcheck P 601 TOPSPIN User Management chpwd NAME chpwd Exit TOPSPIN DESCRIPTION The command chpwd allows you to change the password of the internal user It opens the following dialog PJ chpwd Please define password for user jos New Password Repeat Password Oooo E Figure 14 4 Enter the new password twice and click OK The command can also be started as follows click Opt
172. a name is TEMP the input dataset is the one from which the current 1D dataset was extracted except for the specified expno procno P 187 2D processing commands P 188 lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1 used_from data path of the source 2D data and the row no If no output expno is specified lt dir gt data lt user gt nmr TEMP 1 fid 1DFID lt dir gt data lt user gt nmr TEMP 1 pdata 1 used_from data path of the source 2D data and the row no USAGE IN AU PROGRAMS RSER row expno procno If expno 1 the row is written to the dataset TEMP SEE ALSO wser wserp rser2d rsr rsc wsr wsc slice 2D processing commands rsr NAME rsr Read row from 2D data and store as 1D data 2D 1D SYNTAX rsr lt row gt lt procno gt n DESCRIPTION The command rsr reads a row from a 2D spectrum and stores it as a 1D spectrum When entered on a 2D dataset without arguments rsr opens a dialog box where you can specify the row number and the procno of the output data Please specify row option destination procno ROW F PROCNO 999 Figure 4 15 The row must be specified as a number between 1 and F1 SI The latter is the F1 processing status parameter SI that can be viewed with s si The procno can be any number other that the current procno If the proc no field is left empty the output dataset is stored under data name TEMP When entered
173. a role in F3 tf3 evaluates the processing parameter PKNL On A X spectrometers PKNL true causes a non linear 5th order phase correction of the raw data This corrects possible errors caused by non linear behaviour of the analog filters On Avance spectrometers PKNL must always be set to TRUE For digitally filtered data it causes t 3 to handle the group delay of the FID For analog data it has no effect tf3 evaluates the processing parameter REVERSE If REVERSE TRUE the spectrum will be reversed in F3 i e the first data point be 3D processing commands comes the last and the last data point becomes the first tf3 can be used with the following command line options n tf3 will not store the imaginary data Imaginary data are only needed for phase correction If the phase values are already known and PHCO and PHC1 have been set accordingly t 3 will perform phase correc tion and there is no need to store the imaginary data This will save processing time and disk space If you still need to do a phase correc tion after 3 you can create imaginary data from the real data with a Hilbert transform see tht3 xdim 3D spectra are stored in the so called subcube format The size of the subcubes is calculated by t 3 and depends on the size of the spec trum and the available memory The option xdim allows you to use predefined subcube sizes It causes t 3 to interpret the F3 F2 and F1 processing parameter XDIM which
174. ad OUTPUT FILES For delf delser Delete raw data files of the selected EXPNOs lt dir gt data lt user gt nmr lt name gt lt expno gt audita txt acquisition audit trail For dels de1l2d deli Delete processed data files of the selected PROC NOs lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt auditp txt processing audit trail SEE ALSO del dela delp deldat Dataset handling dir dira dirp dirdat browse NAME dir List datasets nD dira List raw data nD dirp List processed data nD dirdat List data acquired at certain dates nD browse Open data list dialog box nD DESCRIPTION Commands to list data directories can be started from the command line or from the directory dialog box The latter is opened with the command browse see Figure 9 3 Browse Options An entire data set with all EXPNOs PROCNOs Acquisition data Processed data oO Data acquired at certain dates O 1D raw data fid oO 1D processed data 1r 1i 2D4D raw data ser O 2D processed data 2rr 2ii Required parameters Name z Data directory C Bio User guest Figure 9 3 This dialog box has several options each of which selects a certain com P 427 Dataset handling P 428 mand for execution The commands dir dira dirp and dirdat display all datasets con taining raw and or processed data as well as emp
175. addition performs a phase correction gf and gfp automatically perform an FID baseline correction according to BC_mod All composite processing commands can be found under the menu Processing More Transforms Shortcuts INPUT AND OUTPUT PARAMETERS see gm ft and pk INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data input if they exist but are not Fourier trans formed proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters P 98 1D Processing commands auditp txt processing audit trail USAGE IN AU PROGRAMS GF GFP SEE ALSO ef efp fp fme P 99 1D Processing commands P 100 ht NAME ht Hilbert transform 1D DESCRIPTION The command ht performs a Hilbert transform which means the imagi nary part of a spectrum is calculated from the real part This is only useful when the real data have been created from zero filled raw data with SI gt TD Only then will they contain the entire spectral information Imaginary data are required for phase correction They are normally cre ated together with t
176. af The values of ME_mod have the following meaning LPfr forward LP on real data LPfc forward LP on complex data LPbr backward LP on real data LPbc backward LP on complex data LPmifr mirror image forward LP on real data LPmifc mirror image forward LP on complex data Table 2 5 Linear prediction is only performed for NCOEF gt 0 Furthermore LP BIN and for backward prediction TDoff play a role The commands ft xfb xf2 and xf1 evaluate ME_mod but do not distinguish be tween LPfr and LPfc nor do they distinguish between LPbr and LPbc The reason is that the detection mode real or complex is evaluated from the acquisition status parameter AQ_mod However trf xtrf and xtrf2 evaluate the detection mode from ME_mod In 1D a com bination of forward and backward prediction can be done by running trf with ME_mod LPfc and trfp or t with ME_mod LPbce In 2D this would be the sequence xtrf xtrfp or xfb Note that not only Fourier transform but also window multiplication commands per form linear prediction when ME_mod is set This allows you to easily P 29 TOPSPIN parameters see the effect of linear prediction on the FID for example by executing em with LB 0 MI minimum relative intensity for peak picking used in 1D datasets takes a float value cm interpreted by pp 1i lipp only peaks with an intensity greater than MI will appear in the peak list MI can a
177. ain procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS BC SEE ALSO bas P 71 1D Processing commands bcm NAME bcm User defined spectrum baseline correction 1D DESCRIPTION The command bem performs a spectrum baseline correction by subtract ing a polynomial sine or exponential function This involves the following steps 1 Click V or enter bas to change to baseline correction mode 2 Fit the baseline of the spectrum with a polynomial exponential or sine function Click hold the button A and move the mouse to determine the zero order correction Do the same with the buttons B C etc for higher order corrections until the line matches the baseline of the spectrum 3 Click Ejj to return The command bem is automatically executed The interactively determined baseline function is stored in the file base_info This file can be stored for general usage with the command wmisc After that you can read it with rmi sc on another dataset and run bem to perform the same baseline correction In this case bem can be started from the command line or from the baseline dialog box which is opened with the command bas INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data proc processing parameters base_info baseline correction coefficients OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt exp
178. al VNMR parameter file procpar is stored in the TOPSPIN proc essed data directory You can check this ascii file for possible parameters which could not be converted Table 12 2 shows the Varian parameters and there TOPSPIN equivalent vconv can handle Unity and Gemini data acquired with VNMR 4 1 or new er Data from older Varian spectrometers or acquired with older software P 563 versions might also work but have not been tested by Bruker INPUT FILES lt dir gt data lt user gt nmr lt vdata gt fid or lt VNMR gt lt vdata gt fid fid the VNMR raw data procpar the parameters text title file OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid TOPSPIN 1D raw data acqu TOPSPIN acquisition parameters acqus TOPSPIN acquisition status parameters audita txt acquisition audit trail lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1 proc TOPSPIN processing parameters procs TOPSPIN processing status parameters procpar VNMR parameter file For 2D and 3D data the raw data are stored in the file ser and the addi tional parameter files acqu2 s acqu3 s proc2 s and proc3 s are created USAGE IN AU PROGRAMS VCONV vname xwname xwexpno xwdisk xwuser SEE ALSO jconv fconv conv winconv NAME winconv Convert WINNMR type data to TOPSPIN data 1D DESCRIPTION The command winconv converts Bruker WIN NMR data to TOPSPIN for mat It op
179. al is opened Books list available hardcopy printed manuals e Close close the Manuals dialog SEE ALSO help P 576 TOPSPIN Interface Processes edtext NAME edtext Open an empty text file with an editor DESCRIPTION The command edtext open an empty text file with the TOPSPIN editor The file can be stored in any directory SEE ALSO nbook P 577 TOPSPIN Interface Processes NAME exit Exit TOPSPIN DESCRIPTION The command exit exits TOPSPIN and terminates all running processes Before this happens the following warning is displayed Close TopSpin This will terminate all possibly active commands Exit anyway OK Cancel Figure 13 6 Furthermore TopSpin 2 1 and newer displays different warnings and error messages depending on the actual TopSpin use before exiting the pro gramm 1 If Acquisition is running see Figure 13 7 2 Acquisition is in progress Exiting will kill data acquisition Exit anyway OK Cancel Figure 13 7 P 578 TOPSPIN Interface Processes 2 If the spooler contains unfinished jobs see Figure 13 8 v Spooler shutdown EE The spooler contains unfinished jobs Running jobs 1 Priority jobs 3 Delayed jobs 0 Any of the above jobs will be lost upon shutdown Click OK to continue the shutdown OK ji Cancel Figure 13 8 Click OK in the respectively of the three dialogs above to exit
180. all directions takes an integer value between 0 and SI default 0 interpreted ft trf xfb xf2 xf1 xtrf xtrf2 t 3 t 2 tf1 P 37 TOPSPIN parameters P 38 During strip transform only the region determined by STSI and STSR is stored For STSI 0 a normal full transform is done STSI is always rounded in 1D to the next lower multiple of 4 in 2D and 3D to the next higher multiple of 16 Furthermore when the 2D 3D data are stored in submatrix Subcube format STSI is rounded to the next multiple of the submatrix Subcube size STSR strip start first output point of a strip transform used in 1D 2D and 3D datasets in all directions takes an integer value between 0 and SI default 0 interpreted ft xfb xf2 xf1 xtrf xtrf2 t 3 t 2 tf1 During strip transform only the region determined by STSI and STSR is stored TDeff number of raw data points to be used for processing used in 1D 2D and 3D datasets in all directions takes an integer value between 0 and TD default is 0 which means all interpreted by processing commands which work on the raw data The first TDeff raw data points are used for processing For TDeff 0 all points are used with a maximum of 2 SIl TDoff number of raw data points ignored or predicted used in 1D 2D and 3D datasets in all directions integer value between 0 and TD default is 0 interpreted by 2D and 3D processing commands which work on raw data The first r
181. aller size than the original raw data see also genser P 255 2D processing commands P 256 The F1 Fourier transform mode and data storage mode depends on the F1 acquisition mode see INPUT PARAMETERS below and the descrip tion of x b xtrf2 works like xtrf except that it only works in the F2 direction xtrf and xtrf2 take the same options as xfb xtrf can be used to do a combination of forward and backward predic tion Just run xtr with ME_mod LPfc and xtr p or xfb with ME_mod LPbc INPUT PARAMETERS F2 and F1 direction set by the user with edp or by typing si bc_mod bcfw etc SI size of the processed data TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW
182. alog box to move to parame ters further up or down in the dialog box Note that you can also set parameters by entering there names on the command line A dialog window will appear where you can enter the pa rameter value s For example si on a 1D dataset Size of real spectrum SIs 62768 Figure 10 9 or on a 2D dataset Alternatively you can specify the parameter value as an argument on the command line For example si 4k The size will be set to 4k P 476 Parameters lists AU programs Size of real spectrum F2 F1 SI 1024 Figure 10 10 INPUT AND OUTPUT PARAMETERS All processing parameters INPUT FILES lt tshome gt classes prop pared prop parameter properties file lt tshome gt exp stan nmr form proc e format file for edp INPUT AND OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters proc2 processing parameters for the second direction 2D or 3D proc3 processing parameters for the third direction 3D SEE ALSO dpp eda P 477 Parameters lists AU programs edpul edcpd edpy edmac NAME edpul Edit pulse programs edcpd Edit composite pulse decoupling CPD programs edpy Edit Python programs edmac Edit macros DESCRIPTION The commands edpul edepd edpy and edmac open a dialog that lists pulse programs CPD programs Python programs and macros respec tively The
183. alues is encoded in the first digit e DIFF DUP 3 the difference between successive values is encoded suppressing repetition of successive equal values default DIFF DUP For the included data types you have the following choices FID RSPEC ISPEC raw real and imaginary processed data FID RSPEC raw real processed data e FID raw data e RSPEC ISPEC real and imaginary processed data e RSPEC real processed data e PARAMS parameter files Before you can send the data you must fill in the fields To the email address of the recipient From your own email address e SMTP mail server Subject Text INPUT FILES lt tshome gt prog curdir lt user gt curdat current data definition If data type includes FID lt dir gt data lt user gt nmr lt name gt lt expno gt P 455 Dataset handling fid 1D raw data ser 2D raw data If data type includes RSPEC lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data 2rr real processed 2D data If data type includes ISPEC lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt li imaginary processed 1D data 2ir F2 imaginary processed 2D data 2ri F1 imaginary processed 2D data 2ii F2 F1 imaginary processed 2D data All other files which are part of a dataset like parameter files audit trails files etc are sent for all data types OUTPUT FILES lt use
184. alysis commands P 372 autolink NAME autolink Automatic backbone assignment DESCRIPTION The command autolink analyses the peak information available on a given set of protein spectra and calculates a backbone assignment For a step by step description of Autolink Click Help Manuals Analysis and Simulation Protein resonance Assignment Autolink can be started as follows Click Analysis Proteins Automatic Backbone Assignment SEE ALSO ft3d auremol NAME auremol automated protein structure determination DESCRIPTION The command auremo1 allows automated spectrum evaluation and protein structure determination Auremol can be started as follows Click Analysis Proteins Structure determination with AUREMOL For a full description of AUREMOL Click Help AUREMOL manual from the AUREMOL interface Analysis commands P 374 daisy NAME daisy 1D simulation program DESCRIPTION TOPSPIN 2 1 and newer offers the Daisy package for simulating spectra based on chemical shifts and coupling constants Daisy supports the fol lowing input data e TOPSPIN multiplet analysis package e Windaisy e HAM e ACD e Perch Daisy can be started as follows Click Analysis Structure Analysis 1D spectrum Simulation daisy IP exam1d_13 1 1 CABruker TOPSPINwdata guestinmr ees aoe PTSaO O k S R Mim A S S Ss fs ATA ae examld 13C 1 1f C Bruker TOPSPIN data gq
185. ame gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data rtr on 2D data 3rrr 3irr 3rir 3rri 3iii processed data rtr on 3D data A4rrrr 4iiii processed data rtr on 4D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data auditp txt processing audit trail used_ from data path of the source data and the trace number SEE ALSO wtr rpl wpl rcb rser wser wserp nD processing commands wpl NAME wpl Write 2D data to a plane of data gt 3D DESCRIPTION The command wp1 replaces a plane of processed data with dimension gt 3D with a 2D processed dataset It is usually but not necessarily used to write back a plane that was extracted with rp1 This plane can be modi fied and or written back to a different plane number wp takes up to four arguments As an example we take a plane written to a 3D dataset lt plane axis orientation gt 12 13 23 21 31 or 32 The digits refer to the F3 F2 and F1 axes of the 3D data Note that the order of the two digits is relevant e the first digit is the 3D axis that corresponds to the 2D F1 axis e the last digit is the 3D axis that corresponds to the 2D F2 axis This means that for the values 21 31 and 32 the axes are ex changed i e rows are stored as columns and vice versa see be low lt plane number gt 1 Sl SI is the 3D size in the direction orthogo
186. ame gt lt expno gt pdata lt procno gt 4rrrr processed 4D data procs F4 processing status parameters proc2s F3 processing status parameters P 324 nD processing commands proc3s F2 processing status parameters proc4s F1 processing status parameters For 3D data the output data file is 3r rr whereas proc4s does not exist For data of dimension n where n gt 5 output data files are named nr and ni e g 5r 5i 6r 6i etc SEE ALSO ftnd P 325 nD processing commands pknd NAME pknd nD phase correction DESCRIPTION The command pknd performs a phase correction of data of dimension gt 3D applying the values of PHCO and PHC1 It takes one argument the direction to be corrected If no argument is specified on the command line it is requested see Figure 6 4 PJ pknd Enter direction 4 3 2 1 for F4 F3 F2 F1 4 Figure 6 4 Before you execute pknd the phase values must first be determined for example on a 2D plane You can do that by typing x b on the nD data to process a plane do a phase correction on the resulting the 2D dataset and store the phase values in the nD dataset Note that phase correction normally requires the existence of imaginary data Usually however these do not exist for data of dimension gt 4 Therefore pknd automatically creates temporary imaginary data using Hilbert transform Actually the command processes 2D planes of an nD dataset performing a seri
187. ame the selected item in the database if not write protected Export P 481 Parameters lists AU programs Exports one or more items to text files To do that 1 Mark one or more items in the dialog 2 Click File Export 3 Select or enter the storage directory and click Export The selected item s will be stored under their original names provid ed there is write permission Import Imports external item e g pulse program files into the database and lists it in the dialog First it opens a file browser where you can navigate to a direc tory containing your text files which may have been created outside of TOP SPIN Select or enter the desired files in the browser and click the Import button The dialog will be updated showing the imported item Please note that e The owner of imported items is the current TOPSPIN user e Write protected items in the database cannot be overwritten by importing items with the same name e Writable items with the same name are only overwritten by import after user confirmation Close Close the dialog Current TopSpin User The current TOPSPIN user can be one of the following users e the system login user i e the user who started TOPSPIN This is the case if TOPSPIN internal login logoff is disabled e the current internal TOPSPIN user This is the case if TOPSPIN internal login logoff is enabled To enable disable TOPSPIN internal login logoff
188. ameters num TIT WIN NMR title OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid TOPSPIN 1D raw data acqu TOPSPIN acquisition parameters acqus TOPSPIN acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1 1r real processed data li imaginary processed data proc TOPSPIN processing parameters procs TOPSPIN processing status parameters SEE ALSO conv fconv jconv vconv convdta P 566 TOPSPIN Interface Processes Chapter 13 TOPSPIN Interface Processes This chapter describes commands which are related to the User interface and TOPSPIN processes Each user can set up his her own interface includ ing the TOPSPIN menu colours printer usage etc Commands are described for following processes on the screen storing them in the history file or killing them Online help is described as far as it can be started from the command line P 567 TOPSPIN Interface Processes about NAME about Show ToPSPIN version and configuration information DESCRIPTION The command about shows various TOPSPIN version and configuration information see Figure 13 1 CEES lelak The Next Generation in NMR Software 2008 Bruker BioSpin Version info Version 2 1 of January 30 2008 Server patchlevel 0 GUI build number 1149 Java version 1 6 0_04 Sun Microsystems Inc Memory JVM Total memory
189. ameters fitter General Parameters Acquisition Parameters OP Figure 7 4 To select the acquisition parameters to be shown on the plot P 356 Print Export commands 1 Enable the radio button Acquisition Parameters By default all acquisition parameters are shown and the Hide col umn is empty 2 In the Show column select the parameters to be hidden 3 Click the lt button in the center of the dialog 4 If desired you can also select experiment specific ased parame ters by selecting the respective Parameter filter and repeating step 2 and 3 To select the processing parameters to be shown on the plot 5 Enable the radio button Processing Parameters By default some processing parameters are shown while most are hidden In the Show column select the parameters to be hidden Click the lt button in the center of the dialog In the Hide column select the parameters to be shown 9 Click the gt button in the center of the dialog oN O After selecting the acquisition and or processing parameters 10 Click OK to save the selection The dialog offers the following buttons Save as save the current selection under a user defined name Open open a user defined selection Restore Defaults restore the TOPSPIN default selection OK save the current selection Cancel Close the dialog The Save as and Open button allow you to store several selections Note that these can only be activat
190. an be used as follows fromzip opens the above dialog box fromzip lt pathname gt lt dir gt lt user gt converts the ZIP file specified by the pathname and stores it under the specified lt dir gt and lt user gt and the name expno and procno as stored in the ZIP archive In the examples above fromzip stores the output dataset in the direc tory P 545 Conversion commands lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt The TOPSPIN dataset created by fromzip becomes the active dataset INPUT FILES lt pathname gt lt mydata bnmr zip gt TOPSPIN data as stored by tozip OUTPUT FILES For 1D and 2D data lt tshome gt prog curdir lt user gt curdat current data definition lt dir gt data lt user gt nmr lt name gt lt expno gt audita txt acquisition audit trail if input file contains raw data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt auditp txt processing audit trail if input file contains processed data outd output device parameters title title file see edti For 1D data lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data if input file contains 1D raw data acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data if input file contai
191. anation for FnAMODE QF the 2D storage mode is different than for other values see the description of x b As such the size of the resulting 1D data is twice as large as for other values of FnMODE If 2D imaginary data file 2ii exist 1D imaginary file 1i are created P 183 2D processing commands Only in that case the 1D data can be Fourier transformed Example 5 From a 3D dataset a plane is extracted and from this plane a column is extracted On the 3D dataset enter the following commands xf2 s13 48 2 to read the F3 F1 plane 48 to procno 2 rsc 19 3 to read from plane 48 column 19 to procno 3 ft to Fourier transform the resulting 1D data according to Fn MODE Explanation the 3D 2D and 1D dataset are stored in three different procno s all under the same expno i e they share the same acquisi tion parameters 1D processing commands automatically recognize that the 1D dataset is a column from an F3 F1 plane that was extract ed from a 3D dataset As such ft interprets the F1 parameter Fn MODE to determine the Fourier transform mode Note that F1 is the third direction of the 3D dataset The parameter handling however is transparent to the user INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii 2D processed data OUTPUT FILES If no output procno is specified lt dir gt data lt user gt nmr TEMP 1 pdata 1 1r 1i 1D spectru
192. and stores it under the lowest empty expno and procno 1 fromjdx lt pathname gt converts the JCAMP DxX file specified by the pathname and stores it under the lowest empty expno and procno 1 fromjdx lt pathname gt y converts the JCAMP DxX file specified by the pathname and stores it under expno 1 and procno 1 Possibly existing data are overwritten y In the examples above fromjdx stores the output dataset in the direc tory lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt where lt dir gt the data directory of the current dataset lt user gt the user of the currently current dataset lt name gt the name of the JCAMP DX file but without the extension P 541 Conversion commands dx Further examples fromjdx lt pathname gt du converts the JCAMP DX file specified by the pathname and stores it under the dir du user name expno and procno as specified in the input JCAMP DxX file fromjdx lt pathname gt user converts the JCAMP DxX file specified by the pathname and stores it under the dir of the current dataset and the user name expno and procno as specified in the input JCAMP DxX file fromjdx lt pathname gt name converts the JCAMP DxX file specified by the pathname and stores it under the dir and user of the active dataset and the name expno and procno as specified in the input JCAMP DxX file fromjdx lt pathname gt expno converts the JCAMP DxX file spec
193. and 603 exit command 578 expinstall command 405 490 507 508 515 expl command 580 exponential baseline correction 1D 54 72 469 baseline correction 2D 154 broadening factor 78 window multiplication 27 40 75 77 78 exportfile command 350 F f1disco command 160 f1projn command 163 f1projp command 163 f1sum command 167 f2disco command 160 f2projn command 163 f2projp command 163 f2sum command 167 fconv command 444 539 files of a dataset 524 580 filt command 81 filter width 22 find command 435 first order phase correction 32 44 62 110 first point correction 25 fit function 49 fmc command 83 Fourier transform 5 25 41 1D 75 83 85 86 87 98 100 125 133 134 2D 213 223 227 229 250 254 3D 230 267 269 288 289 296 301 308 Fourier transform mode 25 28 41 42 87 134 229 fp command 83 frequency domain data 5 86 96 170 213 223 l 4 227 252 267 288 289 296 301 fromjdx command 444 541 545 fromzip command 444 ft command 75 83 85 98 ft3d command 267 ftf command 85 227 ftnd 314 G Gaussian baseline function 23 69 broadening factor 78 123 deconvolution 91 156 lineshape 91 157 window multiplication 26 27 40 77 98 gdcheck command 605 gdcon command 91 genfid command 96 101 133 genser command 170 252 254 255 geometric sequence of levels 353 gf command 98 gfp command 98 ghelp 583 gm command 77 86 98 135 graphics file 350 group delay 8 33 39 87 231 270 290
194. and adsu This dialog box offers several options each of which selects a certain command for execution Subtract a 1D spectrum from each row retain sign This option selects the command sub2 for execution It subtracts a 1D dataset from each row of the current 2D spectrum It first compares the intensity of each data point of the 1D spectrum with the intensity of the corresponding data point in the 2D spectrum If they have op posite signs no subtraction is done and the 2D data point remains un changed If they have the same sign and the 1D data point is smaller than the 2D data point the subtraction is done If the 1D data point is greater than the 2D data point the latter is set to zero As such the sign of the 2D data points always remains the same Subtract a 1D spectrum from each column retain sign This option selects the command sub1 for execution It works like sub2 except that it subtracts the 1D second dataset from each col umn of the current 2D spectrum Subtract a 1D spectrum from each row This option selects the command sub1d2 for execution It subtracts a 1D dataset from each row of the current 2D spectrum Unlike sub2 it does not compare intensities P 192 2D processing commands ty Add subtract sub2 Options O Add a 2D spectrum ALPHA current GAMMA second Add a 2D fid ser ALPHA current GAMMA second Subtract a 1D spectrum from each row retain sign O Subtract a 1D spectrum f
195. apk and each successive spectrum with pk using the same values see for example AU program proc_noe pk applies but does not change the processing parameters PHCO and PHC1 edp It does however change the corresponding processing status parameters PHCO and PHC1 dpp by adding the applied phase values pk is a part of the composite processing commands efp fp and gfp pk can also be used to perform a phase correction on an FID rather than a spectrum This is automatically done if you enter pk on a dataset which does not contain processed data Phase correction on an FID is used pri or to Fourier transform to induce a shift in the resulting spectrum The spectrum is shifted according to the value of PHC1 one real data point to the left for each 360 A negative value of PHC1 causes a right shift The points which are cut off on one side of the spectrum are appended on the other side Note the difference with performing a left shift 1s or right shift rs after Fourier transform This appends zeroes at the oppo site side If processed data do exist and you still want to do a phase cor rection on the FID you can do this with the command trf The command pk can also be started from the phase correction dialog box which is opened with ph INPUT PARAMETERS set from the ph dialog box with edp or by typing phcO phc1 etc PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value freque
196. ar lt 1D parameter set gt acqu acquisition parameters proc processing parameters outd output device parameters lt tshome gt exp stan nmr par lt 2D parameter set gt acqu F2 acquisition parameters acqu2 F1 acquisition parameters proc F2 processing parameters proc2 F1 processing parameters outd output device parameters clevels 2D contour levels 3D parameter sets also contain the files acqu3 and proc3 for the third direction OUTPUT FILES lt dir gt data lt user gt nmr lt 1D data name gt lt expno gt acqu acquisition parameters lt dir gt data lt user gt nmr lt 1D data name gt lt expno gt pdata lt procno gt proc processing parameters outd output device parameters lt dir gt data lt user gt nmr lt 2D data name gt lt expno gt acqu F2 acquisition parameters acqu2 F1 acquisition parameters lt dir gt data lt user gt nmr lt 2D data name gt lt expno gt pdata lt procno gt proc F2 processing parameters proc2 F1 processing parameters outd output device parameters P 491 Parameters lists AU programs P 492 clevels 2D contour levels In TOPSPIN 2 1 and newer the default directory for user defined parame ter sets is lt tshome gt exp stan nmr par user USAGE IN AU PROGRAMS RPAR name type SEE ALSO wpar delpar expinstall Parameters lists AU programs wpar edpar NAME wpar Write a parameter set edpar Edit a paramete
197. ata DIRECTORY 193 browseDataTres C blokletalg uestinmr exam d_13C 3ipdata DIRECTORY r12 13 15 36 23 224 borowseDetaTree ic DERA d_13C 4 pdata DIRECTORY 12 43 15 36 29 244 browseDataTree Cibio data guestnmr exam1d_13C 5 pdata DIRECTORY 12 43 15 36 29 274 browseDataTree Cibio data guestnmr exam1d_13C 6pdata DIRECTORY 12 43 15 36 29 284 browseDataTree Cibio data guestnmr exam1d_13C 7pdata DIRECTORY 12 13 15 36 29 304 browseDataTree Cibio data guestinmr exam1d_13C Bpdata DIRECTORY 12 13 15 36 29 314_ browseDataTree C bio data guestnmr exam1d_13C 9 pdata DIRECTORY m 2 13 15 36 29 394 getDiscFuncByldent C hio data questnmrfexam1 d_13CH dpdatal amp DF_T T C Documents and Settings Administrator topspin nmr datastation prop protocol txt C tf1 3b1 Siprogicurdir A dministratorthistory C tf13b1 Siprogicurdir Administrator history traffic iC tf13b1 Siprogicurdir Administrator stdout dataserver 1384 Figure 13 12 P 590 TOPSPIN Interface Processes SEE ALSO hist P 591 TOPSPIN Interface Processes set NAME set Open the user preferences window DESCRIPTION The command set allows you to set user preferences It opens the dia log box shown in Figure 13 13 PN User preferences E A Administration items Administration items Spectrum Auto open last used dataset when restarting TopSpin CO Contour plot Show TopSpin data exam
198. ata lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data OUTPUT FILES lt pathname gt lt mydata txt gt text file containing displayed region SEE ALSO tojdx tozip Conversion commands tozip NAME tozip Store current dataset in ZIP file nD DESCRIPTION The command tozip converts a TOPSPIN dataset to ZIP format It opens a dialog box where you can enter the required information amp tozip Please specify destination Name of archive file Directory of archive file C Usersidrud Type of archive file ZIP compress 7 Include these data types FID RSPEC ISPEC v Zip current EXPNO PROCNO only or all of exam_Daisy current x Figure 12 6 This information includes Name of archive file output file name and extension lt datasetname gt topspin zip Directory of archive file directory where output file is stored Type of archive Z IP compress compressed nmr data in zip format ZIP no compress uncompressed nmr data in zip format Data types included FID RSPEC ISPEC raw real and imaginary processed data FID RSPEC raw real processed data P 557 Conversion commands e FID raw data e RSPEC ISPEC real and imaginary processed data e RSPEC real processed data Zip current EXPNO PROCNO only or all of archive current exp no procno or all expnos procnos in current dataset Options for tozip dialog win
199. ata lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS EM GM SEE ALSO sinm qsin sinc qsinc tm traf trafs P 80 1D Processing commands filt NAME filt Digital filtering of the data 1D DESCRIPTION The command filt smoothes the data by replacing each point with a weighted average of its surrounding points By default filt uses the weighting coefficients 1 2 1 which means that the intensity p i of data point i is replaced by 1 p i 1 2 p i 1 pG Figure 3 6 Different weighting algorithms can be set up by creating a new file in the directory lt tshome gt exp stan nmr filt ld Just copy the default file threepoint to a different name and modify it with a text editor The file must look like 3 1 2 1 or 5 1 2 3 2 1 where the first number represents the number of points used for smooth ing and must be odd The other numbers are the weighting coefficients for the data points The processing parameter DFILT determines which file is used by filt This is one of the few cases where file handling cannot be done from TOP SPIN and needs to done on operating system level P 81 1D Processing commands P 82 INPUT PARAMETERS set by the user with edp or by typing dfilt datmod etc DFILT digital filter filename DATMOD data mode w
200. ata lt user2 gt nmr lt name2 gt lt expno2 gt pdata lt procno2 gt 1r 1i processed 1D data input if DATMOD proc OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters P 108 1D Processing commands auditp txt processing audit trail USAGE IN AU PROGRAMS MUL MULC NM DIV SEE ALSO add addc addfid P 109 1D Processing commands pk NAME pk Phase correction according to PHCO PHC1 1D DESCRIPTION The command pk performs a zero and first order phase correction ac cording to user defined phase values These phase values are read from the processing parameters PHCO and PHC1 The data consisting of real points R i and imaginary points I i are phase corrected according to the formula RO i R i cosa i i sina i I0 i I i cosa i R i sina i Figure 3 12 where a i PHC0 i 1 PHC1 Figure 3 13 where i gt 0 RO and 10 represent the corrected values and PHCO and PHC1 are processing parameters pk does not calculate the phase values but uses the preset values Therefore pk is only useful when these values are known They can be determined interactively in Phase correction mode or automatically with apk or apks P 110 1D Processing commands pk is typically used in a series of experiments where the first spectrum is corrected with
201. aw data point that contributes to processing is shifted by TDoff points For 0 lt TDoff lt TD the first TDoff raw data points are cut off at the beginning and TDoff zeroes are appended at the end corresponds to left shift For TDoff lt 0 TDoff zeroes are pre pended at the beginning and e for SI lt TD TDoff 2 raw data are cut off at the end for DIGMOD digital the zeroes would be prepended to the group delay which does not make sense You can avoid that by TOPSPIN parameters converting the raw data with convdta before you process them also interpreted by 1D 2D and 3D processing commands which do linear backward prediction i e ft xfb of t 3 when ME_mod is pbr or lpbc For TDoff gt 0 the first TDoff points are replaced by predicted points For TDoff lt 0 abs TDoff predicted points are added to the beginning and cut off at the end of the raw data If zero filling occurs 2 SI gt TD then only zeroes are cut off at the end as long as abs TDoff lt 2 SI TD Note that digitally filtered Avance data start with a group delay This means that a backward prediction does not make sense unless the data are first converted AMX format with convdta TM1 the end of the rising edge of a trapezoidal window used in 1D 2D and 3D datasets in all directions takes a float value between 0 0 and 1 0 interpreted by tm TM1 represents a fraction of the acquisition time and must be smaller than TM2 TM2 the start
202. be replaced and the destination data path Usage of wser with arguments on the source 1D dataset wser lt row gt the specified row of the 2D raw data is replaced by the current 1D FID The destination 2D dataset is the one from which the current 1D data set was extracted P 206 2D processing commands wser lt row gt lt expno gt the specified row of the 2D raw data is replaced by the current 1D FID The 2D dataset must reside under the current data name the specified expno and procno 1 Usage of wser with arguments on the destination 2D dataset wser lt row gt lt expno gt the specified row of the current 2D raw data is replaced The source 1D dataset must reside under the current data name specified expno and procno 1 INPUT FILES lt dir gt data lt user gt nmr TEMP 1 fid 1D raw data lt dir gt data lt user gt nmr TEMP 1 pdata 1 used_ from data path of the 2D data input of wser ona 1D dataset or lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt used_ from data path of the 2D data input of wser on a 1D dataset wser Can also be started from the dialog box that is opened with the com mand slice OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw 2D data audita txt acquisition audit trail USAGE IN AU PROGRAMS WSER row name expno procno dir user
203. by creating a new data set and initializing its NMR parameters according to the selected experiment type For multi receiver experiments several datasets are created Please define the number of receivers in the box below NAME EXPNO 1 PROCNO 1 DIR CA BrukenT OPSPIN data questinmr solvent CDCI3 z Experiment Dirs C Bruker TOPSPIN exp stan nmr par user v Experiment Use current params v TNE 13C 1H AV500 Cholesterylacetate 1 Receivers 1 2 8 OK Cancel More Info ji Help Figure 9 9 Here you can specify the dataset NAME EXPNO PROCNO DIR disk unit and USER Note that these are all parts of the data pathname lt dir gt data nmr lt user gt lt name gt lt expno gt pdata lt procno gt Furthermore you can select P 440 Dataset handling Solvent sets the acquisition parameter SOLVENT Default is the solvent of the current dataset Experiment parameter set copies the acquisition and processing parameters Default is Use current parameters When you click OK the dataset is created and made the current data win dow If the specified dataset already exists you will be prompted to over write this or not Note that this will only overwrite the parameters not the data files new is equivalent to the command edc INPUT FILES lt tshome gt prog curdir lt user gt curdat current dataset definition If Experiment Use current params lt
204. byteorder or the raw data NC normalization constant F1 parameters set by the acquisition can be viewed with dpa or by typing s fnmode P 224 2D processing commands FnMODE Fourier transform mode OUTPUT PARAMETERS F2 and F1 parameters can be viewed with dpp or by typing s si s tdeff etc SI size of the processed data TDeff number of raw data points that were used for processing STSR strip start first output point of strip transform STSI strip size number of output points of strip transform FTSIZE Fourier transform size XDIM submatrix size F2 parameters can be viewed with dpp or by typing s ft_mod s ymax p etc FT_mod Fourier transform mode YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data F1 parameters set by the acquisition can be viewed with dpp or by typing s mc2 MC2 Fourier transform mode INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data input if 2rr does not exist or is Fourier transformed in F2 acqus F2 acquisition status parameters acqu2s F1 acquisition parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr processed data input if it exists but is not Fourier transformed in F2 proc F2 processing parameters P
205. ce 1D dataset must reside under the current data name specified expno and procno 1 wserp Can also be started from the dialog box that is opened with the command slice INPUT FILES lt dir gt data lt user gt nmr TEMP 1 pdata 1 1r 1i 1D processed data real imaginary used_ from data path of the 2D data input of wserp on a 1D dataset or lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D processed data real imaginary used_ from data path of the 2D data input of wserp on a 1D dataset OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw 2D data audita txt acquisition audit trail USAGE IN AU PROGRAMS WSERP row name expno procno dir user Note that the order of the arguments in AU programs is different from the order on the command line SEE ALSO wser rser rser2d wsr wsc rsr rsc slice P 210 2D processing commands wsr NAME wsr Replace row of a 2D spectrum by 1D spectrum SYNTAX wsr lt row gt lt procno gt DESCRIPTION The command wsr replaces one row of 2D processed data by 1D proc essed data It is normally used in combination with rsr in the following way e run rsr to extract row x from a 2D spectrum manipulate the resulting 1D data with 1D processing commands e run wsr to replace row x of the 2D data with the manipulated 1D data wsr can be entered on the source 1D dataset or on t
206. cessed data used in 1D 2D and 3D datasets in the first direction takes a float value set by all processing commands only exists as processing status parameter dpp YMIN_p minimum intensity of the processed data P 46 used in 1D 2D and 3D datasets in the first direction TOPSPIN parameters e takes a float value e set by all processing commands only exists as processing status parameter dpp 2 6 Relaxation parameters Relaxation parameters can be set with the command edti which can be entered from the Relaxation menu COMPNO number of components contributing to the relaxation curve e used in pseudo 2D relaxation datasets e takes an integer value default is 1 e interpreted by simfit e Peak positions are determined on a row which is specified by the parameter START usually the first row These positions are then used by pd for each row of the 2D data However peak positions sometimes drifts in the course of the experiment i e they might shift one or more points in successive rows Therefore pd searches for the maximum intensity at the predefined peak position plus or minus DRIFT DRIFT drift of the peak positions in the course of the experiment e used in pseudo 2D relaxation datasets e takes an integer value must be 1 or greater default is 5 e interpreted by pd e Relaxation analysis is usually done with a series of relaxation curves one for each peak in the spectrum One curve shows the intensity
207. cified dates day data acquired on the specified date earlier data acquired before the specified date later data acquired later than the specified date Table 9 2 range you select you are further prompted for one or two specific dates A list of datasets which were measured within the specified time range is displayed with a separate entry for each expno When started from the command line dir commands can take one ar gument which may contain wild cards Examples dir examld list all datasets whose name starts with exam d dir examld list all datasets whose name is exam d plus three extra characters INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data ser 2D or 3D raw data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data 2rr 2ir 2ri 2ii processed 2D data 3rrr 3irr 3rir 3iir processed 3D data SEE ALSO dirf dirs dirser dir2d open find re rep rew repw reb P 429 Dataset handling P 430 dirf dirs dirser dir2d browse NAME dirf List raw data 1D dirs List processed data 1D dirser List raw data 2D 3D dir2d List processed data 2D 3D browse Open the list data dialog box nD SYNTAX dir lt name gt DESCRIPTION The dir commands display a list of datasets according to certain crite ria They can be started from the command li
208. cno sinm same process the same row as the previous processing command and store it under the current procno The same option is automatically used by the AU program macros SIN When used on a regular 1D dataset i e with 1D raw data it has no effect The wm command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the wm dialog box with edp or by typing ssb gb etc SSB sine bell shift GB Gaussian broadening factor input of sine and qsinc set by the acquisition can be viewed with dpa or s aq AQ Acquisition time input of sinm and gqsin INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters 1 Usually a result of rsr rsc or a previous 1D processing command on that 2D or 3D data P 123 1D Processing commands lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data input if they exist but are not Fourier trans formed proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS SINM QSIN SINC QSINC
209. command mul instead of a complex multiplica tion mul div mulc and nmwork on raw or on processed data depending on the value of DATMOD The result is always stored as processed data in P 107 1D Processing commands the current dataset The raw data are not overwritten When mul and divare started from the command line they will run with out user interaction if the second dataset is already defined file curdat2 If this is not defined the adsu dialog box will be opened When you run a multiplication or division command from the command line make sure that the required parameters are set Click the Procpars tab or enter edp to do that The adsu command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the adsu dialog box with edp or by typing dc datmod etc DC multiplication factor input of mulc DATMOD data mode work on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if DATMOD proc proc processing parameters curdat2 definition of the second dataset lt dir2 gt data lt user2 gt nmr lt name2 gt lt expno2 gt fid second raw data input if DATMOD raw lt dir2 gt d
210. comment lines The format is suitable to be imported into a spreadsheet program such as Excel for further processing The example is the result of integrating the 3 defined re gions of 3 datasets Intser Processing Finished Data set list full path c intser list1 txt Result file full path c res1 txt Integral info A 1 0 regions in PPM low field high field bias slope 8 44574704397792 8 322631197855793 0 0 0 0 for region 1 7 821960090292476 7 485443444225329 0 0 0 0 for region 2 7 345912151953584 7 206380859681841 0 0 0 0 for region 3 Spectrum number Integral range 0 Integral range 1 Integral range 2 0 0 307 0 587 1 1 0 615 1 174 2 2 1 229 2 348 4 The command intser can also be used to integrate a series of 2D data Note that in this case the file containing the integral regions is int2drng SEE ALSO serial P 519 Automation P 520 qu NAME qu queue a TOPSPIN command for execution DESCRIPTION The command qu queues a command for execution It requires one ar gument the command to be queued For example the command qu xfb queues the command xfb for execution This means that xf b is execut ed as soon as the currently running command and previously queued commands have finished Command queuing can for example be used to process a 2D dataset immediately after acquisition This is done with the command sequence zg qu xfb Note that in
211. corrected shifts from column to column The first column is corrected between F1 ABSF2 and F1 ABSF1 The last column is corrected between F1 SIGF2 and F1 SIGF1 For intermediate columns the low field limit is an interpolation of F1 ABSF2 and F1 SIGF2 and the high field limit is an interpolation of F1 ABSF1 and F1 SIGF1 F1 Auto correct baseline alternate algorithm This option selects the command absd1 for execution It works like abs1 except that it uses a different algorithm It is for example used when a small peak lies on the foot of a large peak In that case absd1 allows you to correct the baseline around the small peak which can then be integrated Usually absd1 is followed by abs1 F1 Auto correct baseline shift correction region alternate algo rithm This option selects the command absoti for execution It works like abst1 except that it has a different algorithm which applies a larger correction If you run a command like abs1 from the command line you have to 2D processing commands make sure that the required parameters are already set Click the Procpars tab or enter edp to do that The bas command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the bas dialog box with edp or by typing absf1 absf2 etc ABSG degree of the polynomial to be subtracted 0 to 5 default is 5 ABSF1 low
212. creates a new dataset Note that the number of data points of the pseudo raw data is twice the size of the processed data they are created from The acquisition status parameter TD dpa is set accordingly TD 2 Sl INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data frequency domain OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt lr 1i processed 1D data time domain auditp txt processing audit trail USAGE IN AU PROGRAMS IFT SEE ALSO genfid ft trf trfp P 101 1D Processing commands Is rs NAME Is Left shift data NSP points 1D rs Right shift data NSP points 1D DESCRIPTION The command 1s shifts 1D data to the left The number of points shifted is determined by the parameter NSP The right end of the data is filled with NSP zeroes rs shifts 1D data to the right The number of points shifted is determined by the parameter NSP The left end of the data is filled with NSP zeroes Depending on the parameter DATMOD rs and 1s work on raw or proc essed data The value of NSP is the number of the real plus imaginary data points that are shifted As such the real data are shifted NSP 2 points and the imaginary data are shifted NSP 2 points For odd values of NSP the real and imaginary data points are interchanged As such the displayed spec trum is not only shifted but also changes f
213. ct1 ct2 dati1 or dat2 do not use the EDGUESS table They calculate the in itial values and step rates of the T1 T2 function variables I 0 P and T1 FCTTYPE function type used for fitting the relaxation curve used in pseudo 2D relaxation datasets takes one of the values listed in Table 2 10 interpreted by simfit Table 2 10 shows the experiment types which simfi t can handle and the corresponding fit functions Note that ct1 ct2 dat1 and dat2 do not evaluate FCTTYPE because they can only handle T1 T2 experiments They do however set FTCTYPE to the value t1 t2 TOPSPIN parameters Exp type Com Fit function p uxnmrtit 1 I t I 0 P exp t T1 2 invrec 1 4 I t I 0 1 2A exp t T1 satrec 1 6 I t I 0 1 exp t T1 cptirho 1 4 I t I 0 1 TIS T1rho exp t T1rho exp t TIS expdec 1 6 I t 1 0 exp t T gaussdec 1 6 I t I 0 exp SQR t T lorgauss 1 3 I t IL exp t TL IG exp SQR t TG linear 1 6 I t A B t varbigdel 1 6 I I 0 exp D SQR 2 PI gamma G LD BD LD 3 1e4 varlitdel 1 6 I I 0 exp D SQR 2 PI gamma G LD BD LD 3 1e4 vargrad 1 6 I I 0 exp D SQR 2 PI gamma G LD BD LD 3 1e4 raddamp 1 6 MZ t A0 MZ O tanh t T0 TRD Table 2 10 e used in pseudo 2D relaxation datasets e takes the value area or intensity default is intensity e interpreted by pd ct1 dat1 and simfit e Before
214. ction used in 1D datasets takes a float value ppm TOPSPIN parameters interpreted by bc when BC_mod sfil or qfil sfil qfil is used to suppress signals in the center of the spectrum BCFW determines the width of the region around the center of the spectrum which is affected by be BC_mod FID baseline correction mode used for 1D 2D and 3D dataset in all directions only useful in the acquisition direction takes one of the values no single quad spol qpol sfil qfil interpreted by be em gm ft trf xfb xf2 xf1 xtrf tf The values of BC_mod and the corresponding functions are shown in table 2 2 Most commands evaluate BC_mod for the function to be subtracted but not for the detection mode The latter is then evalu ated from the acquisition status parameter AQ_mod This means for example it does not matter if you set BC_mod to single or quad Only trf and xtrf evaluate the detection mode from BC_mod and dis tinguish between BC_mod single and BC_mod quad The same counts for the values spol qpol and sfil qfil BC_mo_ Function subtracted from the FID Detection d mode no no function single average intensity of the last quarter of the single channel FID quad average intensity of the last quarter of the quadrature FID spol polynomial of degree 5 least square fit single channel qpol polynomial of degree 5 least square fit quadrature sfil Gaussian function of width BCFW single channel qfil
215. ction on or off It takes two arguments and can be used as follows setdef ackn no commands continue without acknowledgment setdef ackn ok commands require acknowledgment before con tinuing Note that re starting TOPSPIN always sets setdef ackn to its default val ue which is ok setdef can also be used to switch the storage of standard output and standard error message off or on In this case it must be entered in the form setdef stdout on store standard output message setdef stdout off do not store standard output messages The equivalent for standard error messages is setdef stderr ok no OUTPUT FILES lt tshome gt prog curdir lt user gt stdout num standard TOPSPIN output file for setdef stdout ok stderr num Standard TOPSPIN error file for setdef stderr ok P 594 TOPSPIN Interface Processes shell NAME shell Open a Windows Command Prompt or Linux Shell DESCRIPTION The command shell opens a Command Prompt under Windows or a shell under Linux P 595 swin NAME swin Swap the position and geometry of two data windows DESCRIPTION The command swinswaps the position of two data windows If the layout contains exactly two data windows swin simple swaps their position and geometry If the layout contains more than two data windows swin al lows you to swap the currently selected active data window with any of the other data windows The latter can be selected from a list swin
216. ction value frequency independent PHC 1 first order phase correction value frequency dependent Note that this is one of the rare cases where the output parameters of a command are stored as processing edp and as processing status pa rameters dpp INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary proc processing parameters procs processing status parameters auditp txt processing audit trail P 67 1D Processing commands P 68 USAGE IN AU PROGRAMS APK APKF APKS SEE ALSO apk0 apk1 apkOf 1D Processing commands bc NAME bc Baseline correction of the FID 1D DESCRIPTION The command be performs a baseline correction of raw 1D data The type of correction is determined by the processing parameter BC_mod as shown in table 3 1 BC_mod Function subtracted from the FID Detection mode no no function single average intensity of the last quarter of the single channel FID quad average intensity of the last quarter of the quadrature FID spol polynomial of degree 5 least square fit single channel qpol polynomial of degree 5 least square fit quadrature sfil Gaussian functi
217. ctor respectively AQ is an acquisition status parameter which rep resents the acquisition time gm allows you to separate overlapping peaks The quality of the sep aration depends on the choice of the parameters LB and GB Suitable values can be determined with Manual window adjustment The value of LB must be negative typically the half line width of the spectral peaks Note that for exponential window multiplication em LB must be positive The value of GB must lie between 0 and 1 It determines the position of the top of the Gaussian function For example for GB 0 5 the top lies in the middle of the FID Note that for large values of GB close to 1 peaks can become negative at the edges which can impair quantitative analysis of the spectrum emand gmimplicitly perform a baseline correction of the FID according to the processing parameter BC_mod Furthermore they perform linear prediction according to the parameters ME_mod NCOEF and LPBIN P 78 1D Processing commands When executed on 2D or 3D data em and gm take up to four arguments e g em lt row gt lt procno gt n y process the specified row and store it under the specified procno The last two arguments are optional n prevents changing the display to the output 1D data y causes a possibly existing data to be overwritten without warning When executed on a dataset with 2D or 3D raw data but 1D processed data em and gm take one argument e g em lt row g
218. d on a predefined set of data points which are considered to be a part of the baseline The regions between these points are individually fitted In order to execute sab the baseline points must have been determined You can do this as follows 1 Click V or enter bas to change to baseline correction mode 2 Click 4 to switch to Define baseline points mode if the baseline points have been defined before you are first prompted to append to a or overwrite o the existing list of points 3 Move the cursor along the spectrum and click the left mouse but ton at several positions which are part of the baseline 4 Click E to return The command sab is automatically executed The set of baseline points is saved in the file baslpnts This file can be stored for general usage with the command wmisc After that you can read it with rmisc on another dataset and run sab to perform the same baseline correction sab can be started from the command line or from the baseline dialog box which is opened with the command bas INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data baslpnts baseline points points and ppm values OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 127 1D Processing commands P 128 1r real processed 1D data auditp txt processing audit trail USAGE IN AU PROGRAMS SAB
219. d 176 rhpp command 176 right shift 30 102 111 rmisc command 468 rpar command 488 495 550 561 rpl command 334 rs command 102 111 rsc command 134 154 180 203 248 rser command 186 rser2d command 284 rsr command 154 189 211 248 rtr command 338 run command 524 rv command 87 125 rvnp command 176 rvpp command 176 S sab command 127 469 save a data window to a graphics file 350 savelogs command 367 scaling region file 34 37 389 391 405 407 screen dump 350 search criteria 435 result window 437 search command 435 second dataset 26 select a plot layout 364 a printer 363 l 8 sequential data format 233 detection mode 86 serial command 526 set command 592 setdef command 8 594 SGI workstation 41 232 271 291 shear AU program 201 shell command 595 show command 585 signal region 35 36 405 406 signal to noise ratio 36 44 405 simultaneous detection mode 86 sinc squared window multiplication 119 window multiplication 121 sinc command 119 sine baseline correction 1D 54 72 baseline correction 2D 154 squared window multiplication 40 119 window multiplication 40 119 sine bell shift 37 123 sine command 135 single detection mode 23 26 69 86 sinm command 119 sino command 405 slice command 277 slope correction 382 smail command 454 sola command 409 solaguide 404 solvent peak 34 37 389 spline baseline correction 54 127 469 spooler command 529 square brackets 453 sref command 410 standard dev
220. d 252 259 Z zero data 138 zero filling 39 86 230 269 289 zero intensity 31 138 zero order baseline correction 72 154 phase correction 32 43 62 110 zert command 262 zert1 command 262 zert2 command 262 zf command 138 zp command 140 I 10
221. d Line History OUTPUT FILES lt tshome gt exp stan nmr lists mac Macros created by cmdhist Save as SEE ALSO hist edmac P 575 TOPSPIN Interface Processes docs NAME docs Open Manual list DESCRIPTION The command docs opens a list of available documents This list shows all Bruker manuals delivered on the TOPSPIN DVD Figure 13 5 Software And Application Manuals Please click on a manual title General User Manual A description of the TopSpin user interface anc Control amp Function Keys amp list of predefined Control and Function keys Release Letter Describes the changes and new features of th Beginners Guides For Avance Spectrometers Vvith SGU Based Fr English basic description of the Bruker NMR spectror French German Eine grundlegende Beschreibung des Bruker N ttalian AVANCE Manuale per Principianti Spanish Acquisition User Guides 1D and 2D Step by Step Basic amp step by step tutorial of setting up and runnin 1D and 2D Step by Step Advanced A step by step tutorial of setting up and runnin Basic 1D and 2D Experiments A theoretical and practical description of setting 3D Triple Resonance experiments How to set up and run common 3D riple reson Figure 13 5 The manuals are divided in the topics TopSpin Beginners Guides etc Just click the manual name to open it Furthermore the Manual dialog of fer the following buttons e Close this dialog when a manu
222. d as processing edp and as processing status pa rameters dpp INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary proc processing parameters procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS APKO APK1 APKOF SEE ALSO apk apks apkf apkm pk mc ps ph P 64 1D Processing commands apk apks apkm apkf ph NAME apk Automatic phase correction 1D apks Automatic phase correction with a different algorithm 1D apkm Automatic phase correction with a different algorithm 2 1D apkf Customized automatic phase correction 1D ph Open phase correction dialog box 1D 2D DESCRIPTION Phase correction commands can be can be entered on the command line or started from the phase correction dialog box see Figure 3 4 This di alog is opened with the command ph It offers several options each of which selects a certain command for execution Automatic phasing This option selects the command apk for execution It calculates the zero and first order phase values and then corrects the spectrum ac cording to these values The phase values are stored in the parame ters PHCO and PHC1 respectively Note that
223. d data set names can be shown in the display by command md Enter command and full pathname for a specified dataset in the Top Spin command line md lt PathToDataset1 gt lt expnol gt pdata lt procno gt lt PathToDataset2 gt lt expno2 gt pdata lt procno gt The command md no_load ignores the datasets stored in the last multiple display session and enters the multiple display The command md write writes only the assoc file containing the data set list for multiple display Please note that the multiple display module is not started with this command Enter command and full pathname of specified dataset in the TopSpin command line md write lt PathToDataset1l gt lt expnol gt pdata lt procno gt lt PathToDataset2 gt lt expno2 gt pdata lt procno gt Multiple display mode is supported for 1D and 2D spectra For spectra with a dimension gt 2 the selected slice subplane is shown P 355 Print Export commands parplot NAME parplot select parameters to appear on the plot 1D 2D DESCRIPTION The command parplot opens a dialog where you can select the acqui sition and processing parameters that must appear on the plot see Fig ure 7 4 Plot Parameters Show Hide Parameters PPARMOD OFFSET SR HZpPT SW p XDIM PH_mod PKNL PHCO PHC1 BC_mod BCFA FT_mod FCOR ME_mod COROFFS NCOEF v Par
224. dataset in procno 1 Take the plane axis orientation from the current 2D dataset wpl 31 11 2 write the current 2D data to F1 F3 plane number 11 of the 3D data in procno 2 exchanging the F1 and F3 axes Note that if the source 2D dataset does not contain a used_ from file for example because it is not an extracted plane wp1 will prompt the user for the plane axis orientation Entering wpl on the destination 3D dataset In this case wp1 prompts the user for three arguments Alternatively these can be entered on the command line nD processing commands Examples wpl 23 10 999 Write the 2D data in procno 999 to F2 F3 plane 10 of the current 3D data wpl 12 32 101 Write the 2D data in procno 101 to the F1 F2 plane 32 of the cur rent 3D data wpl 12 Prompt the user for the procno of the source 2D dataset and the plane number Write the 2D dataset to the specified F1 F2 plane accordingly Entering wpl on a 4D dataset On a data with dimension gt 3 wp1 works the same as on a 3D dataset except that there are more plane axis orientations For example on 4D dataset possible orientations are 12 13 14 23 24 34 21 31 32 41 42 and 43 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data used_from data path of the source 3D data and the plane number OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno g
225. delete selected jobs e Open the job properties dialog from here also available by double click on the job entry for the selected job type P 529 Tools Allows you show the spooler log file and spooler report es Spooler Spooler Queue Job Tools Data object c bio data Jos van Boxtel c bio data Jos van Boxtel Figure 11 12 Acquisition information Fid Flash Spooler Time queued 0 08 19 no acquisition running delayed 0 cron 2 sep 11 Figure 11 13 Spooler Report To show the spooler report Click Tools Show spooler report To delete entries from the spooler report 1 Mark the entries to be deleted 2 Right click in the dialog and choose Delete To open datasets from the spooler report Double click the respective entry or Right click the respective entry and choose Display ee Spooler report Timestamp Command Data object July 13 2007 7 37 36 4M BST July 9 2007 2 13 09 PM BST July 13 2007 7 37 44 AM BST July 13 2007 7 37 52 AM BST July 13 2007 7 37 56 AM BST c bio data quest nmriexam d_13CH ipdata Cobio Wdatalquestinmriexam2d_HCi pdata cbio data quest nmrexam d_13CH Ipdatal c bio data quest nmriexam d_13CH pdata chio data quest nmr exam d_13CH fpdata Figure 11 14 Note that the spooler report can also be opened from Spooler field if en abled in the Acquisition Status Bar by right clicking the word Spooler and choosing Show spooler report INPUT OUTP
226. dialog offers various functions like edit create search delete import and export In TOPSPIN 2 1 and newer these programs are stored in a database The dialog for the command edpu1 is shown in Figure 10 11 The dialogs for edepd edpy and edmac have the same menu but can offer different buttons Search List Box Database items can be searched in two possible ways as can be chosen from the list box at the upper left of the dialog e Search in names to search for a string in the item names Search in text to search for a string in item text contents Search Text Field Here you can enter one or more characters of the item name or con tents The following wildcards can be used for zero or more occurrences of any character for a single occurrence of any character Here are some examples e xxx finds all occurrences of xxx P 478 Parameters lists AU programs amp Pulse Programs File Options Help Source EAEE v Search in names vi search Class Any vi Dim Any v cosydfgpphi9 2007 05 08 09 00 59 cosydfph 2007 05 08 09 00 59 cosydfphpr 2007 05 08 09 00 59 icosyetgp 2007 05 08 09 00 59 2007 05 08 09 00 59 2007 05 08 09 01 00 2007 05 08 09 01 00 007 05 08 09 01 00 v Graphical Edit Set PULPROG Figure 10 11 e xXX finds all occurrences of xxx preceded by two arbitrary characters A search mask for item names can also be
227. dir gt data lt user gt nmr lt name gt lt expno gt acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters If Experiment Use current params lt tshome gt exp stan nmr par lt experiment gt acqu acquisition parameters proc processing parameters OUTPUT FILES lt tshome gt prog curdir lt user gt curdat current dataset definition If the dataset specified with new does not exist yet the current dataset is P 441 Dataset handling P 442 copied lt dir gt data lt user gt nmr lt name gt lt expno gt acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters For 2D and 3D data the files acqu2 acqu2s etc are also output SEE ALSO open find re rep rew repw reb dir Dataset handling open NAME open Open a dataset pulse program AU program etc nD DESCRIPTION Opening data parameters lists and various other files can be started from the command line or from the open dialog box The latter is opened with the command open Ctr1 o see Figure 9 10 Options Open NMR data stored in standard Bruker format O Open NMR data stored in special formats
228. dow Without argument tozip will open it s dialog showing the default destina tion file lt dataname gt topspin zip You can change this default as fol lows 1 Enter expl prop in TopSpin command line to open the file explorer in the user properties directory 2 Edit the file globals prop 3 Add the line TOZIP_CONFIG option1 option2 where the options must be separated by the character and optioni N NE or NEP for name name expno or name expno proc no respectively option2 any string e g mycompany zip Example Dataset exam1d_13C 102 1 c bruker topspin guest option2 bruker zip If option1 N the default name is exam1d_13C bruker zip If option1 NE the default name is exam1d_13C 102 bruker zip If option1 was NEP the default name is exam1d_13C 102 1 bruker zip Options for the command tozip e Arguments for the command tozip P 558 Conversion commands In TOPSPIN 2 1 and newer the command tozip takes four arguments tozip optionA optionB optionC optionD optionA nmr data which should be transferred to zipfile optionB name and directory of archive data optionC FID_RE_IM FID_RE FID RE_IM RE PARAMS optionD COMPRESS NO_COMPRESS e Zipfile from command line The command tozip can be executed on the command line with the option d and only the pathname of the new zipfile tozip d lt path gt lt filename gt zip This command transfers the raw and processe
229. ds mana NAME mana Switch to multiplet analysis mode 1D DESCRIPTION The command mana switches to multiple analysis mode see Figure 8 8 examid_ ethanol 1 1 Crbio guest HH da alll os A SHIFT 3 6858 ppm amp 00 03 L2 M 4 J 6 908 Im N N N Li M 2 J 4 8632 Hz Nie 5 Me 2 Figure 8 8 It can be started as follows Click Analysis Structure Analysis Multiplet Definition P 384 Analysis commands or from the command line or opened from the Multiplet Analysis Guide command managuide A full description of the Multiplet Analysis package can be found under Help Manuals Analysis and Simulation Structure Analysis Tools SEE ALSO managuide P 385 Analysis commands managuide NAME managuide Open the Multiplet Analysis Guide 1D DESCRIPTION The command managuide opens the Multiplet Analysis Guide which guides you through the multiplet analysis procedure see Figure 8 9 Multiplet Analysis Tutorial 1 MM Peak Picking Connect Enter Analysis et Define Muttiplets i Pail Multilevel Muttiplets fla Define Identifiers Save and Close Figure 8 9 A full description of the Multiplet Analysis package can be found under Help Manuals Analysis and Simulation Structure Analysis Tools SEE ALSO mana P 386 Analysis commands pps ppf ppl pph ppj pp NAME pps Perform peak picking on displayed region p
230. e any command that changes one or more processing status parameters makes an addi tional entry View audit trail of the acquisition data This option selects the command audit acqu for execution It shows P 598 TOPSPIN User Management the acquisition audit trail file audita txt This file is created by the acquisition command that creates the raw data e g zg Any acquisi tion command that modifies updates the raw data e g go makes an additional entry Furthermore any command that changes one or more acquisition status parameters makes an additional entry Verify audit trails This option selects the command audit check for execution It per forms an audit trail check i e a data consistency check If both raw and processed data are consistent you will get the following mes sage amp auditcheck audit file for acquisition OK processing OK raw data checksum OK proc data checksum OK Figure 14 2 If the data have been manipulated e g with third party software or by changing certain status parameters e g SI the checksum will be incon sistent Figure 14 3 shows the message for inconsistent processed data P 599 TOPSPIN User Management amp auditcheck audit file for acquisition OK processing OK raw data checksum OK proc data Invalid data checksum Figure 14 3 Add a comment to audit trail This option selects the command audit com for execution It allows you to add
231. e if you have permission problems or if you want to process or interpret your data with third party software 3D processing commands dosy3d NAME dosy3d Process DOSY dataset 3D DESCRIPTION The command dosy3d processes a 3D DOSY dataset DOSY is a special representation of diffusion measurements Instead of generating just numbers using the T1 T2 fitting package i e diffusion co efficients and error values the DOSY processing gives pseudo 3D data where the F2 or F1 axis displays diffusion constants rather than NMR fre quencies For more information on dosy3d click Help Manuals Acquisition Application Manuals Dosy INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt difflist list of gradient amplitudes in Gauss cm lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr 3D data which are processed in F3 and F2 or in F3 and F1 dosy DOSY processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr 3D processed data auditp txt processing audit trail SEE ALSO eddosy dosy2d P 266 3D processing commands ft3d NAME ft3d Process data including FT in the F3 F2 and F1 direction 3D DESCRIPTION The command t3d processes a 3D dataset in all three directions F3 F2 and F1 It is equivalent to the command sequence t 3 tf 2 tf 1 or tf3 tf1 tf 2 see below t3d per
232. e 3D data to process a 13 or 12 plane do a phase correction on the resulting the 2D dataset and store the phase values to 3D More details on PH_mod can be found in chapter 2 4 The F1 processing parameter SI determines the size of the processed data in the F1 direction This must however be set before t 3 is done and cannot be changed after t 3 See t 3 for the role of TD TDeff and TDoff tf1 can doa strip transform according to the F1 parameters STSR and STSI see t 3 tf1 evaluates the F1 parameter FCOR The first point of the FIDs is mul P 302 1 If FaMODE undefined t 3 sets processing status MC2 to processing MC2 3D processing commands tiplied with the value of FCOR which is a value between 0 0 and 2 0 As such FCOR allows you to control the DC offset of the spectrum tf1 evaluates the F1 parameter REVERSE If REVERSE TRUE the spectrum will be reversed in F1 i e the first data point becomes the last and the last data point becomes the first tf1 evaluates the F1 status parameter MC2 For MC2 QF tf1 uses the file 3rrr as input and the files 3rrr and 3rri as output For MC2 QF tf1 uses the files 3rrr and 3iii as input and output The role of MC2 is described in detail for the 2D processing command x b INPUT PARAMETERS F1 parameters set by the user with edp or by typing be_mod bcfw etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction
233. e created For 3D data the additional parameter files acqu2 acqu2s proc2 and proc2s and acqu3 acqu3s proc3 and proc3s will be created SEE ALSO winconv convdta vconv jconv fconv P 535 Conversion commands convadta NAME convdta Convert Avance type raw data to AMX type 1D 2D 3D DESCRIPTION The command convdta converts Avance type raw data to AMX type raw data It can handle 1D 2D and 3D data This is useful if you want to proc ess data that have been acquired on an Avance spectrometer on an AMX or ARX spectrometer convdta takes up to six arguments and can be used as follows 1 convdta You will be prompted for an expno under which the raw data must be stored 2 convdta lt expno gt The raw data will be stored under the specified expno 3 convdta lt expno gt lt name gt y The output will be stored under the specified name and expno The last argument y causes convdta to overwrite existing data with out a warning 4 convdta lt expno gt lt name gt lt user gt lt dir gt yn The output will be stored under the specified expno name user and dir The second last argument y causes convdta to overwrite existing data without a warning The last argument n causes the display to remain on the current dataset rather than change to the output dataset You can use any other combination of arguments as long they are en tered in the correct order The processed data number procno of the new
234. e phase sensitive spectrum This option selects the command syma for execution It works like sym except that it compares each data point with the corresponding data point on the other side of the diagonal and determines which one has the lowest absolute intensity Then both data points are set to that intensity while each point keeps its original sign Table 4 2 shows the intensities of four pairs of data points before and after syma before syma after syma 370000 12000 12000 12000 1000 700 700 700 18000 6000 6000 6000 13000 8000 8000 8000 Table 4 2 syma is typically used on phase sensitive cosy spectra Symmetrize J resolved spectrum This option selects the command sym j for execution It symmetrizes P 196 2D processing commands a 2D spectrum about a horizontal line through the middle It is similar to sym i e it compares each data point with the corresponding data point on the other side of the horizontal line and determines which one has the lowest most negative intensity Then both data points are set to that intensity Table 4 3 shows the intensities of 5 pairs of data points before and after symj before symj after symj 370000 370000 370000 12000 1000 700 700 700 18000 6000 6000 6000 13000 8000 13000 13000 8000 25000 25000 25000 Table 4 3 symj is typically used on J resolved spectra wh
235. e regions specified in the reg file If it does not exist global is used pireg as ireg but the peak must also lie within the plot region sreg The highest peak in the regions specified in scal ing region file This file is specified by the parame ter SREGLST If SREGLST is not set or it specifies a file which does not exist global is used psreg as sreg but the peak must also lie within the plot region noise The intensity height of the noise of the spectrum Table 8 2 a reg file click fF to switch to integration mode click and select Save regions to reg The reg file can be viewed or edited with the command edmisc reg For PSCAL sreg or psreg the scaling region file is interpreted This is used to make sure the solvent peak is not used as reference The name of a scaling region file is typically of the form NUCLEUS SOL VENT e g 1H CDCI3 For most common nucleus solvent combina tions a scaling region file is delivered with TOPSPIN They can be viewed or edited with edlist scl In several 1D standard parameter sets which are used during automation PSCAL is set to sreg and SREGLIST to NUCLEUS SOLVENT as defined by the parameters NUCLEUS and SOLVENT pps evaluates the parameter PSIGN which can take three possible value P 389 Analysis commands pos only positive peaks appear in the list neg only negative peaks appear in the list both both positive and n
236. ecify three arguments the axis orientation is taken from the first argument rather than from the 3D dataset Examples wtr P 344 nD processing commands prompt the user for the trace number and destination 3D procno take the axis orientation from the current 1D dataset and write the trace accordingly wtr 11 1 write the current 1D data to trace 11 of the 3D dataset in procno 1 Take the axis orientation from the current 1D dataset wtr 3 11 2 write the current 1D data to F3 trace number 11 of the 3D data in procno 2 Note that if the source 1D dataset does not contain a used_ from file for example because it is not an extracted trace wtr will prompt the user for the axis orientation Entering wtr on the destination 3D dataset In this case wtr prompts the user for three arguments Alternatively these can be entered on the command line Examples wtr 2 10 999 Write the 1D data in procno 999 to F2 trace 10 of the current 3D data wtr 1 32 101 Write the 1D data in procno 101 to the F1 trace 32 of the current 3D data wtr 1 Prompt the user for the trace number and the procno of the source 1D dataset Write the 1D dataset to the specified F1 trace accord ingly Entering wtr on a 4D dataset On a data with dimension gt 3 wtr works the same as on a 3D dataset except that there are more axis orientations For example on 4D data set possible orientations are 7 2 3 and 4 P 345 nD processing
237. ectory lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt From the browser you can e select the data name to be displayed in the current data window move up in the data directory tree to select a different user and or dir e double click a data name to move down the directory tree and select a desired expnolprocno Once you have selected the desired name expno or procno click Display P 449 Dataset handling or hit Enter to display the dataset in the current data window In Topspin 2 0 and newer reb allows opening datasets stored in the fol lowing directories structures lt mydata gt lt dataname gt lt expno gt pdata lt procno gt Note that this will create a copy the dataset in the standard Topspin da tapath lt tshome gt data lt user gt nmr lt dataname gt lt expno gt pdata lt procno gt where lt user gt is the current internal Topspin user This copy can be proc essed delete or overwritten even if the original dataset is write protect ed The original data set is left unchanged SEE ALSO open re rep rew repw new find P 450 Dataset handling rel repl NAME rel Open a list of expnos procnos in current dataset repl Open a list of procnos in the current expno DESCRIPTION The command re1 lists the available expnos procnos under the current dataset and allows you to select and open one see Figure 9 14 EJ exam1d_13C This data set con
238. ectory To view the peak list click the Peaks tab of the data window toolbar The peak picking dialog window has two extra buttons Reset all to allows you to reset all parameters to the stored parameters or to the P 396 1 Only active when peak picking was already done Analysis commands most recent values stored in the peak list Note that the stored param eters and the parameters in the peak list can be different since param eters can also be set with edp or from the command line However right after peak picking they are the same Start manual picker To switch to interactive peak picking mode equivalent to clicking the button in the TOPSPIN upper toolbar The options specified in square brackets in the dialog window and further options can also be specified on the command line For example Pp append open peak picking dialog with the Append option checked pp noduplicates open peak picking dialog with the Discard new peaks option checked pp silent perform peak picking on the displayed region with the last stored op tions no dialog Equivalent to the command pps pp nodia perform peak picking on the last stored region with the last stored op tions no dialog pp append noduplicates nodia perform peak picking on the last stored region with the specified op tions The pp command can be used on 1D 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appr
239. ed 2D dataset 4 xf1 Perform 2D processing in the F1 direction Processing the four directions in separate steps Normally ftnd with the argument 0 or one of the arguments 4321 4312 etc to process all directions In some cases you may want to process the different directions in individual steps and perform the sequence ftnd 4 ftnd 3 etc The first direction to be processed must be F4 the other three directions can be processed in any order Note that every order in which the data are processed in F3 F2 an and F1 gives the same result unless linear prediction is done ME_mod and NCOEF z 0 Delayed linear prediction Linear prediction is a valuable method for improving the resolution of nD data with small TD values and often truncated FIDs The effect of linear prediction in one direction can however be distorted by modulations in troduced by other untransformed directions The dlp argument allows you to perform linear prediction in a certain direction while all other direc tions have already been Fourier transformed Let s take an example to nD processing commands see how this works Suppose you have a 4D dataset with acquisition or der 4321 parameter AQSEQ which you want to processed in all 4 di rections including Window Multiplication WM and Fourier transform FT Furthermore you want to increase the resolution with linear predic tion LP in the third F2 and fourth F1 direction As such you have
240. ed between F2 SIGF2 and F2 SIGF1 For intermediate rows the low field limit is an interpola tion of F2 ABSF2 and F2 SIGF2 and the high field limit is an interpolation of F2 ABSF1 and F2 SIGF1 zert2 works exactly like abst2 except that the data points are ze roed instead of baseline corrected Zero trapezoidal region in F1 This option selects the command zert1i for execution The trapezoi dal region to be zeroed is defined as follows e only the columns between F2 ABSF2 and F2 ABSF1 are zeroed e the part region of each column which is zeroed shifts from col umn to column The first column is zeroed between F1 ABSF2 and F1 ABSF1 The last column is zeroed between F1 SIGF2 and F1 SIGF1 For intermediate columns the low field limit is an interpolation of F1 ABSF2 and F1 SIGF2 and the high field limit is an interpolation of F1 ABSF1 and F1 SIGF1 zert1 works exactly like abst1 except that the data points are ze roed instead of baseline corrected INPUT PARAMETERS set from the zert dialog box with edp or by typing absf1 absf2 etc ABSF1 low field limit of the zero region in the first row ABSF2 high field limit of the zero region in the first row SIGF1 low field limit of the zero region in the last row SIGF2 high field limit of the zero region in the last row INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc2 F1 processing parameters
241. ed for processing TDoff first point of the FID used for processing default 0 XDIM subcube size FT_mod Fourier transform mode P 320 nD processing commands FTSIZE Fourier transform size F4 parameters can be viewed with dpp or by typing s si s tdeff etc AQORDER Acquisition order YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data F3 F2 and F1 parameters can be viewed with dpp or by typing s mc2 etc MC2 Fourier transform mode INPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data acqus F4 acquisition status parameters acqu2s F3 acquisition status parameters acqu3s F2 acquisition status parameters acqu4s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc F4 processing parameters proc2 F3 processing parameters proc3 F2 processing parameters proc4 F1 processing parameters For 3D data proc4s does not exist For data of dimension n where n gt 5 the additional files proc5 etc exist OUTPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 321 nD processing commands 4rrrr processed 4D data procs F4 processing status parame
242. ed from the parplot dialog by using the Open and OK buttons respectively and then count for all dataset Only parameters selected with parplot will appear on the plot This counts for both interactive plotting command plot and automated plot ting command autoplot P 357 Print Export commands INPUT AND OUTPUT FILES lt tshome gt exp stan nmr form acqu normp1 acquisition parameters that appear on the plot lt tshome gt exp stan nmr form proc normpl processing parameters that appear on the plot lt tshome gt exp stan nmr form lt name gt user defined selection of acquisition processing parameters INPUT AND OUTPUT FILES plot autoplot 1 On datasets created with TOPSPIN 1 3 or older first remove the files format temp in the dataset EXPNO and parm txt in the dataset PROCNO P 358 Print Export commands edti NAME edti Set the dataset title 1D 2D 3D DESCRIPTION The command edti allows you to define the dataset title Entering this command is equivalent to clicking the Title tab Changes in the title will automatically appear in the data window after clicking the Spectrum or Fid tab The title defined with edti will also appear on plots created with prnt or autoplot The command edti replaces the formerly used command setti which is still available INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt title plot title OUTPUT
243. eda or by typing chemstr CHEMSTR molecule structure filename INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt lt name gt molecule structure file acqu TOPSPIN acquisition parameters lt tshome gt classes prop StructureSamples molecule structure files SEE ALSO edstruc P 380 Analysis commands li lipp lippf int NAME li List integrals 1D lipp List integrals and peaks within F1P F2P 1D lippf List integrals and peaks of the full spectrum 1D int Open integral dialog box 1D 2D 3D DESCRIPTION Integral commands can be started from the command line or from the in tegration dialog box see Figure 8 7 The later is opened with the com Integration abs li Options Define integral regions manually O Integrate existing regions file intrng amp display result O List peaks and integrals using regions file intrng within the displayed region O List peaks and integrals using regions file intrng of the entire spectrum Required parameters Integration sensitivity factor ABSL 0 100 3 Minimum separation between independent integral regions AZFYY ppm 0 5 Integral region extension factor amp ZFE ppm 0 1 Integral sensitivity factor with reference to the largest integral ISEN 0 30 Degree of polynomial ABSG 0 5 5 219 160903930664 19 160918955445 Scale 1D integrals relative to a reference dataset INTSCL 1 0 0 1 Automat
244. eg file If the reg file does not exist global is used pireg as ireg but the peak must also lie within the plot region sreg The highest peak in the regions specified in scaling region file This file is specified by the parameter SREGLST If SREGLST is not set or specifies a file which does not exist g obal is used psreg as sreg but the peak must also lie within the plot region noise The intensity of the noise Table 2 7 For PSCAL ireg or pireg the req file is interpreted The req file can be created in interactive integration mode and can be viewed or edited with the command edmisc reg For PSCAL sreg or psreg the scaling region file is interpreted This feature is used to exclude the region in which the solvent peak is expected The name of a scaling region file is typically of the form NUCLEUS SOLVENT e g 1H CDCI3 For all common nucleus sol vent combinations a scaling region file is delivered with TOPSPIN These can be viewed or edited with the command edlist scl In several 1D standard parameter sets which are used during automa tion PSCAL is set to sreg and SREGLIST to NUCLEUS SOLVENT as defined by the parameters NUCLEUS and SOLVENT PSIGN peak sign for peak picking P 34 used in 1D datasets takes the value pos neg or both default is pos interpreted by pp lipp in most 1D standard parameter sets PSIGN is set to pos which means only positive peaks are picked TOPS
245. egative peaks appear in the list Auto Pick peaks on full spectrum This option selects the command ppf for execution It works like pps except that it picks peaks on the full spectrum Auto Pick peaks in predefined regions file peakrng This option selects the command pp1 for execution It pick the peaks in predefined regions To define those regions e click Define regions peaks manually in the peaks dialog box or click the j button in the toolbar to switch to peak picking mode e click the button and drag the cursor inside the data win dow to defined the regions e right click inside the data window and select Pick Peaks on ranges or enter pp1 on the command line Like 1st option but peak list with histogram This option selects the command pph for execution It works like pps except that it also shows an intensity histogram This allows you to get a quick overview over the intensity distribution Like 1st option but peak in JCAMP format This option selects the command ppj for execution It works like pps except that the peak list is stored in JCAMP DX format in the file pp dx This file resides in the processed data directory and can be used for external programs which require JCAMP peak lists As the file created by tojdx it contains the acquisition and processing pa P 390 Analysis commands rameters but instead of data points it contains a list of peaks The H NPOINTS 4 PEAK
246. el complex iqc inverse quadrature complex Table 2 3 GAMMA multiplication factor e used in 2D datasets in F2 e takes a float value e interpreted by add2d GAMMA is the multiplication factor for the second dataset see also parameter ALPHA GB Gaussian broadening factor for Gaussian window multiplication e used in 1D 2D and 3D datasets in all directions e takes a float value between 0 0 and 1 0 e interpreted by gm e interpreted by trf xfb xf2 xf1 xtrf tf if WOW EM or GM INTBC automatic baseline correction of integrals created by abs e used in 1D datasets e takes the value yes or no e interpreted by 1i lipp lippf P 26 TOPSPIN parameters e INTBC has no effect on integrals which were created interactively in the Integration mode INTSCL scale 1D integrals relative to a reference dataset e used in 1D datasets e takes an integer value e interpreted by 1i lipp lippf INTSCL is used as follows For INTSCL gt 0 the integral values are scaled individually for each spectrum For INTSCL 0 the integrals on the plot will obtain the same numeric values as defined interactively in the integration mode For INTSCL 1 scaling is performed relatively to the last spectrum plotted ISEN integral sensitivity factor with reference to the largest integral e used in 1D datasets e takes a positive float value default 128 e interpreted by abs absd absf e Only the regions of integ
247. en peaks for independent integration AZFE integral extension factor ISEN integral sensitivity factor with reference to the largest integral P 54 1 It uses the same algorithm as the command abs in DISNMR 1D Processing commands INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data procs processing status parameters intrng integral regions output of abs absf absd auditp txt processing audit trail USAGE IN AU PROGRAMS ABS ABSD ABSF SEE ALSO bem sab bc basl P 55 1D Processing commands P 56 add duadd addfid addc adsu NAME add Add two datasets point wise multiply 2nd with DC 1D duadd Add two datasets ppm Hz wise mult 2nd with DC 1D addfid Add two FIDs multiply 2nd with DC 1D addc Add the constant DC to the current dataset adsu Open add subtract multiply dialog box 1D 2D DESCRIPTION Addition commands can be entered on the command line or started from the add subtract multiply dialog box The latter is opened with the com mand adsu This dialog box offers several options each of which selects a certain command for execution Add a 1D spectrum point wise This option selects the command add for execution It adds the sec ond dataset
248. en the parameter set was created see wpar Usually however user defined parameter sets are also stored with all parameter types Bruker parameter sets are delivered with TOPSPIN and installed with the command expinstall User defined parameter sets are created with wpar which stores the pa rameters of the current dataset under a new or existing parameter set name rpar allows you to read parameters sets of various dimensionalities 1D 2D etc If the dimensionality of the current dataset and the parameter set you want to read are the same e g both 1D the current parameter files are overwritten If the current dataset contains data raw and or proc essed data these are kept Furthermore the status parameters are kept so you still have a consistent dataset However as soon as you process the data the new processing parameters are used the processed data files are overwritten and the processing status parameters are updated When you start an acquisition the new acquisition parameters are used the raw data are overwritten and the acquisition status parameters are updated Parameters lists AU programs If the dimensionality of the current dataset and the parameter set you want to read are different the current parameter files are overwritten all data files are deleted and status parameters are kept If the dimension ality is reduced the superfluous parameter files are deleted INPUT FILES lt tshome gt exp stan nmr p
249. en truncated FIDs The effect of linear 1 If imaginary data do not exist they are automatically created with Hilbert transform P 323 nD processing commands prediction in one direction can however be distorted by modulations in troduced by other untransformed directions Therefore it is a good idea to first process the data in all directions and then perform Ipnd This en tire procedure including the correct window handling is automatically performed by the command ftnd d1p delayed linear prediction How ever if you want both backward and forward prediction the latter must be done with Ipnd In this case you have to perform the following steps 1 Backward prediction with ftnd while ME_mod LPbr or LPbc and WDW no 2 Forward prediction with 1pnd while ME_mod LPfr or LPfc and WDW set to the desired window function For more information see the description of ftnd INPUT AND OUTPUT PARAMETERS see ftnd INPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr processed 4D data proc F4 processing parameters proc2 F3 processing parameters proc3 F2 processing parameters proc4 F1 processing parameters For 3D data the input data file is 3rrr whereas the proc4 does not ex ist For data of dimension n where n gt 5 input data files are named nr and ni e g 5r 5i 6r 6i etc OUTPUT FILES For 4D data lt dir gt data lt user gt nmr lt n
250. ens a browser where you can navigate to the WIN NmR input da tasets A WIN NMR dataset is a directory with several files Each file has anumber as filename e the extension FID 1R 1I AQS or FQS for raw data proc essed real data processed imaginary data acquisition parame ters and processing parameters respectively Just select any of these files and click convert This will open the dialog box shown in Figure 12 8 EY wincony C bio1 winnmr 011002 1R The selected WWINNMR data will be converted Define destination dataset NAME Ethanol EXPNO 11 PROCNO 2 DIR C Bio USER guest Figure 12 8 Here you can specify the TOPSPIN destination dataset The datapath fields are initialized as follows NAME the WIN NwR data directory EXPNO the first three digits of the WIN NMR data name PROCNO the second three digits of the WIN NMR data name Conversion commands DIR DIR of the active TOPSPIN dataset USER USER of the active TOPSPIN dataset Specify a the datapath or accept the initial values and click OK to start the conversion To display the dataset just open it from the TOPSPIN browser or use the command re INPUT FILES lt name gt num FID WIN NMR raw data num 1R WIN NMR real processed data num 1I WIN NMR imaginary processed data num 1I WIN NMR imaginary processed data num AQS WIN NMR acquisition parameters num FQS WIN NMR processing par
251. ent to n m The command to be executed can be specified before or after the exp no s Examples of argument strings The argument efp 1 3 4 6 8 11 will preselect the command efp and the expnos 1 3 4 5 6 8 and 11 The argument 1 8 10 15 20 will preselect the expnos 1 2 3 4 5 6 7 8 10 15 16 17 18 19 and 20 and leave the command field empty Specified expnos which do not exist are ignored The preselected com mand and expnos can be modified extended in the dialog To select or deselect all expnos in the opened dialog P 522 Automation Right click in the dialog and choose Select all or Deselect all respec tively If qumulti is entered without argument only the current expno is prese lected On clicking OK a priority job is created for each selected expno starting with the lowest expno and sent to the queue Queued commands can be viewed in the command spooler which can be started with the command spooler and is available in the spectrom eter status bar Note that if you try to exit TOPSPIN while a priority job is still active you will be warned about this and requested to confirm exiting SEE ALSO cron qu at atmulti spooler P 523 Automation run NAME run Open dialog for starting macro AU Python or serial DESCRIPTION The command run opens the run dialog window Open Command PromptGhell Serial Processing Execute AU Program Execute Python Progra
252. enter hist and look for the entry User properties directory P 569 TOPSPIN Interface Processes P 570 where lt name gt is the name of the button panel 3 Enter the button definitions including Panel title Colors Toggle buttons Top buttons Panel layout Panel buttons and Tooltips 4 Save the file Make sure the extension of the file is prop and not txt prop txt or anything else 5 Enter bpan lt name gt on the command line to open the button panel Here is the contents of the properties file for the button panel above Color definitions used in this file RGB BLUE1 51 204 255 YELLOW1 255 255 0 GREEN1 84S 196 20 T Title definition TITLE 1D Processing Panel ELE E_COLOR 0 0 255 Toggle button definition TOGGLE BUTTON To 2D TOGGLE CMD bpan bproc2d TOGGLE TIP Switch to 2D processing Top row button definition TOP BUTTONS EM SFTS SPKS TOP COLORS YELLOW1 YELLOW1S S YELLOW1 TOP _CMDS em ft pk TOP _TIPS Exponential multiplication Fourier transform Phase correction T Panel button definitions LAYOUT format rows columns hgap vgap PAN LAYOUT 1 3 8 8 PAN BUTTONS Print EXPORTS SSEND TOS PAN COLORS BLUE1 BLUE1 BLUE1 PAN CMDS prnt exportfile smail PAN TIPS Print the spectrum lt br gt as it appears on the screen Export the dataset lt br gt to png jpg bmp etc
253. er for some datasets no value of AQ_mod translates to a correct Fourier transform mode An exam ple of this is when you read a column with rsc from a 2D dataset which was measured with FnMODE or MC2 States TPPI and Fourier transformed in the F2 direction only The resulting FID can only be Fourier transformed correctly with trf The parameter FT_mod is automatically set to the correct value by the rse com mand trf can also be used manipulate the acquisition mode of raw data by Fourier transforming the data with one FT_mod and inverse Fourier transforming them with a different FT_mod From the resulting data you could create pseudo raw data using gen fid with a different acquisition mode than the original raw data Finally tr allows you to process the data without Fourier trans form FT_mod no Table 3 3 shows a list of FT_mod values FT_mod Fourier transform mode no no Fourier transform fsr forward single channel real fqr forward quadrature real fsc forward single channel com plex fqc forward quadrature complex isr inverse single channel real iqr inverse quadrature real isc inverse single channel complex iqc inverse quadrature complex Table 3 3 The command trfp works like trf except that it always works on proc essed data If no processed data exist trfp stops with an error mes sage trfp can be used to perform multiple
254. ered on this 1D dataset This takes two arguments and can be used as follows rsc opens the above dialog box rsc lt column gt reads the specified column from the 2D dataset from which the current 1D dataset was extracted rsc lt column gt lt procno gt reads the specified column from the 2D dataset that resides under the current data name 1 the current expno and the specified procno Spec ifying the procno allows you to read a column from a 2D dataset other than the one from which the current 1D dataset was extracted Fur thermore the AU macro RSC requires two arguments no matter if it is used on a 1D or on a 2D dataset rsr can also be started from the dialog box that is opened with the com mand slice A special case is a 2D dataset that has been Fourier transformed in F2 but not in F1 rse then stores 1D processed data that are in the time do main rather than the frequency domain Below are five different exam ples of this case Example 1 1 However if the current data name is TEMP rsc lt column gt lt procno gt reads from the specified PrOcno in the dataset from which the current 1D dataset was extracted P 181 2D processing commands P 182 A 2D dataset is Fourier transformed in F2 column 17 time domain is extracted and stored under the same name and expno in procno 2 The resulting 1D dataset is Fourier transformed On the 2D dataset enter the following commands xf2 to Fourier tran
255. es e g LB PHCO ABSF1 P 17 TOPSPIN parameters parameters using a predefined list of values e g BC_mod WDW PSCAL You can easily see to which group a parameter belongs from the parameter editor opened by entering edp or clicking Procpars Note that the values of parameters which use a predefined list are actually stored as integers The first value of the list is always stored as 0 the second value as 1 etc Table 2 1 shows the values of the parameter PH_mod as an example Parameter Integer stored in the proc s value file no 0 pk 1 mc 2 ps 3 Table 2 1 2 3 Parameter files TOPSPIN parameters are stored in various files in the dataset directory tree In a 1D dataset lt dir gt data lt user gt nmr lt name gt lt expno gt acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters In a 2D dataset lt dir gt data lt user gt nmr lt name gt lt expno gt acqu F2 acquisition parameters acqu2 F1 acquisition parameters acqus F2 acquisition status parameters acqu2s F1 acquisition status parameters P 18 TOPSPIN parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc F2 processing parameters proc2 F1 processing parameters procs F2 proce
256. es of xht2 xf2p or xht1 xf1 commands On 3D data the commands pknd 3 pknd 2 and pknd 1 are equivalent to t 3p tf2p and tf1p respectively INPUT PARAMETERS set by the user with edp or by typing phcO phc1 etc PHCO zero order phase correction value frequency independent P 326 nD processing commands PHC 1 first order phase correction value frequency dependent OUTPUT PARAMETERS can be viewed with dpp or by typing s phcO s phc1 etc PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value frequency dependent INPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr processed 4D data proc F4 processing parameters proc2 F3 processing parameters proc3 F2 processing parameters proc4 F1 processing parameters For 3D data the input data file is 3rrr whereas the proc4 does not ex ist For data of dimension n where n 5 input data files are named nr and ni e g 5r 5i 6r 6i etc OUTPUT FILES For 4D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr processed 4D data procs F4 processing status parameters proc2s F3 processing status parameters proc3s F2 processing status parameters proc4s F1 processing status parameters For 3D data the output data file is 3r rr whereas proc4s does not exist For data of dimension n where n g
257. esponding orthogonal trace in the 2D spectrum Par tial means that only a specified range of rows or columns is are evalu ated i e only a part of the orthogonal trace is scanned for the highest intensity Negative projections contain only negative intensities positive projections contain only positive intensities A special case is the command fiprojp or flprojn on a hypercom plex 2D dataset MC2 QF that has been processed in F2 only Sup pose you would perform the following command sequence xf2 to process the data in F2 only s si to check the F1 size of the 2D data click Cancel s mc2 to check status MC2 QF click Cancel f1projp to store the F1 projection in TEMP and change to that da taset s si to check the size of the resulting 1D dataset click Cancel You will see that the size of the 1D data is only half the F1 size of the 2D data The reason is that 1projp unshuffles the input data file 2rr As such f lprojp behaves like the command rsc If you want to prevent the unshuffling of the input data file 2r1r you can use the following trick Set the status parameter MC2 to QF before you run flprojp s mc2 click QF Then the size of the 1D data will be the same as the F1 size of the 2D data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr processed data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata
258. essing commands A 2D dataset with an F1 acquisition mode States TPPI is Fourier transformed in F2 Column 17 time domain is extracted and stored under data name TEMP The resulting 1D dataset is Fourier trans formed On the 2D dataset enter the following commands s nmode check the FnMODE value States TPPI click Cancel xf 2 to Fourier transform in F2 only s mc2 check the MC2 value States TPPI click Cancel rsc 17 to read column 17 to TEMP and switch to that dataset f t_mod check the FT_mod value fsc click Cancel trfp to Fourier transform the resulting 1D data according to FT_mod Explanation the source 2D and the destination 1D have a separate a set of acquisition parameters Since there is no value for AQ_mod that corresponds to States TPPI rsc sets the processing parameter FT_mod instead of the acquisition status parameter AQ_mod As such the resulting 1D dataset can only be Fourier transformed cor rectly with tr p Example 4 A 2D dataset with an F1 acquisition mode QF is Fourier transformed in F2 Column 17 time domain is extracted and stored under data name TEMP From the 2D dataset enter the following commands s nmode check the FnMODE value QF click Cancel xf 2 to Fourier transform in F2 only s mc2 check the MC2 value QF click Cancel rsc 17 to read column 17 to TEMP and switch to that dataset s si check the size of the 1D dataset click Cancel Expl
259. eter set Write New Write the parameters of the current dataset to a new experiment name You will be prompted to enter this name Close Close the wpar dialog The parameters are written to the Source directory as selected at the up per right of the dialog wpar Can be used with arguments e wpar lt name gt opens a dialog box where you can select individual parameter files of the parameter set lt name gt Upon clicking OK this file is copied to the current dataset wpar lt name gt acqu reads the acquisition parameters file acqu of the parameter set lt name gt to the current dataset wpar lt name gt proc reads the processing parameters file proc of the parameter set lt name gt to the current dataset e wpar lt name gt acqu proc reads the acquisition and processing parameters files acqu and proc of the parameter set lt name gt to the current dataset wpar lt name gt all reads all parameter files of the parameter set lt name gt to the cur rent dataset The first argument may contain wildcards e g wpar C shows all parameter sets beginning with the letter C Bruker standard experiment names should not be used when storing your own experiments with wpar The reason is that they are overwritten P 494 Parameters lists AU programs when a new version of TOPSPIN is installed wpar is often used in the following way 1 Define a new dataset with the command new 2 Enter rpar to read a
260. eters For example the phase correction button offers var ious automatic algorithms as well as an option to switch to interactive phasing mode Experienced users normally enter the individual processing commands from the command line This requires that for each command the processing parameters are set correctly The Processing Guide can be used for 1D and 2D processing SEE ALSO aqguide tl guide managuide solaguide P 113 1D Processing commands NMR Data Processing Guide Close Automatic mode o Open Data Set Advanced ee Window Function ae Peak Picking Fourier Transform Se Integration Phase Correction Plot Print om gt amp s S Axis Calibration m E E mail Archive Baseline Corr Figure 3 14 P 114 1D Processing commands procid NAME proc1d Open 1D Processing dialog DESCRIPTION The command procid opens a 1D processing dialog see Figure 3 15 es procid Press OK to process plot the selected dataset using the enabled options The command proc1d y will process data without this dialog using the last settings Exponential Multiply em M LB Hz h Fourier Transform ft Auto Phasing apk Set Spectrum Reference sref Auto Baseline Correction abs Plot autoplot Figure 3 15 This dialog can be used for standard 1D processing including exponen tial multiplication Fourie
261. eters clevels 2D contour levels 3D parameter sets also contain the files acqu3 and proc3 for the third direction Note that in TOPSPIN 2 0 and older the user subdirectory does not exist and user defined parameter sets are stored in lt tshome gt exp stan nmr par the same location as Bruker parameter sets USAGE IN AU PROGRAMS WPAR name type SEE ALSO rpar expinstall P 496 Parameters lists AU programs xmac NAME xmac Execute macro DESCRIPTION The command xmac opens a dialog showing all available macros see Figure 10 16 Just select the desired macro and click the Execute button to execute it i amp Macros File Options Help Source C ABruker TOPSPIN exp stan nmrilistsimac Search in names v Search exam_efp ss exam_Ib_si_efp lexam_Ibefp _ exam_Ibefp2 Edit Execute Close Figure 10 16 Macros can also be executed from the command line by entering the macro name e g exam_efp or xmac exam_efp The difference is that using the xmac command searches for macros on ly whereas only entering just the name searches for a TOPSPIN com mand AU program Python program or macro of that name In TOPSPIN 2 0 and newer macros are stored in a database xmac opens the same dialog as the corresponding commands edmac For more de tails see the description of this command SEE ALSO edmac delmac xpy P 497 xpy NAME xpy Execute Python p
262. ets which contain 1D 2D or 3D imaginary data showing a separate entry for each processed data number procno Each entry shows the da taset NAME EXPNO PROCNO PROC DATA and SIZE Only the im aginary processed data files are deleted Raw data processed data and parameter files are kept To delete data mark one or more data sets and click the button Delete imaginary processed data of the selected PROCNOs When started from the command line del commands can take one ar gument which may contain wild cards Examples delf examid list all datasets whose name starts with exam d delf exam1ld list all datasets whose name is exam d plus three extra characters de1 commands only list and delete the datasets of current user The current user here refers to the user part of the data path of the currently P 425 Dataset handling P 426 selected dataset Please distinguish e the user part of the data path the owner of the dataset e the user who runs TOPSPIN Usually these three things are the same i e a user works on his own da ta However the user part of the data path can be any character string and does not have to correspond to a user account on the computer Fur thermore the user who runs TOPSPIN might work on someone else s data In this case he she may or may not have the permission to delete this dataset In the latter case the del commands will not delete the dataset but show an error message inste
263. ever FnMODE undefined the processing status parameter MC2 is set according to the processing parameter MC2 Furthermore status MC2 is interpreted during 2D processing in F1 on processed data for example by xf1 on data which have already been processed with xf2 NC_proc intensity scaling factor used in 1D 2D and 3D datasets in the first direction takes an integer value set by all processing commands only exists as processing status parameter Processing in TOPSPIN performs calculations in double precision float ing point but stores the result in 32 bit integer values During double to integer conversion the data are scaled up or down such that the highest intensity of the spectrum lies between 278 and 22 This means the 32 bit resolution is not entirely used This allows for the highest intensity to be increased for example during phase correc tion without causing data overflow NC_proc shows the amount of scaling that was done for example NC_proc 3 data were scaled up multiplied by 2 three times NC_proc 4 the data were scaled down divided by 2 four times TOPSPIN parameters Although NC_proc is normally calculated by processing commands 2D processing also allows you to predefine the scaling factor with the argument nc_proc for example xfb nc_proc 2 scales down the data twice However you can only scale the data more down or less up than the command would have done without the argument nc_proc
264. experiment number ex pno Note that genser does not modify the data but only stores them in a dif ferent format The number of data points of the pseudo raw data is twice the size SI of the processed data they are created from The acquisition status parameter TD type dpa is set accordingly TD 2 SI This count for both the F2 and F1 direction genser takes three arguments and can be used as follows genser opens a dialog box where you can specify the output data 2D processing commands genser lt expno gt stores the output under the specified expno and opens a new data window displaying this expno genser lt expno gt n stores the output under the specified expno but does not open and display this expno If the specified expno already exists you will be prompted to overwrite it or not You can force the overwrite by specifying the extra argument y on the command line genser lt expno gt yn stores the output under the specified expno overwriting it if it exists but does not open and display this expno The processed data number procno of the new dataset is always set to l genser can be useful if you want to reprocess a 2D spectrum for exam ple with different processing parameters but the raw data do not exist any more An example of such a procedure is xi f2 if the data are Fourier transformed in F2 xif1 if the data are Fourier transformed in F1 genser to create the pseudo raw da
265. expno n and m n m equivalent to n m The command to be executed can be specified before or after the exp no s Examples of argument strings The argument efp 1 3 4 6 8 11 P 504 Automation New schedule Schedule Command Time 10 38 AM Date April 10 2007 2 Experiment IDs Cancel Figure 11 2 will preselect the command efp and the expnos 1 3 4 5 6 8 and 11 The argument 1 8 10 15 20 will preselect the expnos 1 2 3 4 5 6 7 8 10 15 16 17 18 19 and 20 and leave the command field empty Specified expnos which do not exist are ignored The preselected com mand and expnos can be modified extended in the dialog P 505 Automation To select or deselect all expnos in the opened dialog Right click in the dialog and choose Select all or Deselect all respec tively On clicking OK a delay job is created for each selected expno starting with the lowest expno and sent to the queue Scheduled commands can be viewed in the command spooler which can be started with the command spooler and is available in the spec trometer status bar Note that if you try to exit TOPSPIN while a priority job is still active you will be warned about this and requested to confirm exiting SEE ALSO at qu qumulti cron spooler P 506 Automation compileall NAME compileall Compile all Bruker and User AU programs DESCRIPTION The command compileal1 co
266. f add and addc procs processing status parameters auditp txt processing audit trail output of add and addc USAGE IN AU PROGRAMS ADD ADDFID ADDC SEE ALSO mul mulc div add2d P 59 1D Processing commands accumulate NAME accumulate Accumulate 1D datasets ppm Hz wise 1D SYNTAX accumulate start offset scale Hz ppm procno expno name user dir DESCRIPTION The command accumulate accumulates 1D datasets It adds a speci fied processed dataset to the current dataset accumulate has the fol lowing features e the specified data can be shifted and scaled with respect to the current data e addition can be performed ppm wise or hz wise e the specified data can overwrite the current data or can be added to the current data All required information must be specified by command line arguments As such accumulate takes 4 to 9 arguments Here are some examples of its usage accumulate lt offset gt lt scale gt ppm hz lt procno gt Add the processed data of the specified procno to the current procno as follows e shift the added data by lt offset gt ppm e scale added data by the value lt scale gt perform the addition ppm wise or hz wise as specified Example accumulate 0 0 1 0 ppm 3 accumulate start lt offset gt lt scale gt ppm hz lt procno gt Same as above except that the processed data of the specified proc no are copied to the current procno overwriting possibly existing dat
267. ference manual INPUT FILES lt tshome gt exp stan nmr au src AU programs source files OUTPUT FILES lt tshome gt prog au bin AU programs executable files SEE ALSO expinstall compileall edau xau xaua xaup delau P 508 Automation cron NAME cron schedule a TOPSPIN command for execution DESCRIPTION The command cron performs command scheduling It allows you to ex ecuted commands periodically at predefined times It is more versatile then the commands at and atmul ti offering full flexibility in time defini tion off schedule execution and user control When entered without ar guments it opens the dialog shown in Figure 11 3 Here you can specify the command to be scheduled some scheduling options and the starting time and date The following fields are available Command The command to be executed Description A description of the command Execution Scope The scope of the command execution User or Topspin For scope User the scheduled command will only be executed if TOPSPIN is run by the same internal user that is active during cron definition If the scope is TOPSPIN the scheduled command will be executed for any internal user Scheduled commands with TOPSPIN execution scope can only be defined cancelled or modified after entering the NMR Administra tion password Off schedule execution This flag allows you to execute commands that were scheduled to run at the time when T
268. ff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm P 319 nD processing commands GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk set by the acquisition can be viewed with dpa or s aq_mod etc TD time domain number of raw data points F4 parameters set by the user with edp or by typing agorder pkn1 etc AQORDER Acquisition order PKNL group delay compensation Avance or filter correction A X set by the acquisition can be viewed with dpa or s aq_mod etc AQ_mod acquisition mode determines the status FT_mod AQSEQ acquisition sequence 3 2 1 or 3 1 2 BYTORDA byteorder or the raw data NC normalization constant F3 F2 and F1 parameters set by the acquisition can be viewed with dpa or by typing s fnmode etc FnMODE Fourier transform mode OUTPUT PARAMETERS F4 F3 F2 and F1 can be viewed with dpp or by typing s si s stsi etc SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points that were us
269. field limit of the correction region in the first row ABSF2 high field limit of the correction region in the first row SIGF1 low field limit of the correction region in the last row SIGF2 high field limit of the correction region in the last row INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc2 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc2s F1 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS ABS1 ABST1 ABSD1 ABSOT 1 SEE ALSO abs2 abst2 absd2 absot2 P 149 2D processing commands add2d mul2d addser adsu NAME add2d Add or subtract two datasets 2D mul2d Multiply two datasets 2D addser Add two raw datasets 2D 3D adsu Open add subtract multiply dialog box 1D 2D DESCRIPTION Addition commands can be started from the command line or from the add subtract dialog box The latter is opened with the command adsu PN Add subtract add2d Options Add a 2D spectrum ALPHA current GAMMA second O Add a 2D fid ser ALPHA current GAMMA second Subtract a 1D spectrum from each row retain sign O Subtract a 1D spectrum from each column retain sign Subtract a 1D spectrum from each row Subtract a 1D spectrum from each column Multiply
270. fined by tiltfactor ALPHA SI2 SI1 nsrow total number of rows row the row number where SI2 and SI1 are processing status parameter SI in F2 and F1 respectively Tilt along columns This option selects the command ptilt1 for execution It tilts the 2D spectrum about a user defined angle by shifting the data points in the F1 direction The tilt factor is determined by the F1 processing param eter ALPHA which can take a value between 2 and 2 Each column of the 2D matrix is shifted by n points where n is defined by 2D processing commands n tiltfactor nscol 2 col The variables in this equation are defined by tiltfactor ALPHA SI1 SI2 nscol total number of columns col the column number where SI2 and SI1 are processing status parameter SI in F2 and F1 respectively For F2 ALPHA 1 and F1 ALPHA 1 e the sequence ptilt ptilti1 rotates the spectrum by 90 e the sequence ptilt1 ptilt rotates the spectrum by 90 The command ptilti1 is used in the AU program shear which can be viewed with the command edau shear When executed from the command line the command tilt ptilt and ptilt1 select the corresponding option in the dialog box This means you can just click OK or hit Enter to start the command In contrast symt selects the last used tilt command INPUT PARAMETERS set from the symt dialog box with edp or by typing alpha ALPHA tilt factor used by ptilt and ptilt1 set by initial pr
271. for the plane axis orientation the plane number and source 3D procno and read the plane accordingly rpl 23 10 999 Read F2 F3 plane 10 and store it in procno 999 rpl 3210 999 Read F2 F3 plane 10 and store it in procno 999 exchanging the F2 and F3 axes rpl 12 64101 Read F1 F2 plane 64 and store it in procno 101 rpl 12 64 Read F1 F2 plane 64 prompt the user for the destination procno rpl 311 10n Read an F1 F3 plane number 1 and store it in procno 10 exchang ing the F1 and F3 axes Do not display activate the destination da taset rpl entered on a destination 2D dataset This is typically done on a 2D dataset which is a plane extracted by a previous rp1 command which was entered on the source 3D dataset In that case rp1 requires only one argument the plane number By de fault the same plane axis orientation and source 3D dataset procno are used as with the previous rp1 command as defined in the used_from file of the 2D dataset You can however use two or three arguments to specify a different plane axis orientation and or 3D source procno Ona regular 2D dataset not a plane from a 3D rp1 requires three argu ments P 335 nD processing commands P 336 Here are some examples of rp1 executed on a 2D dataset where the 2D dataset is a plane from a 3D dataset rpl Prompt the user for the plane number use the plane axis orientation and source 3D procno as defined in the current 2D dataset and read the
272. foreground abs2 water 2007 11 14 16 51 45 Performs an F2 baseline correction on a 2D dataset left and right of abs2D 2007 11 14 16 51 45 Performs a baseline correction on a 2D dataset in both dimensions accept_best 2007 11 14 16 51 45 Accept_1 08 02 2006 Intensity and Backmixing of series of BEST acqu_fid_ser 2007 11 14 16 51 45 This AU program acquires a single FID of the current 2D experiment all_fromjdx 2007 11 14 16 51 45 all_tojdx 2007 11 14 16 51 45 datasets the AU program will stop The AU program converts the first lamplstab 2007 11 14 16 51 45 This program calculates the amplitude stability based on a peaklist file langle 2007 11 14 16 51 45 Program to perform multiple acquisitions and ft s This program is apkO noe 2007 11 14 16 51 45 AU program does automated zero order phase correction for s l Edit Compile Execute J Close Figure 11 5 P 514 Automation Manage Source Directories Add modify AU programs source directories AU programs will be searched for in the order of the directories specified Detailed information about Manage Source Directories are described in Chapter 1 9 Export Sources Opens a dialog to export an entire AU program library to a user de fined directory Note the difference to the Export function under the File menu see below When you edit a Bruker AU program it is shown in view mode which means it cannot be modified Howe
273. forms a Fourier transform which transforms time domain data FID into frequency domain data spectrum Depending on the process ing parameters BC_mod WDW ME_mod and PH_mod it also performs baseline correction window multiplication linear prediction and spec trum phase correction t3d executes the following processing steps 1 Baseline correction The time domain data are baseline corrected according to BC_mod This parameter takes the value no single quad spol qpol sfil or qfil 2 Linear prediction Linear prediction is done according to ME_mod This parameter takes the value no LPfr LPfc LPbr LPbc LPmifr or LPmifc Usu ally ME_mod no which means no prediction is done Forward prediction LPfr LPfc LPmifr or LPmifc can for example be used to extend truncated FIDs Backward prediction LPbr or LPbc is usually only done in F3 e g improve the initial data points of the FID Linear prediction is only performed if NCOEF gt 0 Further more the parameters LPBIN and for backward prediction TDoff are evaluated 3 Window multiplication The time domain data are multiplied with a window function according to WDW This parameter takes the value em gm sine qsine trap user sinc qsinc traf Or trafs 4 Fourier transform The time domain data are Fourier transformed in F3 according to P 267 3D processing commands the acquisition status parameter AQ_mod see table 5 6
274. from the File Explorer This involves two steps 1 Copy In the File Explorer Go to a dataset e Right click a dataset folder or file e g the data name expno or procno folder or any file in it and click Copy 2 Paste In TOPSPIN e Click File Paste or type paste Note that if you select and copy a the dataset in the File Explorer its data path is copied to the Clipboard The command Paste reads this path from the Clipboard If you run Paste without first copying a dataset from the Ex plorer TOPSPIN tries to read whatever is currently stored in the Clipboard If that is a data path TOPSPIN will read it otherwise you will get an error message OUTPUT FILES lt tshome gt prog curdir lt user gt curdat current data definition SEE ALSO copy P 445 Dataset handling re rep rew repw NAME re Read data of specified name or expno nD rep Read data of specified procno nD rew Read data of specified name expno in new window nD repw Read data of specified procno in new window nD DESCRIPTION The commands re and rew allow you to read and display a new dataset They open a dialog box with the corresponding option selected see Fig ure 9 11 These options are r amp re Options Display data in new window NAME exam1d_13C EXPNO 1 PROCNO 1 DIR C Bruker T OPSPIN data questinmr ok Cancel Browse Find Help Figure 9 11
275. functions each of which selects a certain command for execution Sine bell This window function selects the command sinm for execution It per P 119 1D Processing commands forms a sine window multiplication according to the function SINM t sin n PHI t AQ PHI Figure 3 19 where 0 lt t lt AQand PHI n SBB Figure 3 20 where AQ is an acquisition status parameter and SSB a processing parameter Typical values are SSB 1 for a pure sine function and SSB 2 fora pure cosine function Values greater than 2 give a mixed sine cosine function Note that all values smaller than 2 for example 0 have the same effect as SSB 1 namely a pure sine function Squared sine bell This window function selects the command qsin for execution It per forms a sine squared window multiplication according to the function OSIN t sin n PHD t AQ PHI Figure 3 21 P 120 1D Processing commands where 0 lt t lt AQand PHI n SBB Figure 3 22 where AQ is an acquisition status parameter and SSB a processing parameter Typical values are SSB 1 for a pure sine function and SSB 2 fora pure cosine function Values greater than 2 give mixed sine cosine functions Note that all values smaller than 2 have the same effect as SSB 1 namely a pure sine function Sinc This window function selects the command sinc for execution It per forms a sinc window multiplication according to the functi
276. g box offers several options each of which selects a certain command for execution Magnitude spectrum F2 This option selects the command x 2m for execution It calculates the real and F2 imaginary data according to P 217 2D processing commands O09 rr Nrr ir fs Ds 29 ri Ari il Figure 4 22 Magnitude spectrum F1 This option selects the command xf1m for execution It calculates the real and F1 imaginary data according to according to 2 2 rr rr Tri eee r ir Til Figure 4 23 Magnitude spectrum F12 and F1 This option selects the command xfbm for execution It calculates the real andF1 F2 imaginary data according to according to i er ee rr rr vir Trl Til Figure 4 24 where rr real data 2 rr file ir F2 imaginary data 2ir file ri F1 imaginary data 2 ri file ii F2 F1 imaginary data 211 file The commands xf mare for example used to convert a phase sensitive spectrum to magnitude spectrum This is useful for data which cannot be phased properly or data which are not phase sensitive but have been ac quired as such P 218 2D processing commands The ph command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data OUTPUT FILES lt di
277. g factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum set by the x 2 can be viewed with dpp or by typing s mc2 MC2 Fourier transform mode input of x 1 on processed data set by the acquisition can be viewed with dpa or by typing s fnmode FnMODE Acquisition mode input of x 1 on raw data OUTPUT PARAMETERS F1 parameters can be viewed with dpp or by typing s ft_mod etc P 214 2D processing commands FT_mod Fourier transform mode FTSIZE Fourier transform size F2 parameters can be viewed with dpp or by typing s ymax_p s ymin _petc YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data input if 2rr does not exist or is Fourier transformed in F1 acqu2s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2r
278. gh Saturday For each of these fields you can define an interval by selecting a value in the From and a value in the To field Setting the To field to Zgnore schedules the command for execution only at the time date selected in the From field An asterix in the From field indicated all possible times Clicking the button to the right of a field adds an extra field of the same type allowing multiple interval definition Clicking the button removes the extra field The cron dialog also offers a right click menu which allows following op tions e Add new rule adding new scheduling rules e Remove rule removing scheduling rules e Favorites define favorites for scheduling rules SEE ALSO at atmulti qu qumulti spooler P 511 Automation NAME edau Edit an AU program xau Execute an AU program delau Delete an AU program edau xau delau SYNTAX edau lt name gt xau lt name gt delau lt name gt DESCRIPTION ee AU Programs File Options Help Search in names search When entered without arguments the AU program commands edau xau and delau all open the AU program dialog box see Figure 11 4 Source Cits 1 expistaninmriauisre 2df1 shift abs2 water 2dgetref 2dshift 2nde 2ndn abs2D accept_best lacqu_fid_ser lacqulist all_fromjdx all_tojdx amplstab jangle apkO noe asclev atpplot au_cp au_diff lau
279. gh field right limit of the signal region set by the acquisition can be viewed with dpa or by typing s nuc1 etc NUC1 observe nucleus SOLVENT sample solvent OUTPUT PARAMETERS can be viewed with dpp or by typing s sino SINO signal to noise ratio INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data li imaginary processed data not used for sino real proc processing parameters lt tshome gt exp stan nmr lists scl lt NUC1 SOLVENT gt scaling region file OUPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 407 Analysis commands P 408 procs processing status parameters USAGE IN AU PROGRAMS SINO SEE ALSO mc abs Analysis commands sola NAME sola Switch to solids lineshape analysis mode DESCRIPTION The command sola switches to solids lineshape analysis mode This procedure is completely described in the TOPSPIN Users Guide To open this click Help Manuals Analysis and Simulation Structure Analysis Tools SEE ALSO solaguide P 409 Analysis commands sref cal NAME sref Calibrate the spectrum set the TMS signal to 0 ppm 1D 2D cal Open calibration dialog box 1D 2D DESCRIPTION Spectrum calibration can be started from the command line with sref or from the calibration dialog box which is opened with the cal command S Ax
280. h the possibility of graphical editing Set PULPROG for pulse programs only Sets the acquisition parameter PULPPROG to the name of the select ed pulse program The Options menu The Options menu offers the following functions Show Comment Toggles between displaying items with without comments P 480 Parameters lists AU programs Show Date Toggles between displaying items with without date Sort by Date Sort items by date when selected Manage Source Directories Add modify item source directories Items will be searched for in the order of the directories specified For detailed information about Source Directory Handling and Manage Source Directories please refer to Chapter 1 9 Export Sources Opens a dialog to export an entire item library to a user defined direc tory Note the difference to the Export function under the File menu see below The File menu The File menu offers the following functions New Opens an empty editor for creating a new item e g a pulse program Saving the text will prompt you for the item name and will store it in the database The owner of the item will be the current TOPSPIN user Save As Saves the selected item under a new name Opens a dialog where you can selected a source directory and specify a filename Delete Deletes all selected items from the database if not write protected You will be prompted to confirm deletion Rename Allows you to ren
281. h the source and binary AU program are deleted Rename Rename the selected AU program Note that both the source and bi nary AU program are deleted Note that only user defined AU pro P 513 Automation grams can be renamed Export Export the selected AU program to an arbitrary directory A file dialog will appear where you can select specify the destination directory Import Import an AU program from an arbitrary directory A file dialog will ap pear where you can select specify the AU program The Options menu The Options menu offers the following functions Show Comment Toggles between displaying AU programs with without comments see Figure 11 5 Show Date Toggles between displaying AU programs with without date see Fig ure 11 5 Sort by Date Sort AU programs by date when selected see Figure 11 5 7 AU Programs x File Options Help Source C Bruker TOPSPINexpistaninmriauisre oa Search in names 2007 11 14 16 51 45 Program to shift a 2D spectrum along the F1 axis Keywords shift 2dgetret 2007 11 14 16 51 45 AU program which gets parameters for a 2D spectrum from the 1D 2dshitt 2007 11 14 16 51 45 Program to shift 2D time domain data left or right over NSP points 2nde 2007 11 14 16 51 45 Set 2nd data set to new expno and 3rd data set equal to foreground 2ndn 2007 11 14 16 51 45 Set 2nd data set to new name and 3rd data set equal to
282. he F1 direction and stores it as a 1D dataset Read negative projection on rows This option selects the command rhnp for execution It calculates the full negative projection of a 2D spectrum in the F2 direction and stores itas a 1D dataset Read negative projection on columns This option selects the command rvnp for execution It calculates the full negative projection of a 2D spectrum in the F1 direction and stores itas a 1D dataset A projection is a 1D trace where every point has the highest intensity of all points of the corresponding orthogonal trace in the 2D spectrum r p commands only take the projection of the first quadrant data file 2rr and store it as real 1D data file 1r r p commands can be started from the command line When entered without arguments they open a dialog box as shown in Figure 4 12 DESTINATION janelle PROCNO 999 Figure 4 12 P 177 2D processing commands The required arguments can also be specified on the command line rhpp lt procno gt stores the projection under the specified procno of the current data name rhpp lt procno gt n stores the projection under the specified procno but does not change the display to that procno The three other r p command have the same syntax A special case is the command rvpp or rvnp on a hypercomplex 2D da taset MC2 QF that has been processed in F2 only Suppose you would perform the following command sequence xf2 to p
283. he destination 2D dataset Examples of the usage of wsr on the source 1D dataset wsr prompts for the row of the destination 2D data which must be replaced by the current 1D data The 2D dataset is the one from which the cur rent 1D dataset was extracted wsr lt row gt the specified row of the destination 2D data is replaced by the current 1D data The 2D dataset is the one from which the current 1D dataset was extracted wsr lt row gt lt procno gt the specified row of the destination 2D data is replaced by the current 1D data The 2D dataset must reside under the current data name A 1 However if the current data name is TEMP wsr lt row gt lt procno gt writes to the specified procno in the dataset from which the current 1D dataset was extracted P 211 2D processing commands the current expno and the specified procno Examples of usage of wsr on the destination 2D dataset wsxr lt row gt the specified row of the current 2D processed data is replaced The source 1D data must reside under the data name TEMP wsr lt row gt lt procno gt the specified row of the current 2D processed data is replaced The source 1D data must reside under the current data name the current expno and the specified procno wsr can also be started from the dialog box that is opened with the com mand slice INPUT FILES lt dir gt data lt user gt nmr TEMP 1 pdata 1 1r 1i 1D processed data used_from data path
284. he following parameters settings are used In F2 TD 8 Sl is 4 In F1 TD 4 Sl 2 Furthermore the following notation is used for individual data points e rnrm point n of FID m This point is real in F2 and F1 e inrm point n of FID m This point is imaginary in F2 and real in F1 e rnim point n of FID m This point is real in F2 and imaginary in F1 e inim point n of FID m This point is imaginary in F2 and F1 Input F2 processing raw data F2 r r1 idrd4 r2r1 i2r1 r3r1 i3r1 r4r1 i4r1 Fl rit i1i1 r2i1 i2i1 r3i1 i3i1 r4i1 i4i1 r4r2i1r2 r2r2i2r2 r3r2i3r2 r4r2 i4r2 r1i2 i1i2 r2i2 i2i2 r3i2 i3i2 r4i2 i4i2 ser file For F2 processing r1r1 i1r1 is the first hypercomplex input data point r2r1 i2r1 the second etc P 237 2D processing commands Output F2 processing Input F1 processing F2 rird r2r4 ss r3r1 sr4r1 i1ri i2r4 ss i3r1 i4r Fl qi r2i4r3i1 rit i1i1 i2i1 i3i1 i4i1 mr r2r2 r3r2 r4r2 i1r2 i2r2 i3r2 i4r2 rmi2 r2i2 r3i2 r4i2 i1i2 i2i2 i3i2 i4i2 2rr file 2ir file Below the F1 input data are simply redisplayed with the first F1 com plex input points in bold Input F1 processing F2 r ird r2r4 r3r4i r4r1 idr4 i2r1 i3r1 i4r1 Fl r1i1 r2i1 r3i1 r4i1 i1i1 i2i1 i3i1 i4i1 mr r2r2 r3r2 r4r2 i1r2 i2r2 i3r2 i4r2 r1i2 r2i2 r3i2 r4i2 i1i2 i2i2 i3i2 i4i2 2rr file 2ir file Output F1 processing F2 rir r2r1 r3r4i r4r1 itrt i
285. he last modification unused for status parameters S Switch between processing and processing status parameters 4 Search for the parameter specified in the search field Processing status parameters can also be viewed by entering their names on the command line For example s f t_mod display the processing status parameter FT_mod s nc_ proc display the processing status parameter NC_proc INPUT FILES lt tshome gt classes prop pared prop parameter properties file lt tshome gt exp stan nmr form proc e processing parameter format file lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt procs processing status parameters On 2D and 3D data the files proc2s and proc3s are used for the sec ond and third direction respectively see also chapter 2 3 SEE ALSO edp dpa P 463 Parameters lists AU programs eddosy NAME eddosy Edit DOSY processing parameters 2D 3D DESCRIPTION The command eddosy opens a dialog box in which you can set DOSY processing parameters exam2d_HC 1 1 C ibio guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid gt YP GetPrev amp panera b General A First Second First component Third Baseline Contin vary Yes v Fit intensity i 1000000000 Intensity Mmin 2147483647 Minirnurn intensity imax 2147483647 Maximum intensity Di vary Yes v Fit diffusion coefficient
286. he real data by Fourier transform Directly after the Fourier transform real and imaginary data are consistent and can be used for phase correction If however the real data are manipulated e g by abs they are no longer consistent with the imaginary data In that case or when the imaginary data have been deleted ht can be used to create new imaginary data Hilbert transform is based on the so called dispersion relations or Kram ers Kronig relations see for example R R Ernst G Bodenhausen and A Wokaun Principles of nuclear magnetic resonance in one and two di mensions Clarendon Press Oxford 1987 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt li imaginary processed data auditp txt processing audit trail USAGE IN AU PROGRAMS HT SEE ALSO ft ift trf trfp 1D Processing commands ift NAME ift Inverse Fourier transform 1D DESCRIPTION The command ift performs an inverse Fourier transform of a 1D spec trum thus creating an artificial FID Normally i t is done when the raw data do not exist any more If however raw data do exist they are not overwritten ift stores the resulting FID as processed data i e it over writes the current spectrum After ift you can create pseudo raw data with the command genfid which
287. her information about deconvolution please look up the User Manual P 95 1D Processing commands P 96 genfid NAME genfid Generate pseudo raw data 1D DESCRIPTION The command genfid generates pseudo raw data from processed da ta When entered without arguments it opens a dialog box where you can specify the destination dataset genfid i e Please specify destination NAME examid_13C EXPNO ok Cancel Help Figure 3 9 genfid is normally used in combination with the command ift which performs an inverse Fourier transform converting a spectrum into an FID Actually ift transforms processed frequency domain data into processed time domain data genfid converts these processed time do main data into pseudo raw time domain data and stores them under a new name or experiment number expno Note that genfid does not modify the data but only stores them in a dif ferent format The number of data points of the pseudo raw data is twice the size SI of the processed data they are created from The acquisition status parameter TD types s td or dpa is set accordingly TD 2 Sl genfid takes arguments and can be used as follows 1 genfid lt expno gt The FID will be stored under the specified expno 2 genfid lt expno gt lt name gt y 1D Processing commands The FID will be stored under the specified name and expno The last argument y causes genfid to overwrite
288. ian lineshape to determine the ratio of each individual peak Use Gaussian shape This option selects the command gdcon for execution It deconvolves the spectrum by fitting a Gaussian function to the peaks It is typically used for overlapping peaks with a Gaussian lineshape to determine the ratio of each individual peak Use mixed shape auto peak pick into file peaklist This option selects the command mdcon auto for execution It first picks the peaks for deconvolution and stores them in the peaklist file Then it deconvolves the spectrum by fitting a mixed Lorentz ian Gaussian function to these peaks This command is typically used to deconvolve spectra which cannot be approximated by a pure Lorentzian or a pure Gaussian lineshape P 91 1D Processing commands Yine deconvolution Ideon Options C Use Gaussian shape C Use mixed shape auto peak pick into file peaklist C Use mixed shape use peaks from file peaklist Generate file peaklist no deconvolution C Re Display peak list from last deconvolution Display the Lorentz Gauss curves of the last deconvolution Required parameters Left deconvolution limit F1P ppm fi 6 4569606781 005686 Right deconvolution limit F2P ppm 4 106147707164844 Minimum intensity MI rel fi Maximum intensity MAXI rel hi 0000 Peak detection sensitivity PC fi Peak overlapping factor AZFY ppr fo Destination PROCNO for fitted data 999
289. iation 20 53 215 status parameter display 476 storage order 3D data 265 strip size 37 45 86 233 271 292 start 38 86 233 271 292 transform 37 38 45 transform 1D 86 transform 2D 233 transform 3D 271 292 297 302 sub1 command 192 sub1d1 command 192 sub1d2 command 192 sub2 command 192 subcube format 38 45 271 272 291 292 subcube size 46 272 292 submatrix format 38 45 232 255 submatrix size 46 224 225 233 243 subtract a 1D from a 2D 192 subtract two 2D datasets 150 sumcb command 328 sumpl command 275 susceptibility 411 swin command 596 sym command 195 197 syma command 195 symj command 195 symmetrize a 2D spectrum 44 195 symt command 195 199 T t1guide command 414 tabs1 command 286 tabs2 command 286 tabs3 command 286 tf1 command 41 301 306 tf1p command 306 308 tf2 command 296 306 tf2p command 306 308 tf3 command 21 288 296 297 301 306 tf3p command 306 308 third party software 232 233 250 265 271 272 291 292 308 tht1 command 308 tht2 command 308 tht3 command 270 291 306 308 tilt a 2D spectrum 199 tilt command 199 tilt factor 21 200 time domain data 5 86 96 170 227 252 278 title bar 453 tm command 129 tojdx command 390 551 totxt command 555 tozip command 557 trace 143 165 177 traf command 129 Traficante window multiplication 40 129 trafs command 129 trapezoidal window multiplication 39 40 129 trf command 87 88 111 133
290. ic baseline correction of integrals if regions auto detected INTBC yes v Figure 8 7 P 381 Analysis commands P 382 mand int This dialog box has several options each of which selects a certain com mand for execution Auto find regions integrate amp display results This option executes the command sequence abs li The com mand abs determines the integral regions creating the intrng file The command 1i calculates the integral value for each integral region and shows the result in on the screen Integrate existing regions and display results This option executes the command 1i This command calculates the integral value for each integral region and shows the result in on the screen List peaks and integrals within the displayed region This option executes the command lipp It works like 1i except that it also performs peak picking and shows a list of integral regions and peaks within the region F1P F2P List peaks and integrals of the entire spectrum This option executes the command lippgf It works like lipp except that it only determines the integrals and peaks over the entire spec trum The Zi commands evaluates the parameter INTSCL if the regions have been determined interactively For INTSCL 1 the current dataset is defined as reference dataset for integral scaling For INTSCL 1 the integrals of the current dataset are scaled relative to the reference data set
291. ich have been tilted with the command tilt sym commands only work on the real data After using it the imaginary data no longer match the real data and cannot be used for phase correc tion When executed from the command line the command sym syma and symj select the corresponding option in the dialog box This means you can just click OK or hit Enter to start the command In contrast symt selects the last used symmetrization command OUTPUT PARAMETERS can be viewed with dpp or by typing s symm SYMM type of symmetrization no sym syma or symj done INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data P 197 2D processing commands OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS SYM SYMA SYMJ SEE ALSO tilt ptilt ptilt P 198 2D processing commands tilt ptilt ptilt symt NAME tilt Tilta 2D spectrum ptilt Tilt a 2D spectrum by shifting the data in the F2 direction ptilt1 Tilt a 2D spectrum by shifting the data in the F1 direction symt Open the symmetrize tilt dialog box DESCRIPTION All ti1t commands open the symmetrize tilt dialog box see Figure 4 18 EN Symmetrize tilt tilt Options Symmetrize COSY type spectrum oO Symmetrize phase sensitive spectrum Symmetrize J
292. ified by the pathname and stores it under the dir user and name of the active dataset and the expno and procno as specified in the input JCAMP DxX file fromjdx lt pathname gt procno converts the JCAMP DxX file specified by the pathname and stores it under the dir user and name of the active dataset expno 1 and the procno as specified in the input JCAMP DxX file All the above examples can be used with the y option to overwrite pos sibly existing data INPUT FILES lt pathname gt lt mydata dx gt TOPSPIN data in JCAMP DX format OUTPUT FILES For 1D and 2D data lt tshome gt prog curdir lt user gt curdat current data definition lt dir gt data lt user gt nmr lt name gt lt expno gt P 542 Conversion commands t acquisition audit trail if input file contains raw data x audita t lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt t processing audit trail if input file contains processed x auditp t data outd output device parameters title title file see edti For 1D data lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data if input file contains 1D raw data acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data if input file contains 1D real processed data li imaginar
293. igatory vconv converts all VNMR parameters which have a TOPSPIN equivalent First the VNMR parameter SEQFIL is interpreted If it is set to a certain name veconv checks the existence of a TOPSPIN parameter set with that name If it exists it is copied to the destination dataset If it does not exist a standard parameter set standard D for 1D data is copied Then veonv converts all VNMR parameters which have a TOPSPIN equivalent and over writes the values of the parameter set which was previously copied The parameters of the TOPSPIN parameter set which do not have a VNMR equivalent keep their original values If you frequently convert Vnmr data with typical values of SEQFIL you might want to create the TOPSPIN pa rameter sets with the corresponding names This can be done by reading a standard parameter set with rpar modify it with eda and edp and then store it with wpar Conversion commands VNMR XWIN NMR VNMR XWIN NMR ct NS status rfl rfp OFFSET d1 D1 rfl1 rfp1 OFFSET 2D date DATE rfl2 rfp2 OFFSET 3D dfrq BF2 rp PHCO dfrq2 BF3 rp Ip PHCO PHC1 dmf P31 rp1 lp1 PHCO0 PHC1 2D dn DECNUC rp2 lp2 PHCO PHC1 3D dn2 DECBNUC seqfil PULPROG dof 02 sfrq BF1 dof2 O3 solvent SOLVENT fb FW spin RO fn SI ss DS Ip PHC1 Sw SW_h np TD sw1 SW_h 2D nt NS foreground sw2 SW_h 3D pp P3 temp TE an AUNM tn NUCLEUS pw PO tof 01 pw90 P1 Table 12 2 The origin
294. ile called threepoint is delivered with TOPSPIN TOPSPIN parameters FCOR first FID data point multiplication factor used in 1D 2D and 3D datasets in all directions takes a float value between 0 0 and 2 0 interpreted by ft trf xfb xf2 xf1 xtrf xtrfp tf3 t 2 tf1 For 1D digitally filtered Avance data DIGMOD digital FCOR does not play a role because the first raw data point is always zero FCOR however allows you to control the DC offset of the spectrum in the following cases on A X data on Avance data measured in analog mode DIGMOD analog on 2D 3D Avance data in the second secondt third direction FT_mod Fourier transform mode used in 1D 2D and 3D in all directions takes one of the values no fsr fqr fsc fqc isr igr iqc isc interpreted by trf xtrf xtrfp the Fourier transform commands ft 1D xfb x 2 xf1 2D and tf 3D do not interpret FT_mod because they evaluate the Fourier transform mode from the acquisition status parameter AQ_mod They do however set the processing status parameter FT_mod P 25 TOPSPIN parameters The values of FT_mod have the following meaning FT mod Fourier transform mode no no Fourier transform fsr forward single channel real fqr forward quadrature real fsc forward single channel com plex fqc forward quadrature complex isr inverse single channel real iqgr inverse quadrature real isc inverse single chann
295. imaginary data are created during Fourier transform If however the imaginary data are missing or do not match the real data and you want to do a phase correction you can re create them with Hilbert transform Imaginary data do not match the real data if the latter have been manipulated after the Fourier transform for example by base line correction or third party software INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3irr F3 imaginary processed data output of tht3 3rir F2 imaginary processed data output of tht2 P 308 3D processing commands 3rri F1 imaginary processed data output of tht1 auditp txt processing audit trail SEE ALSO tf3 tf2 tfl P 309 Chapter 6 nD processing commands TOPSPIN 2 0 and newer offers nD processing Datasets up to 5D have been tested by Bruker nD data can be displayed by reading cubes planes or traces nD processing commands P 312 absnd NAME absnd nD automatic baseline correction DESCRIPTION The command absnd performs an automatic baseline correction of data of dimension 23D It takes one argument the direction to be corrected If no argument is specified on the command line it is requested see Figure 6 1 amp absnd Enter direction 4 3 2 1 for F4 F3 F2 F1
296. ime domain data into frequency domain data Depending on the processing parameters BC_mod WDW ME_mod and PH_mod xfb also performs baseline correction window multiplication linear prediction and spectrum phase correction The processing steps done by xfb can be described as follows 1 Baseline correction of the 2D time domain data Each row and or column is baseline corrected according to BC_mod This parameter takes the value no single quad spol qpol sfil or qfil More details on BC_mod can be found in chapter 2 4 2 Linear prediction of the 2D time domain data Linear prediction is done according to ME_mod This parameter takes the value no LPfr LPfc LPbr LPbc LPmifr or LPmifc Usu P 227 2D processing commands Fourier transform xfb Options O Advanced Fourier transform Required parameters F2 and F1 Enable transform for one both dimensions Size of real spectrum Sl pnts Figure 4 29 ally ME_mod no which means no prediction is done Forward prediction LPfr LPfc LPmifr or LPmifc can for example be used to extend truncated FIDs Backward prediction LPbr or LPbc can be used to improve the initial data points of the FID Linear predic tion is only performed for NCOEF gt 0 Furthermore LPBIN and for backward prediction TDoff play a role see these parameters in chapter 2 4 3 Window multiplication of the 2D time domain data P 228 2D processing commands
297. ing FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 BC_mod FID baseline correction mode 1 Usually a result of rsr rsc or a previous 1D processing command on that 2D or 3D data P 135 1D Processing commands BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap FT_mod Fourier transform mode REVERSE flag indicating to reverse the spectrum PKNL group delay compensation Avance or filter correction A X STSR strip start first output point of strip transform STSI strip size number of output points of strip transform PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk set by the acquisition can be viewed with dpa or by typing s td TD time domain number of raw data points OUTPUT PARAMETERS can be viewed with dpp or by typing s tdeff etc TDeff number of raw data poi
298. ing status parameters OUTPUT FILES lt pathname gt lt mydata dx gt TOPSPIN data in JCAMP DX format USAGE IN AU PROGRAMS TOJDX name data mode title origin owner for example TOJDX tmp mydata dx 0 2 mytitle BRUKER joe SEE ALSO fromjdx tozip totxt P 554 Conversion commands totxt NAME totxt Save the currently displayed region as a text file 1D 2D DESCRIPTION The command totxt saves the currently displayed spectral region as text file It will open the following dialog box Please specify destination Name of archive file exami d_13C txt Directory of archive file es Include imaginary data yes no no in which you can enter the text filename and directory totxt works on 1D and 2D datasets and only stores the real processed data The 1D file format is File created Wednesday March 3 2004 11 52 01 AM CET Data set examld 13C 1 1 C bio guest Spectral Region LEFT 145 2549493926 ppm RIGHT 116 58206350384 ppm SIZE 3940 number of points In the following ordering is from the left to the right limits Lines beginning with must be considered as comment 4 1 4612096E7 3084512 0 4615664 0 1 6594048E7 4898192 0 4555792 0 P 555 Conversion commands P 556 INPUT FILES For 1D data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data For 2D d
299. ion 4D data F4 first direction acquisition or direct direction F3 second direction indirect direction F2 third direction indirect direction 1 If C if the default drive P 4 Introduction F1 fourth direction indirect direction Commands like t 3 and tabs3 work in F3 t 2 tabs2 etc work in F2 tf1 tabs1 etc work in F1 Data with dimension gt 3 can be processed with the command ftnd 1 4 About time and frequency domain data The result of an acquisition is a representation of intensity values versus acquisition time seconds the data are in the time domain The result of a Fourier transform is a representation of intensity values versus frequency Hz or ppm the data are in the frequency domain Examples of time domain data are e raw data 1D 2D and 3D e 1D data processed with be em or gm e 2D data processed with xf 2 time domain in F1 e 3D data processed with t 3 time domain in F2 and F1 Examples of frequency domain data are e 1D data processed with ft ef gf efp gfp trf 2D data processed with xfb xf2 xf1 xtrf 3D data processed tf 3 tf2 tf1 Be aware the commands trf and xtrf only perform a Fourier trans form if the processing parameter FT_mod type edp is set see trf Time and frequency domain data can usually be distinguished by the data type FID versus spectrum and axis labelling Hz or ppm versus sec The only unequivocal way to distinguish the
300. ion can be viewed with dpa or by typing s fnmode FnMODE F1 Acquisition transform mode set by the user with edp or by typing mc2 MC2 FT mode in F1 only used if F1 FnMODE undefined OUTPUT PARAMETERS F2 and F1 parameters can be viewed with dpp or by typing s si s tdeff etc SI size of the processed data TDeff number of raw data points that were used for processing FTSIZE Fourier transform size STSR strip start first output point of strip transform STSI strip size number of output points of strip transform XDIM submatrix size FT_mod Fourier transform mode F2 parameters can be viewed with dpp or by typing s ymax_p s ymin _petc YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data P 244 2D processing commands INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data input if 2rr does not exit or is Fourier transformed lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data input if it exists but is not Fourier trans formed proc F2 processing parameters proc2 F1 processing parameters acqus F2 acquisition status parameters acqu2s F1 acquisition status parameters Note that if 2rr is input then 2ir and 2ri can also be inpu
301. ion commands can be started from the command line or from the baseline dialog box The latter is opened with the command bas amp Baseline correction bcm2 Options Auto correct baseline using polynomial oO Auto correct baseline shift correction region Auto correct baseline alternate algorithm O Auto correct baseline shift correction region altern algo Correct baseline using correction result from 1D rov column Required parameters F2 and F1 Apply to axis F2 F1 Figure 4 4 see Figure 4 4 This dialog box offers several options each of which selects a certain command for execution P 153 2D processing commands Correct baseline using correction result from 1D row column F2 This option selects the command bem2 for execution It performs a baseline correction in the F2 direction by subtracting a polynomial sine or exponential function Before you can use bem2 you must first do the following 1 2 3 6 Read a row with rsr TOPSPIN will switch to the 1D data window Click or enter bas1 to switch to baseline mode Click Ly fy or L to select the baseline correction func tion Fit the baseline of the spectrum with the function you selected in step 2 initially represented by a straight horizontal line Click hold button A and move the mouse to determine the zero order correc tion Do the same with the buttons B C for higher order correc tions until the line ma
302. ions Administration Change internal user password SEE ALSO uadmin esign logoff P 602 TOPSPIN User Management esign NAME esign Exit TOPSPIN DESCRIPTION The command esign adds an electronic signature to the raw data and or to the processed data of a dataset It opens the following dialog esign Add Electronic Signature To Data Set examid_13C 1 1 C bio guest Data component to be signed Raw amp Processed Data Select Signature Meaning all our commen Comment Figure 14 5 Just select the data component to be signed the signature meaning and optionally add a comment Then click Sign now The signature will appear with the parameters on the plot commands plot autoplot and in the Audit file command audit proc It con sists of four lines e g USER ID larry USER NAME Larry Hill MEANING approval COMMENT Spectrum quality is OK The command esign can also be started as follows Click Options Administration E Sign Data Set P 603 TOPSPIN User Management P 604 esign requires that the NMR administrator has set up a list of users who are allowed to sign a data set along with definitions of signature mean ings e g review approval INPUT FILES lt tshome gt conf topspin users prop TOPSPIN users properties file OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt auditp txt processing audit trail SEE
303. irectory for user defined lists is lt tshome gt exp stan nmr lists lt listhame gt SEE ALSO edmisc P 467 Parameters lists AU programs P 468 edmisc rmisc wmisc delmisc NAME edmisc Edit miscellaneous lists rmisc Read miscellaneous lists wmisc Write miscellaneous lists delmisc Delete miscellaneous lists DESCRIPTION The commands misc allow you to read edit write or delete miscella neous lists When entered without arguments they all open an akin win dow for Miscellaneous Files The difference is that wmisc only offers writing possibilities for Miscellaneous Files rmisc only offers reading possibility whereas with edmisc and delmisc you can read write and edit the correesponding selected Miscellaneous File as shown in Figure 10 4 amp Miscellaneous Files edmisc Ex File Options Help Source C My_intrng_files X Search in names x Search Misc type intrng 1D integral range intrng 1D integral ranges peakrng 1D peak ranges basipnts baseline points for abs base_info baseline function for ocm peaklist peak file for dcon clevels 2D contour levels reg reference regions for pp int2drng 2D integral ranges exam1d_1H bt intrng test tt Edit Read Write Write New Close Figure 10 4 On the topright you can change the Source and specifiy the Miscellane ous type that should be shown in
304. is calibration sref Options Manual calibration Figure 8 15 This dialog box offers two options one for manual and one for automatic calibration Manual calibration This option selects the ca1 command for execution This is equiva lent to clicking the button in the toolbar and switches to interactive calibration mode Click inside the data window at the reference peak enter the frequency value in the appearing dialog box and click OK Automatic calibration This option selects the sref command for execution It calibrates the spectrum by setting the TMS signal of a spectrum to exactly 0 ppm It works on 1D and 2D spectra sref makes use of the lock table This must be set up once after install ing TOPSPIN with the command edlock On 1D spectra sref involves three steps which are discussed below P 410 Analysis commands During the first step sref sets the value of the processing parameter SF according to the formula SF BF 1 1 0 RShift 1e 6 where RShift is taken from the edlock table and BF1 is an acquisition status parameter Changing SF automatically changes the processing parameters SR the spectral reference and OFFSET the ppm value of the first data point according to the following relations SR SF BF1 where BF 1 is an acquisition status parameter OFFSET SFO1 SF 1 1 0e6 0 5 SW SFO1 SF where SW and SFO1 are acquisition status parameters Actually the relation for OF
305. k Delete to actually delete them An entire dataset with all expnos procnos This option selects the command de1 for execution It lists datasets only showing the dataset name To delete data mark one or more da tasets and click Delete The marked datasets are entirely deleted in cluding data files parameter files and the data name directory Acquisition data This option selects the command dea for execution It It lists data sets showing a separate entry for each experiment number expno Each entry shows the dataset NAME EXPNO ACQU DATA and SIZE Datasets which do not contain raw data are displayed with AC QU DATA none To delete data mark one or more datasets and click P 419 Dataset handling Browse Options An entire data set with all EXPNOs PROCNOs Acquisition data Processed data Data acquired at certain dates O 1D raw data fid O 1D processed data ri 205D raw data ser 2D processed data 2rr 2ii O Imaginary processed data 1i oO Macro AU program Python program Pulse program Parameter list Miscellaneous file Required parameters Name Data directory C Bio User Figure 9 1 one of the following buttons Delete selected EXPNOs to delete the expno directory Delete raw data files of the selected EXPNOs Processed data This option selects the command dep for execution It lists datasets showing a separate en
306. l direction which is displayed vertically The names of most 2D processing commands express the direction in which they work e g x 2 works in F2 xf1 in F1 and x b in both directions F2 traces are usually referred to as rows F1 traces as columns Some commands express this terminology e g rsr reads and stores rows and rsc reads and stores columns of a 2D spectrum For each command the relevant input and output parameters are men tioned Furthermore the relevant input and output files and their location are mentioned Although file handling is completely transparent it is some times useful to know which files are involved and where they reside For example if you have permission problems or if you want to process or interpret your data with third party software 2D processing commands abs2 abst2 absd2 absot2 bas NAME abs2 Automatic baseline correction in F2 2D abst2 Automatic selective baseline correction in F2 2D absd2 Automatic baseline correction in F2 diff algorithm 2D absot2 Automatic selective baseline correction in F2 diff algorithm 2D bas Open baseline correction dialog box 1D 2D DESCRIPTION Baseline correction commands can be started from the command line by entering abs2 abst2 etc or from the baseline dialog box The latter is opened with the command bas i Baseline correction abs2 O Auto correct baseline shift correction region O Auto correct baseline alternate alg
307. l options each of which selects a certain command for execution Additive phasing using PHC0 1 F2 and F1 This option selects the command xfbp for execution It performs a zero and first order 2D phase correction in the F2 and F1 direction xfbp works like the 1D command pk This means it does not calculate P 247 2D processing commands the phase values it simply applies the current values of PHCO and PHC1 Additive phasing using PHC0 1 F2 This option selects the command x 2p for execution It works like xfbp except that it only corrects the phase in the F2 direction Additive phasing using PHC0 1 F1 This option selects the command x 1p for execution It works like xfbp except that it only corrects the phase in the F1 direction xf p are only useful when the PHCO and PHC1 values are known If they are not you can perform 2D interactive phase correction To do that select the option Manual Phasing in the ph dialog box or click 4 in the toolbar The interactive phase correction procedure is described in the TOPSPIN Users Guide The phase values can also be determined by the 1D interactive phase correction of a row or column To do that read a row rsr and or column rsc and click 4 in the toolbar see TOPSPIN Users Guide Alternative ly you can phase correct a row or column with apk and view the calcu lated phase values with dpp Then you can go back to the 2D dataset set the determined phase values with ed
308. l then prompt you for an output procno e dlp Delayed linear prediction Optional argument only applicable when all directions are processed This argument ensures that when lin ear prediction is performed in a certain direction all other directions are already Fourier transformed see below If the arguments are not specified on the command line ftnd will nor mally only prompt you for the direction The output procno is only prompt ed for if inplace operation is not possible P 314 nD processing commands Here are some example of specifying arguments on the command line ftnd 0 Process the data in all directions in the order defined by the acquisition status parameter AQSEQ ftnd 4 Process data in direction F4 ftnd 4312 999 Process the data in all directions in the order F4 F3 F1 F2 and store the result in procno 999 ftnd 0 dlp Process the data in all directions in the order defined by AQSEQ per forming delayed linear prediction according to ME_MOD and NCOEF Missing arguments are prompted for except for the dlp argument Note that for the first argument the direction only the allowed directions are displayed and the next logical direction is suggested Figure 6 2 shows the dialog opened by ftnd on a 4D dataset that has already been proc essed in F4 and F3 Enter direction s 4 2 1 for F4 F2 F1 or 0 4321 4312 4213 4231 4123 4132 for all 0 all directions according to AQORDER 3
309. le nD processing commands rpl 12 1 10 keepsize Note that a plane read with keepsize cannot be written back to the source dataset because the sizes do not match Note that the command rp1 replaces the old commands r12 r13 and r23 which do not allow axes exchange For compatibility reasons these commands are still available Note however their usage in AU programs has changed compared to TOPSPIN 1 1 and XWIN NMR see the descrip tion of r12 The behaviour of the command rp1 is similar to the commands rsr and rsc in the sense that it can be entered from the source and destination dataset On a data with dimension gt 3 rp1 works the same as on a 3D dataset except that there are more plane axis orientations For example on 4D dataset possible orientations are 34 24 14 23 13 12 43 42 41 32 31 and 27 For an example if the inmem option see the AU program ift3d INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr 3irr 3rir 3rri 3iii processed data rp1 on 3D data 4rrrr 4iiii processed data rp1 on 4D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data auditp txt processing audit trail used_from data path of the source 3D data and the plane number SEE ALSO wpl rtr wtr rcb rser wser wserp rser2d P 337 nD processing commands rtr NAME
310. le menu The File menu offers the following functions New Create a new Shape File Note that new Shape Files can only be stored in user defined directories Save as Save the selected Shape Files under a new name A dialog will ap pear where you can specify the Shape File name and destination di rectory Delete Delete the selected Shape File Rename Rename the selected Shape file Note that only user defined Shape Files can be renamed Export Export the selected Shape File to an arbitrary directory A file dialog will appear where you can select specify the destination directory Import Import a Shape File from an arbitrary directory A file dialog will appear where you can select specify the Shape File Close Close the Shape File lists The Options menu The Options menu offers the following functions Show Comment Toggles between displaying Shape File with without comments see Figure 10 7 Show Date Toggles between displaying Shape File with without date see Figure P 473 Parameters lists AU programs P 474 10 7 Sort by Date Sort Shape Files by date when selected see Figure 10 7 amp Shape Files S File Options Help Source CABrukeTOPSPINexpistaninmrilistsiwave X Search in names Search 2007 10 23 10 31 48 Type SmoothedChirp Adiabatic Inversion 2007 10 23 10 31 50 Type CompositeSmoothedChirp Add Const
311. les of reb executed on a 3D dataset where the 3D dataset is a cube from a 4D dataset rcb Prompt the user for the cube number Use the cube axis orientation and source 4D procno as defined in the current 3D dataset rcb 11 Read cube 11 Use the cube axis orientation and Source 4D procno as defined in current 3D dataset rcb 123 11 Read F1 F2 F3 plane 11 Use the source 4D procno as defined in current 3D dataset rcb 123 11 2 Read F1 F2 F3 plane 11 from the 4D dataset under procno 2 As described above the reb argument cube axis orientation determines whether the axes are exchanged Axes exchange is sometimes required to match nuclei when you compare a 4D cube with a 3D dataset INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr 4iiii processed 4D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr 3iii processed 3D data auditp txt processing audit trail P 332 nD processing commands used_ from data path of the source 4D data and the cube axis orienta tion SEE ALSO rpl wpl rtr wtr P 333 nD processing commands rpl NAME rpl Read plane from data gt 3D and store as 2D data DESCRIPTION The command rpi reads a plane from processed data with dimension gt 3D and stores it as a 2D dataset in a different procno rpl takes up to five arguments As an example we take a plane read fr
312. lick the Bruker Utilities lt topspin version gt icon on your desktop An Explorer will be opened e Double click Miscellaneous e Execute the script savelogs Under Linux Open a shell Type savelogs INPUT FILES User specific installation files like history files etc named lt tshome gt prog curdir lt user gt OUTPUT FILES Windows XP lt userhome gt AppData Local Settings Temp TopSpinSupportFiles_ lt Support Token gt lt operating system user gt lt year gt lt month gt lt day gt lt hour gt lt minute gt tar gz e Windows Vista lt userhome gt AppData Local Temp TopSpinSupportFiles_ lt Support Token gt lt operating system user gt lt year gt lt month gt lt day gt lt hour gt lt minute gt tar gz P 368 e Linux tmp TopSpinSupportFiles_ lt Support Token gt _ lt operating system user gt lt year gt lt month gt lt day gt lt hour gt lt minute gt tar gz SEE ALSO hist Print Export commands P 370 Analysis commands Chapter 8 Analysis commands This chapter describes TOPSPIN analysis commands for 1D 2D and 3D data Although they do not really process manipulate the data they are part of the processing part of TOPSPIN Some of them merely interpret the data and display their output i e they do not change the dataset in any way Others change parameters like sref and sino or create new files like edti and pps None of them however change the processed data P 371 An
313. line or from the de lete dialog box The latter is opened with the command delete see Fig ure 9 2 This dialog box has several options each of which selects a certain com mand for execution The commands delf dels delser del2d and deli display a list of datasets Such a list only includes datasets which contain data files As opposed to commands like del and dela they do not show empty da tasets You can click one or more datasets to mark them for deletion and then click Delete to actually delete them 1D raw data This option selects the command def for execution It lists 1D data sets which contain raw data showing a separate entry for each exper iment number expo Each entry shows the dataset NAME EXPNO ACQU DATA and SIZE To delete data mark one or more datasets and click one of the following buttons Delete selected EXPNOs to delete the expno directory Delete raw data files of the selected EXPNOs 1D processed data P 423 Dataset handling P 424 EN delf Browse Options An entire data set with all EXPNOs PROCNOs Acquisition data Processed data Data acquired at certain dates O 1D processed data 1r i 205D raw data ser 2D processed data 2rr 2ii O Imaginary processed data 1i oO Macro AU program Python program Pulse program Parameter list Miscellaneous file Required parameters Name Data directory CBio User
314. ling This chapter describes all TOPSPIN commands which can be used to read or write or delete datasets P 415 Dataset handling copy NAME copy Copy the contents of the current data window to the Clipboard nD DESCRIPTION Under Windows the command copy copies the contents of the current data window to the clipboard The data are copied as a bitmap 1 To copy the data as a windows metafile use the command copy wmf On Linux is the screen dump png format copied to a temporary file the pathname of this file is copied to clipboard Entering copy on the command line is equivalent to clicking File Copy in the menu SEE ALSO paste 1 In Topspin 2 0 and older data were copied in WMF format P 416 Dataset handling dalias NAME dalias Create an alias name for a dataset nD DESCRIPTION The command dalias creates or interprets alias names for TOPSPIN da ta The command requires various arguments and can be used as fol lows Create alias names dalias add lt alias gt lt name gt lt eno gt lt pno gt lt dir gt lt usr gt create the alias name lt alias gt for the specified dataset e g dalias add elh examld_1H 1 1 C bio joe dalias add lt alias gt lt pathname gt create the alias name lt alias gt for the specified dataset e g dalias add elh C bio data guest nmr examld_1H 1 pdata 1 Show full names on the screen dalias pr lt alias gt print the name expno procno
315. ll be prompted for For example if you enter projcbp without any arguments it will start with the dialog shown in Figure 6 5 nD processing commands amp projcbp Enter cube axis orientation 234 134 124 123 432 321 E4 Figure 6 5 Note the following aspects the maximum first and last cube is determined by the size of the data in the direction not included cube orientation i e the direction along which the projection is calculated e XDIM is a processing parameter which must be set in each direc tion included cube orientation when with the xdim argument is used e the numerical arguments must be specified in the above order whereas the arguments all xdimand ncan be specified at any position INPUT FILES For a 4D dataset lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 4rrrr real processed 4D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data procs F3 processing status parameters proc2s F2 processing status parameters proc3s F1 processing status parameters auditp txt processing audit trail SEE ALSO projplp projpln sumpl P 329 nD processing commands rcb NAME rcb Read cube from data gt 4D and store as 3D data DESCRIPTION The command rcb reads a cube from processed data of dimension gt 4 It stores the extracted cube in a different procno as a 3D da
316. lso be set from the pp dialog box and interactively in peak picking mode NCOEF number of linear prediction coefficients used in on 1D 2D and 3D datasets in all directions takes a positive integer value default is 0 interpreted by ft trf xfb xf2 xf1 xtrf tf also interpreted by em gm sin tm traf NCOEF is typically set to 2 3 times the number of expected peaks For NCOEF 0 no prediction is done Linear prediction also depends on the parameters ME_mod LPBIN and TDoff NOISF1 low field left limit of the noise region used in 1D datasets takes a float value ppm interpreted by sino The noise in the region between NOISF1 and NOISF2 is calculated according to the algorithm described for the command sino NOISF2 high field right limit of the noise region used in 1D datasets takes a float value ppm interpreted by sino The noise in the region between NOISF1 and NOISF2 is calculated according to the algorithm described for the command sino NSP number of data points shifted during right shift or left shift P 30 TOPSPIN parameters used in 1D datasets takes a positive integer value default is 1 interpreted by 1s and rs NSP points are discarded from one end and NSP zeroes are added to the other end of the spectrum NZP number of data points set to zero intensity used in 1D datasets takes a positive integer value default is 0 interpreted by zp zp sets the intensity of the fi
317. lude the EA direction For example to process F2 F3 plane 17 of a 3D dataset which is EA in F1 enter xfb eao s23 17 2 y If you omit the eao option the plane is still processed but no EA cal culation is done Using the eao option allows you to determine the cor rect phase values for EA data or compare the processed plane with a plane extracted from a 3D processed data Note that if the processed plane includes the EA direction or if the 3D data are not EA in any di rection the option eao has no effect When executed on a dataset with 3D raw data but 2D processed da ta xfb takes one argument P 242 1 Usually a result of a previous 2D processing command on that 3D dataset 2D processing commands xfb lt plane gt process the specified plane and store it under the current procno xfb same process the same plane as the previous processing command and store it under the current procno The same option is automatically used by the AU program macro XFB When used on a regular 2D da taset i e with 2D raw data it has no effect INPUT PARAMETERS F2 and F1 parameters set from the ftf dialog box with edp or by typing be_mod bcfw etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction
318. m Execute Macro Start Text Editor Figure 11 9 This dialog box has various options each of which selects a certain com mand for execution Open the file explorer This option selects the command exp for execution It opens the File Explorer showing the processed data files the files in the procno di rectory of the active dataset Under Linux the KDE konqueror will be opened If no dataset is open in the TOPSPIN data area the Explorer will show the users home directory exp1 allows you access to the current data files as well as the entire data directory tree An alternative way to access data files is to right click inside the data window and select Files in the appearing popup menu P 524 Automation Open Command Prompt Shell This option selects the command she11 for execution It opens a Win dows COmmand Prompt or Linux Shell depending on your operating system Serial Processing This option selects the command serial for execution It opens a di alog window where you can set up and start data processing of a se ries of datasets using TOPSPIN Commands macros or Python programs Execute an AU program This option selects the command xau for execution It opens the AU dialog box showing a list of available AU program Here you can select an AU program and click Execute to execute it xau can also be en tered on the command line in which case you can specify the AU pro gram as an argument Execute
319. m FTSIZE Fourier transform size TDeff number of raw data points that were used for processing TDoff first point of the FID used for processing default 0 XDIM subcube size FT_mod Fourier transform mode F3 parameters can be viewed with dpp or by typing s ymax _p etc YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data P 273 3D processing commands F2 and F1 parameters can be viewed with dpp or by typing s mc2 MC2 Fourier transform mode INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data acqus F3 acquisition status parameters acqu2s F2 acquisition status parameters acqu3s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc F3 processing parameters proc2 F2 processing parameters proc3 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data 3rri real imaginary processed data for AQSEQ 321 FnMODE QF 3rir real imaginary processed data for AQSEQ 312 FnMODE QF 3iii imaginary processed data for FNMODE QF procs F3 processing status parameters proc2s F2 processing status parameters proc3s F1 pr
320. m however is the processing parameter FT_mod type dpp FT_mod no no FT was done and the data are still in the time domain e FT_mod f FT was done and the data are in the frequency domain FT_mod i FT and IFT was done and the data are again in the time domain P 5 Introduction 1 5 About raw and processed data 1 5 1 1 5 2 P 6 The result of an acquisition are raw data Raw data are data which have not been processed in any way They are stored in lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data ser 2D or 3D raw data The result of processing are processed data They are stored in lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D processed data 2rr 2ir 2ri 2ii 2D processed data 3rrr 3irr 3rir 3rri 3D processed data Concerning their input data processing commands can be divided into commands which only work on raw data commands which only work on processed data commands which work on raw or processed data Commands that only work on raw data The following commands only work on raw data If no raw data exist they stop with an error message e 1D commands be trf addfid convdta e 2D commands xtrf xtrf2 addser convdta 3D commands tf3 convdta Commands that work on raw data or processed data The following processing commands work on raw or processed 1D data em gm sinm qsin sinc qsi
321. m used_ from data path of the source 2D data and the column no auditp txt processing audit trail If the output procno is specified lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i 1D spectrum used_from data path of the source 2D data and the column no P 184 2D processing commands auditp txt processing audit trail USAGE IN AU PROGRAMS RSC column procno If procno 1 the column is written to the dataset TEMP SEE ALSO rtr rsr wsr wsc rser rser2d wser wserp slice P 185 2D processing commands P 186 rser NAME rser Read row from 2D raw data and store as 1D FID 2D 1D SYNTAX rser lt row gt lt expno gt n DESCRIPTION The command rser reads a row from 2D or 3D raw data a series of FIDs and stores it as a 1D dataset It opens a dialog box where you can specify the FID number and the expno of the output data FID EXPNO 999 Figure 4 14 For 2D data the row must be specified as a number between 1 and F1 TD The latter is the F1 acquisition status parameter TD that can be viewed with s td rser is normally entered on the 2D dataset It then takes up to three ar guments and can be used as follows rser prompts for the row number and stores it under data name TEMP rser lt row gt stores the specified row under data name TEMP rser lt row gt lt expno gt stores the specified row under the current data name
322. m plane in F1 F3 This option selects the command r13 for execution It reads an F1 F3 plane from a 3D dataset and stores it as a 2D dataset see Table 5 4 Extract an orthogonal spectrum plane in F2 F3 This option selects the command r23 for execution It reads an F2 F3 plane from a 3D dataset and stores it as a 2D dataset see Table 5 5 3D processing commands 3D data processed 3D input data 2D output data with F3 F2 F3 F2 F1 tf3 realtima FID FID FID FID g tf3 tf2 real realtima FID realtima FID g g tf3 tf2 tf1 real real realtima_ real realtima g g tf3 tf1 tf2 real realtima real realtima real g g Table 5 3 r12 input output data 3D data processed 3D input data 2D output data with F3 F2 F1 F2 F1 tf3 realtima FID FID realtima FID g g tf3 tf2 real realtima FID real FID g tf3 tf2 tf1 real real realtima_ real realtima g g tf3 tf1 tf2 real realtima real real real g Table 5 4 r13 input output data P 279 3D processing commands 3D data processed 3D input data 2D output data with F3 F2 F1 F2 F1 tf3 realtima FID FID realtima FID g g tf3 tf2 real realtima FID real realtima g g tf3 tf2 tf1 real real realtima_ real real g tf3 tf1 tf2 real realtima real real realtima g g Table 5 5 r23 input output data The parameters required by r12
323. macro which takes a TOPSPIN command as argument Examples are XCMD edp XCMD setdef ackn no AU programs can be set up with the command edau Most TOPSPIN commands can also be used in a TOPSPIN macro see edmac or Python program see edpy Introduction 1 8 Clicking commands from the TOPSPIN menu This manuals describes all processing commands as they can be entered on the command line However they can also be clicked from the TOPSPIN popup menus Most commands can be found under the Processing or Anal ysis menu The corresponding command line commands are specified in square brackets or appear on right clicking the menu item 1 9 Userspecific handling of Source Directories 1 9 1 Source Directory Handling Introduction The following paragraphe describes the fundamental handling how Top Spin 2 1 and newer is searching for information like pulse programs pa rameter sets AU programs lists like VD list and files like intrng files see listing below paragraphe 1 9 3 The information where to find these files is stored in the definition of Source Directories in TopSpin There each TopSpin user can add remove directories and change the order of direc tories The order of the directories defines the priority for TooSpin when searching for a file This function is complemented now with the function called Manage Source Directories There all user preferences regarding Directory Han dling can be defined and are keeped
324. mand you must select the desired region and perform peak picking Command pp Then enter the command dcon or dcon2d to open the dialog box see Figure 4 5 amp Deconvolution 2D dcon2d Options Use Gaussian shape Use mixed shape View fitted parameters of the last deconvolution O View calculated spectrum of the last deconvolution Required parameters Destination PROCNO for fitted data 1000 O Save individual peak lineshapes Marquardt stop criteria Optimization O Memory Speed Figure 4 5 2D processing commands This offers several options each of which selects a certain command for execution Use Lorentzian shape This option deconvolves the spectrum by fitting a Lorentzian function to the peaks It is typically used for overlapping peaks with a Lorentz ian lineshape to determine the ratio of each individual peak Use Gaussian shape This option deconvolves the spectrum by fitting a Gaussian function to the peaks It is typically used for overlapping peaks with a Gaussian lineshape to determine the ratio of each individual peak Use mixed shape This option deconvolves the spectrum by fitting a mixed Lorentz ian Gaussian function to the peaks It requires the parameter Gaus sian percentage for mixed shape to be set A mixed shape deconvolution is typically used for spectra which cannot be approxi mated by a pure Lorentzian or a pure Gaussian lineshape View fitted parameters of the last deco
325. mmand 419 delete 1D processed data 423 1D raw data 423 2D processed data 423 2D raw data 423 imaginary data 423 integral lists 468 processed data 419 raw data 419 delete command 419 423 delf command 423 deli command 250 423 delmac 486 delmisc command 468 delp command 419 delpul 486 delpy 486 dels command 423 delser command 423 detection mode 23 29 69 88 133 255 diagonal line in 2D 195 plane in 3D 282 digital filtering 24 acquisition 8 processing 81 digitally filtered data 8 25 33 87 231 270 290 dimensionality 490 491 dimensionality of data 43 dir command 427 dir2d command 430 dira command 427 dirdat command 427 dirf command 430 dirp command 427 dirs command 430 dirser command 430 disco projection 160 161 disk space 231 270 291 disk unit 457 Display button 437 display found dataset 437 div command 106 docs 576 dosy2d command 159 dosy3d command 266 dpl command 354 dpp command 462 dt command 74 duadd command 56 E edau command 8 444 512 edc2 command 433 edcpd 478 edcpd command 444 eddosy command 464 edgp command 444 edlev command 352 edlist command 444 466 edmac 478 edmisc command 444 468 edp command 475 edpar command 493 edpul command 444 478 edpy 478 edpy command 444 edshape command 471 edstruc command 376 edtext command 577 edti command 359 edtix command 360 ef command 75 efp command 75 em command 75 77 86 135 equidistant sequence of levels 353 esign comm
326. mming INPUT OUTPUT FILES lt tshome gt exp stan nmr au src AU program source files A tshome gt prog au bin AU program executable binary files SEE ALSO expinstall compileall cpluser Automation intser NAME intser integrate a list of spectra 1D 2D DESCRIPTION The command intser integrates a series of 1D or 2D data It starts by opening opens the dialog window shown in Figure 11 6 Intser Processing Define Datasets Please define the full path name of the dataset list to be processed Click on gt Browse For List locate an existing dataset list gt Find Datasets search for datasets and use the selected ones as the list gt Edit List edit the current or a new dataset list gt Next continue with command definition F DOCUME 1 WOSVAN 1 LOCALS 1 Tempidatasets_25379 txt Figure 11 6 Here you can specify find or edit the list of datasets to be processed The functions of the buttons are described in the dialog A dataset list is a list of full pathnames e g C bio data guest nmr examld_13C 1 pdata 1 C bio data guest nmr examld_13C 2 pdata 1 C bio data guest nmr examld_13C 3 pdata 1 The first dataset in the list serves as reference dataset Its PROCNO direc tory must contain an int rng file with the spectral regions to be integrated This file is created by automatic integration command abs or by interac tive integration command int
327. mpiles all Bruker and User AU programs In order to compile Bruker AU programs these must have been installed This can be done with the command expinsta11 with the option In stall Bruker library AU programs enabled For more information on AU programs please refer to the AU reference manual INPUT FILES lt tshome gt exp stan nmr au src AU programs source files OUTPUT FILES lt tshome gt prog au bin AU programs executable files SEE ALSO expinstall cplbruk cpluser edau xau xaua xaup delau P 507 Automation cplbruk cpluser NAME cplbruk Compile Bruker AU programs cpluser Compile user defined AU programs SYNTAX cplbruk lt name gt all cpluser lt name gt all DESCRIPTION The command cplbruk allows you to compile one or more Bruker AU programs Before you can use it the command expinsta11 must have been executed once with the option Install Bruker library AU programs enabled Then you can use cplbruk in three different ways cplbruk lt name gt compile the Bruker AU program lt name gt cplbruk all compile all Bruker AU programs cplbruk lists Bruker AU programs double click one to compile it If you specify an argument then it may contain wildcards for example cplbruk a compiles all Bruker AU programs which start with a cpluser works like cplbruk except that it compiles user defined AU programs For more information on AU programs please refer to the AU re
328. n The xtrfp commands can for example be used to perform multiple additive baseline corrections This can be necessary if the raw data con tain multiple frequency baseline distortions You cannot do this with xfb or xtrf because these commands always work on the raw data i e they are not additive xtrfp xtrfp2 and xtrfp1 can also be used for inverse Fourier trans form To do that 1 Type dpp to check the status FT_mod 2 Type edp to set the processing parameters set BC_mod WDW ME_mod and PH_mod to no and FT_mod to the inverse equiva lent of the status FT_mod 3 Perform xtrfp xtrfp2 or xtrfp1 An alternative way to do an inverse Fourier transform is the usages of the commands xif2 and xif1 INPUT PARAMETERS F2 and F1 parameters P 259 2D processing commands set by the user with edp or by typing be_mod bcfw etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for
329. n F2 diff algorithm 2D abst1 Autom selective baseline correction in F1 2D abst2 Autom selective baseline correction in F2 2D accumulate Add two datasets ppm Hz wise 1D add Add two datasets point wise multiply 2nd with DC 1D add2d Add or subtract two datasets 2D addc Add the constant DC to the current dataset 1D addfid Add two FIDs multiply 2nd with DC 1D addser Add two raw datasets 2D adsu Open the add subtract command dialog apk Automatic phase correction 1D apkO Zero order automatic phase correction 1D apkOf Customized zero order autom phase correction 1D apk1 First order automatic phase correction 1D apkf Automatic phase correction using absF1 2 region 1D apks Automatic phase correction special algorithm 1D na JiK LIM N O P Q R S T U VIW X Y 2 lsinc Sinc window multiplication of the FID 1D sinm Sine window multiplication of the FID 1D sino Calculate signal to noise ratio 1D slice Open the slice plane command dialog 2D 3D smail Send the current dataset by Email 1D 2D 3D sola Switch to solids lineshape analysis mode spdisp Symbolic graphical pulse program display sref Calibrate spectrum set TMS signal to 0 ppm 1D 2D st Generate manipulate and analyse RF shapes and gradient stdisp Shape Tool to generate manipulate analyze shapes stop Stop the acquisition immediately sub1 Subtract 1D data from 2D data columns
330. nal to the plane axis orien tation lt procno gt destination 3D procno source 3D procno if wp1 is entered on the destination 2D dataset lt inmem gt optional argument for usage in AU programs only improves performance by data caching Caution nD data must not be modified by any command other than wp1 between two consec utive rpl inmem or wpl inmem commands P 341 nD processing commands P 342 do not write imaginary data Only the real data plane is written to the real destination data This option prevents wp1 to abort when nD destination data exist but 2D source data do not Caution this options makes the nD imaginary data inconsis tent wp can be entered on the 2D source dataset or on the destination 3D dataset The number of required arguments is different see below wp1 entered on the source 2D dataset In this case wp1 prompts the user for two arguments only the plane number and the 3D destination procno The plane axis orientation is taken from the 2D dataset used_fromfile The two arguments can also be specified on the command line If however you specify three argu ments the plane axis orientation is taken from the first argument rather than from the 2D dataset Examples wpl prompt the user for the plane number and destination 3D procno take the plane axis orientation from the current 2D dataset and write the plane accordingly wpl 11 1 write the current 2D data to plane 11 of the 3D
331. nc tm traf trafs ft ef gf efp gfp They work on raw data if one of the following is true no processed data exist file 1r and or 1i do not exist processed data exist but they are already Fourier transformed Introduction They work on processed data if the following is true e processed data exist but they are not Fourier transformed add addc and div filt 1s mul mulc or rs rv xor zf zp They work on raw data if the parameter DATMOD raw They work on processed data if the parameter DATMOD processed The following processing commands work on raw or processed 2D data xfb xf2 xf1 They work on raw data if one of the following is true e the option raw is added e g xfb raw no processed data i e the file 2rr exist e the processing status parameter files procs or proc2s do not exist or are not readable e for x 2 data are already Fourier transformed in F2 for xf1 data are already Fourier transformed in F1 e for xfb data are already Fourier transformed in both F2 and F1 e the processing status parameter PH_mod is set to ps power spectrum or mc magnitude spectrum in F2 and or F1 They work on processed data if one of the following is true e the option proc is used e g xfb proc e none of the conditions for using raw data is fulfilled 1 5 3 Commands that always work on processed data Several processing commands can by definition only work on processed data If no processed data exist they s
332. ncy dependent OUTPUT PARAMETERS can be viewed with dpp or by typing s phcO s phc1 etc PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value frequency dependent INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt P 111 1D Processing commands P 112 fid raw data input if no processed data exist lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if they exist proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS PK SEE ALSO mc ps apk trf trfp 1D Processing commands prguide NAME prguide Open the Processing Guide 1D 2D DESCRIPTION The command prguide opens the TOPSPIN Processing Guide see Fig ure 3 14 This contains a workflow for processing data especially suited for new or occasional users In Automatic mode the Processing Guide will simply execute a processing command when you click the corresponding button This requires the processing parameters to be set correctly In in teractive mode Automatic mode unchecked the Processing Guide will at each step open a dialog box offering you the available options and re quired param
333. nd F1 can be viewed with dpp or by typing s si s stsi etc SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points that were used for processing TDoff first point of the FID used for processing default 0 XDIM subcube size P 293 3D processing commands P 294 F3 parameters can be viewed with dpp or by typing s si s tdeff etc FTSIZE Fourier transform size FT_mod Fourier transform mode YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data F2 and F1 parameters can be viewed with dpp or by typing s mc2 etc MC2 Fourier transform mode INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser raw data acqus F3 acquisition status parameters acqu2s F2 acquisition status parameters acqu3s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc F3 processing parameters proc2 F2 processing parameters proc3 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data 3irr real imaginary processed data for FnMODE
334. nd F1 processing status parameter XDIM and can be viewed with dpp Predefining subcube sizes is for example used to read the processed data with third party software which can not interpret the processing status parameter XDIM big little t3d stores the data in the data storage order of the computer it runs on e g little endian on Windows PCs Note that TOPSPIN s predeces sor XWIN NMR on SGI UNIX workstations stores data in big endian The storage order is stored in the processing status parameter BYTORDP type s bytordp If however you want to read the processed data with third party software which can not interpret this parameter you can use the big little option to predefine the storage order p lt du gt the option p allows you to store the processed data on a different top level data directory typically a different disk The rest of the data di rectory path is the same as that of the raw data If the specified top level directory does not exist it will be created Normally t3d stores the entire spectral region as determined by the spectral width However you can do a so called strip transform which means that only a certain region of the spectrum is stored This can be done by setting the parameters STSR and STSI which represent the strip start and strip size respectively They both can take a value between 0 and SI The values which are actually used can be a little different STSI is always rounded to the next highe
335. nds in the sense that they manipulate the data The manual however also includes several commands that ana lyse data or send information to the screen or printer 1 2 Conventions Font conventions abs commands to be entered on the command line are in courier bold italic ProcPars commands to be clicked are in times bold italic fid filenames are in courier name any name which is not a filename is in times italic Introduction File directory conventions lt tshome gt the TOPSPIN home directory default C Bruker topspin under Windows and opt topspin under LINUX lt userhome gt the user home directory Header conventions SYNTAX only included if the command described requires arguments USED IN AU PROGRAMS only included if an AU macro exist for the command described 1 3 About directions TOPSPIN Can process data up to 8 dimension TOPSPIN 2 1 has been tested for data up to dimension 6 The directions of a dataset are indicated with the terms F6 F5 F4 F3 F2 and F1 which are used as follows 1D data F1 first and only direction 2D data F2 first direction acquisition or direct direction F1 second direction indirect direction Commands like xf2 and abs2 work in the F2 direction xf1 abs1 etc work in F1 xfb xtrf etc work in both F2 and F1 3D data F3 first direction acquisition or direct direction F2 second direction indirect direction F1 third direction indirect direct
336. ne or from the browse dia log box see Figure 9 4 The commands dirf dirs dirser and dir2d display a list of data sets This list only includes datasets which contain certain data files As opposed to commands like dir and dira they do not show empty da tasets You can mark one or more datasets in the list and click e Display to display the data in the current data window or Display in new window to display the data in a new data window When multiple entries were marked the will be shown in one data win dow in multi display mode 1D raw data This option selects the command dirf for execution It lists 1D data sets which contain raw data showing a separate entry for each exper iment number expo Each entry shows the dataset NAME EXPNO ACQU DATA and SIZE 1D processed data Dataset handling EN dirf Browse Options An entire data set with all EXPNOs PROCNOs Acquisition data oO Processed data O Data acquired at certain dates O 1D processed data r i 2D 8D raw data ser 2D processed data 2rr 2ii Required parameters Name z Data directory C Bio User Figure 9 4 This option selects the command dirs for execution It lists 1D data sets which contain processed data showing a separate entry for each processed data number procno Each entry shows the dataset NAME EXPNO PROCNO PROC DATA and SIZE 2D 3D raw data This option selects the command dirser for exec
337. ng the 2D dataset and store the phase values to 3D tf2p works like t 3p except that it works in the F2 direction applying the F2 parameters PHCO and PHC1 These can be determined on a 2D plane extracted with r23 or r12 tf1p works like t 3p except that it works in the F1 direction applying the F1 parameters PHCO and PHC1 These can be determined on a 2D plane extracted with r13 or r12 tf3p can only be done e directly after 3 not after t 2 or tf 1 e ifthe F3 imaginary data exist Note that the command t 3 n does not store the imaginary data You can however create them data from the real data with a Hilbert trans form command tht3 Phase correction is already done as a part of the commands t 3 t 2 and tf1 if PH_mod pk and PHCO and PHC1 are set INPUT PARAMETERS set by the user with edp or by typing phcO phci etc PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value frequency dependent P 306 3D processing commands OUTPUT PARAMETERS can be viewed with dpp or by typing s phcO s phc1 etc PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value frequency dependent INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data 3irr F3 imaginary processed data input of t 3p 3rir F2 imaginary processed data input of
338. nly PKNL Yes y OK Cancel Help Figure 3 7 This dialog box offers two options both of which select the t command P 85 1D Processing commands P 86 for execution Standard Fourier transform This option only allows you to set the parameter SI the size of the real spectrum Advanced Fourier transform This option allows you to set all FT related parameters Fourier transform is the main step in processing NMR data The time do main data FID which are created by acquisition are transformed into fre quency domain data spectrum Usually Fourier transform is preceded by other processing steps like FID baseline correction bc and window multiplication em gm etc and followed by steps like phase correction apk and spectrum baseline correction abs The size of the resulting spectrum is determined by the parameter SI An FID of TD time domain points is transformed to a spectrum of SI real and SI imaginary data points A typical value for SI is TD 2 In that case all points of the FID are used by the Fourier transform and no zero filling is done The size of the spectrum and the number of FID points which are used can be determined in the following ways e Sl gt TD 2 the FID is zero filled e SI lt TD 2 only the first 2 SI points of the FID are used e 0 lt TDeff lt TD only the first TDeff points of the FID are used In the latter two cases the spectrum will contain less information then the F
339. no gt pdata lt procno gt 1r real processed 1D data procs processing status parameters P 72 1D Processing commands auditp txt processing audit trail USAGE IN AU PROGRAMS BCM SEE ALSO bas sab basl P 73 1D Processing commands P 74 dt NAME dt Calculate the first derivative of the data 1D DESCRIPTION The command dt calculates the first derivative of the current dataset Depending on the value of DATMOD dt works on the raw or on the proc essed data INPUT PARAMETERS set by the user with edp or by typing datmod DATMOD data mode work on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if DATMOD proc proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS DT 1D Processing commands ef efp NAME ef Exponential window multiplication Fourier transform 1D efp Exponential window multiplication FT phase correction 1D DESCRIPTION The composite processing command ef is a combination of em and ft i e it performs an exponential window
340. ns 1D real processed data li imaginary processed 1D data if input file contains 1D imaginary data proc processing parameters procs processing status parameters For 2D data lt dir gt data lt user gt nmr lt name gt lt expno gt P 546 Conversion commands ser 2D raw data input if Output Data raw acqu F2 acquisition parameters acqu2 F1 acquisition parameters acqus F2 acquisition status parameters acqu2s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data if input file contains 2D real processed data proc F2 processing parameters proc2 F1 processing parameters procs F2 processing status parameters proc2s F1 processing status parameters clevels 2D contour levels For 3D data the additional parameter files acqu3 acqu3s proc3 and proc3s will be created SEE ALSO tozip tojdx totxt fromjdx P 547 Conversion commands jconv NAME jconv Convert Jeol type data to Bruker ToPSPIN data 1D 2D 3D DESCRIPTION The command jconv converts Jeol raw data to TOPSPIN format It opens a dialog window where you can navigate to the Jeol input data file Just select the desired file and click JNMR data conversion This will open the dialog box shown in Figure 12 4 EN jconv The selected Jeol data will be converted Define destination dataset JNMR name C biot jeolalpha50
341. ns dialog box 2D 3D DESCRIPTION The disco projection commands open the projections dialog box see Figure 4 6 selecting the corresponding command BN f2disco Options Calculate positive projection oO Calculate negative projection Calculate sum Calculate disco sum O Read positive projection O Read negative projection oO Update rows cols from display Required parameters Projection sum of Display projection First rowicol 1 Last row col 10 Destination PROCNO 999 Disco reference colrow 1 Figure 4 6 This dialog box has several options each of which selects a certain com mand for execution P 160 2D processing commands Calculate disco sum of rows This option selects the command 2disco for execution Like 2sum it calculates the sum of all rows between firstrow and lastrow However for each row the intensity at the intersection with the reference col umn is determined If this intensity is positive the row is added to the total If it is negative the row is subtracted from the total Calculate disco sum of columns This option selects the command 1disco for execution It works like 2disco except that it calculates the sum of the specified columns considering the intensities at the intersections with a reference row The calculated disco sum is stored under the specified Destination procno The Required parameter Display projection can be set to on 2D to
342. nse You can avoid that by converting the raw data with convdta before you process them 6 0 lt STSR lt SI only the processed data between STSR and STSR STSI are stored if STSI 0 STSR is ignored and SI points are stored 7 0 lt STSI lt SI only the processed data between STSR and STSR STSI are stored Note that only in the first case the processed data contain the total infor mation of the raw data In all other cases information is lost Before you run t 3 you must set the processing parameter SI in all three directions F3 F2 and F1 The commandt 2 does not evaluate the F2 processing parameter SI it evaluates the processing status parameter SI as it was set by t 3 t 3 evaluates the acquisition status parameter AQSEQ This parameter defines the storage order of the raw data 3 2 1 or 3 1 2 For processed data F2 and F1 are always the second and third direction respectively For raw data this order can be the same or reversed as expressed by AQSEQ tf3 evaluates the processing parameter FCOR The first point of the FIDs is multiplied with the value of FCOR which lies between 0 0 and 2 0 For digitally filtered Avance data FCOR has no effect in F3 because the first point is part of the group delay and as such is zero In that case it only plays a role in the F2 and F1 direction see t 2 and t 1 However on A X data or Avance data measured with DIGMOD analog there is no group delay and FCOR also plays
343. nsform mode in the processing status parameter FT_mod Phase correction of the F3 frequency domain data Each row is phase corrected according to PH_mod This parame ter takes the value no pk mc or ps For PH_mod pk t 3 applies the values of PHCO and PHC1 This is only useful if the phase val ues are known You can determine them by typing x b on the 3D data to process a 23 or 13 plane do a phase correction on the resulting the 2D dataset and store the phase values to 3D More details on PH_mod can be found in chapter 2 4 The size of the processed data is determined by the processing param eter SI SI real and SI imaginary points are created A typical value for SI is TD 2 in which case all raw data points are used and no zero filling is done In fact several parameters control the number of input and output data points for example 1 SI gt TD 2 the raw data are zero filled before the Fourier transform 2 SI lt TD 2 only the first 2 SI raw data points are used 3 4 0 lt TDoff lt TD the first TDoff raw data points are cut off and TDoff 0 lt TDeff lt TD only the first TDeff raw data points are used zeroes are appended at the end TDoff lt 0 TDoff zeroes are prepended at the beginning Note that e for SI lt TD TDoff 2 raw data are cut off at the end P 289 3D processing commands P 290 for DIGMOD digital the zeroes would be prepended to the group delay which does not make se
344. nsidered noise ALPHA correction factor P 20 used in 2D datasets in F2 and F1 TOPSPIN parameters takes a float value interpreted by ptilt ptilt1 and add2d For ptilt F2 ALPHA is the tilt factor For ptilt1 F1 ALPHA is the tilt factor They must have a value between 2 0 and 2 0 For add2d F2 ALPHA is the multiplication factor for the current dataset see also parameter GAMMA AQORDER Acquisition order used in datasets with dimensionality gt 3 takes one of the values 32 3 2 for 3D data takes one of the values 4321 43 2 4231 etc for 4D data takes etc only interpreted if AQSEQ is not set by the processing commands ftndand t 3 AQORDER describes the order in which the indirect directions have been acquired For example a 3D pulse program usually contains a double nested loop with loop counters tdi and ta2 If tdi is used in the inner loop and ta2 in the outer loop the acquisition order is 312 Otherwise it is 321 Caution the acquisition order is normally evaluated from the acquisi tion status parameter AQSEQ Only if this parameter is not set AQORDER is used ASSFAC assign the highest or second highest peak as reference for scal ing used in 1D datasets takes a float value default is 0 0 interpreted by pp lipp This parameter is interpreted as follows If ASSFAC gt 1 the second highest peak is used as reference for scal ing if the following is true 42 lt hmax ASSFAC
345. nts that were used for processing STSR strip start first output point of strip transform STSI strip size number of output points of strip transform NC_proc intensity scaling factor YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data BYTORDP data storage order INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input of trf acqus F2 acquisition status parameters P 136 1D Processing commands lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input of trfp proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS TRF TRFP SEE ALSO ftf ft bc em pk P 137 1D Processing commands zf NAME zf Zero all data points 1D DESCRIPTION The command z sets the intensity of all data points to zero Depending on the value of the parameter DATMOD zf works on raw or processed data The result is always stored as processed data the raw data are never overwritten The output of z is usually the same for DATMOD raw or processed namely SI processed data points with zero intensity However for DAT MOD proc the existing processed data are set to zero whereas for DA
346. nvolution This option shows the fitted parameters and peaks of the last per formed deconvolution on the current dataset View calculated spectrum of the last deconvolution This option shows the graphical result of the last deconvolution the original and the deconvolved spectrum in multi display mode The result of deconvolution is e The quality of the fit expressed by the minimized chi square value e alist of peaks within the selected region and for each peak its fre quency width intensity and integral This list is displayed on the screen e the fitted lineshape which is shown together with the original spectrum in multi display mode Note that the deconvolution can be optimized for memory usage or speed Furthermore you can check the option Save individual peak line shapes to store the deconvolution result for each peak in a separate proc P 157 2D processing commands no All resulting procnos are shown superimposed in multi display mode As such each deconvolved peak can be separately scaled and shifted INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data peaklist xml peak list proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata 1000 2rr deconvolved processed 2D data first individual peak dcon2dpeaks txt deconvolution parameters and peaks procs processing status parameters
347. o NAME sino Calculate signal to noise ratio 1D SYNTAX sino real noprint DESCRIPTION The command sino calculates the signal to noise ratio of a 1D spectrum according to the formula SINO maxval 2 noise where maxval is highest intensity in the signal region The signal region is determined by the processing parameters SIGF1 and SIGF2 If SIGF1 SIGF2 the signal region is defined by e the entire spectrum minus the first 16th part if the scaling region file is not defined e the regions defined in the scaling region file NUC1 SOLVENT where NUC1 and SOLVENT are acquisition status parameters Standard scaling region files can be installed with expinstal1l and can be edited with edlist scl The factor noise is calculated according to the algorithm shown in Figure 8 13 where N is the total number of points in the noise region n N 1 2 and y i is the nth point in the noise region The limits of the noise region is determined by the processing parameters NOISF1 and NOISF2 If they are equal the first 1 16th of the spectrum is used as the noise region The parameters SIGF1 SIGF2 NOISF1 and NOISF2 can be set from the command line from the Procpars tab command edp or interactively in Signal Noise display mode The latter can be entered by clicking Analysis gt Signal Noise Calculation or by entering sino on the command line P 405 Analysis commands n P n 3 i y i y i swt x oj 00
348. o Process Selected Datasets below Add Selection to dataset group Add the list of selected datasets to a dataset group You will be prompted to enter the group name The created or modified group can be accessed from the browser File properties Show main dataset parameters like Dimension Pulse program Acquisition Date Nuclei Spectrometer frequency and Solvent Files Show the files in the processed data directory of the selected dataset Process Selected Datasets Perform serial processing on the selected datasets Opens a dialog where you can change or edit the dataset list and specify the command macro or Python program to be executed starts the command serial The Close button allows you to close the search result dialog P 438 Dataset handling INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data acqu acquisition parameters acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data proc processing parameters procs processing status parameters Note that these are only the main 1D data files SEE ALSO open new re rep rew repw reb dir P 439 Dataset handling new NAME new Define a new dataset nD DESCRIPTION The command new Ctr1 n opens a dialog box in which you can define a new dataset amp New pS Prepare for a new experiment
349. ocessing command e g xfb can be viewed with dpp SW_p spectral width of the processed data used by tilt SI size of the processed data OUTPUT PARAMETERS can be viewed with dpp TILT shows whether tilt ptilt or ptilti1 was done true or false INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data P 201 2D processing commands OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS TILT PTILT PTILT1 SEE ALSO sym syma symj P 202 2D processing commands WSC NAME wsc Replace column of 2D spectrum by 1D spectrum SYNTAX wsc lt row gt lt procno gt DESCRIPTION The command wsc replaces one column of 2D processed data by 1D processed data It is normally used in combination with rsc in the follow ing way 1 Run rsc to extract column x from a 2D spectrum 2 Manipulate the resulting 1D data with 1D processing commands 3 Run wsc to replace column x of the 2D data with the manipulated 1D data wsc can be entered on the source 1D dataset or on the destination 2D dataset Examples of the usage of wsc on the source 1D dataset WSC prompts for the column of the destination 2D data which must be re placed by the current 1D data The 2D dataset is the one from which the 1D dataset was ex
350. ocessing commands F2 parameters set by the t 3 can be viewed with dpp or by typing s mc2 MC2 Fourier transform mode F1 parameters set by the acquisition can be viewed with dpa or by typing s td etc TD time domain number of raw data points OUTPUT PARAMETERS F2 parameters can be viewed with dpp or by typing s ft_mod FT_mod Fourier transform mode FTSIZE Fourier transform size F3 parameters can be viewed with dpp or by typing s ymax_p s ymin_p etc YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt acqu2s F2 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr processed 3D data Fourier transformed in F3 3iii real imaginary processed data if MC2 QF proc2 F2 processing parameters procs proc2s proc3s F3 F2 F1 processing status parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data P 299 3D processing commands P 300 3rir real imaginary data if MC2 QF 3iii real imaginary processed data if MC2 QF procs F3 processing status parameters proc2s F2 processing status parameters auditp txt processing audit trail USAGE
351. ocessing parameters 15 18 processing status parameters 15 18 462 PROCNO 524 580 proj command 160 163 167 176 projcbn command 328 projcbp command 328 projd command 173 projection disco 2D 160 negative full 2D 176 negative partial 2D 163 positive 3D 275 328 positive full 2D 176 positive partial 2D 163 projpln command 275 projplp command 275 properties of a printer 363 ps command 116 pseudo raw data 96 101 170 252 ptilt command 199 ptilt command 199 ptrace 589 pulse program edit 478 486 Q qsin command 119 qsinc command 119 qu command 520 quad spike correction 223 230 quadrature detection mode 26 69 134 255 qumulti command 521 R r12 command 277 306 12d command 282 r13 command 277 306 13d command 282 r23 command 277 306 123d command 282 raw data 5 6 8 24 41 58 rcb command 330 re command 443 446 reb command 443 449 reference column for disco projections 161 data for integral scaling 27 382 frequency 35 37 411 peak for frequency calibration 410 peak for scaling 21 33 37 388 391 row for disco projections 161 shift 411 substance 411 reg file 34 389 392 469 rel 451 reopen command 453 rep command 443 446 rep command 451 repw command 446 reset search mask 435 resolution of a screen dump 350 rev1 command 175 231 rev2 command 175 231 reverse 1D spectrum 87 125 2D spectrum 175 231 3D spectrum 270 290 298 303 flag 35 rew command 446 rhnp comman
352. ocessing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS FT3D SEE ALSO tf3 tf2 tfl P 274 3D processing commands projplp projpin sumpl NAME projplp Calculate positive projection nD projpln Calculate negative projection nD sumpl Calculate sum projection nD DESCRIPTION The commands projpl1p projpln and sump1 calculate the 2D posi tive negative and sum projection respectively When entered without ar guments they all open the same dialog see Figure 5 1 amp Projections projplp Options Calculate positive projection Calculate negative projection Calculate sum Required parameters First row col 1 Last row col 10 Destination PROCNO 999 Figure 5 1 Here you can select the desired command in the Options section and specify the plane orientation first and last row column and output PROC NO in the Parameter section The parameters can also be specified as arguments Up to 5 arguments can be used lt plane orientation gt 23 13 12 3D data 34 24 14 23 13 12 43 21 4D data P 275 3D processing commands lt first plane gt the plane included in the calculation lt last plane gt the last plane included in the calculation lt dest procno gt the procno where the 2D output data are stored n prevents the destination dataset from being displayed activated op tional Here is an example projplp 13 10
353. ockgui command 607 logoff command 609 Lorentzian broadening factor 27 deconvolution 91 156 lineshape 91 157 Ipnd command 323 Is command 102 111 macros in AU programs 8 in TOPSPIN 8 478 486 497 498 magnet field drifts 200 magnitude calculation 1D 33 83 104 407 magnitude spectrum 1D 104 2D 7 196 217 218 220 mana command 384 managuide command 386 maximum intensity in 1D peak picking 94 391 of a spectrum 46 mc command 83 104 mdcon command 91 469 minimum intensity in 1D peak picking 94 391 of a spectrum 46 miscellaneous lists 468 mixed Gaussian Lorentzian deconvolution 91 469 Mixed Lorentzian Gaussian deconvolution 156 mixed sine cosine function 120 121 most significant byte 41 mul command 106 mul2d command 150 mulc command 106 multiplication factor 1D 24 2D 21 26 first point acquisition 25 multiply two datasets 106 multiply with increment in 2D levels 353 N nbook 586 negate a dataset 106 new command 440 new dataset 101 252 440 495 536 newtop command 587 newwin command 588 nextwin command 588 nm command 106 noise region 30 405 O objects of a dataset 453 open command 443 orthogonal trace 165 177 output parameters 16 overlapping peaks 53 78 91 157 P parameter sets 461 490 501 549 561 parplot command 356 paste command 445 peak highest 34 389 second highest 21 22 391 seperation 22 l 6 sign 34 390 391 peak picking 1D 406 2D 394 3D 399 maximum
354. of the falling edge of a trapezoidal window used in 1D 2D and 3D datasets in all directions takes a float value between 0 0 and 1 0 interpreted by tm TM2 represents a fraction of the acquisition time and must be greater than TM1 WDW FID window multiplication mode used in 1D 2D and 3D datasets in all directions takes one of the values no em gm sine qsine trap user sinc qsinc traf trafs interpreted by trf xfb xf2 xf1 xtrf tf On 1D data window multiplication is usually done with commands like em gm sinm etc which do not interpret WDW These com P 39 TOPSPIN parameters mands are already specific for one type of window multiplication The values of WDW have the following meaning WDW Function Depend Specific 1D value ent command parame ters em Exponential LB em gm Gaussian GB LB gm sine Sine SSB sinm qsine Sine squared SSB qsin trap Trapezoidal TM2 TM1 tm sinc Sine SSB GB sinc qsinc Sine squared SSB GB qsinc traf Traficante JMR 71 1987 traf 237 trafs Traficante JMR 71 1987 trafs 237 Table 2 8 2 5 Processing status parameters P 40 After processing most processing status parameters have been set to the same value as the corresponding processing parameter For some processing status parameters however this is different The reason can be that e the corresponding processing parameter does not
355. og box with the appropriate options and parameters 1D Processing commands INPUT PARAMETERS set from the ftf dialog box with edp or by typing si stsr etc SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points to be used for processing FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum PKNL group delay compensation Avance or filter correction A X ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb set by the acquisition can be viewed with dpa or by typing s aq_mod etc AQ_mod acquisition mode determines the Fourier transform mode TD time domain number of raw data points BYTORDA byteorder or the raw data NC normalization constant OUTPUT PARAMETERS can be viewed with dpp or by typing s ft_mod s tdeff etc FT_mod Fourier transform mode TDeff number of raw data points that were used for processing STSR strip start first output point of strip transform STSI strip size number of output points of strip transform NC_proc intensity scaling factor YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data BYTORDP da
356. om a 3D dataset lt plane axis orientation gt 23 13 12 32 31 or 21 The digits refer to the F3 F2 and F1 axes of the 3D data Note that the order of the two digits is relevant e the first digit is the 3D axis that corresponds to the 2D F1 axis e the last digit is the 3D axis that corresponds to the 2D F2 axis This means that for the values 21 31 and 32 the axes are ex changed storing rows as columns and vice versa see below lt plane number gt 1 Sl SI is the 3D size in the direction orthogonal to the plane orientation lt procno gt destination 2D procno source 3D procno if rp1 is entered on the destination 2D dataset lt inmem gt optional argument for usage in AU programs only improves performance by data caching Caution nD data must not be modified by any command other than wp1 between two con secutive rpl inmem or wpl inmem commands n optional argument prevents the destination dataset from being displayed activated Obligatory arguments which are not specified on the command line will be prompted for P 334 nD processing commands rpl can be entered on the source 3D dataset or if it already exists on the destination 2D dataset The number of required arguments is differ ent see below rpl entered on a source 3D dataset In this case rp1 prompts the user for three arguments Alternatively these can be entered on the command line Here are some examples rpl Prompt the user
357. on SINC t Figure 3 23 where 27 SBB GB lt t lt 2r SSB 1 GB Figure 3 24 P 121 1D Processing commands and SSB and GB are processing parameters Squared sinc This window function selects the command gsinc for execution It performs a sinc squared window multiplication according to the func tion sin OSINC t Figure 3 25 where 27 SBB GB lt t lt 2r SSB 1 GB Figure 3 26 and SSB and GB are processing parameters The sin commands implicitly perform a baseline correction of the FID according to the processing parameter BC_mod Furthermore they per form linear prediction according to the parameters ME_mod NCOEF and LPBIN If you run a command like sinm from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that When executed on 2D or 3D data the sin commands take up to four arguments e g P 122 1D Processing commands sinm lt row gt lt procno gt n y process the specified row and store it under the specified procno The last two arguments are optional n prevents changing the display to the output 1D data y causes a possibly existing data to be overwritten without warning When executed on a dataset with 2D or 3D raw data but 1D processed data1 the sin commands take one argument sinm lt row gt process the specified row and store it under the current pro
358. on a 2D dataset rsrtakes up to three arguments and can be used as follows rsr lt row gt stores the specified row under data name TEMP rsr lt row gt lt procno gt stores the specified row under the current data name the current exp P 189 2D processing commands no and the specified procno It changes the display to the output 1D data rsr lt row gt lt procno gt n stores the specified row under the current data name the current exp no and the specified procno It does not change the display to the out put 1D data After rsr has read a row and the display has changed to the destination 1D dataset a subsequent rsr command can be entered on this 1D da taset This takes two arguments and can be used as follows rsr opens the dialog box where you can specify the row and procno of the 2D data rsr lt row gt reads the specified row from the 2D dataset from which the current 1D dataset was extracted rsr lt row gt lt procno gt reads the specified row from the 2D dataset that resides under the cur rent data name 1 the current expno and the specified procno Specify ing the procno allows you to read a row from a 2D dataset other than the one from which the current 1D dataset was extracted Further more the AU macro RSR requires two arguments no matter if it is used on a 1D or on a 2D dataset rsr can also be started from the dialog box that is opened with the com mand slice INPUT FILES lt dir gt
359. on of width BCFW single channel qfil Gaussian function of width BCFW quadrature Table 3 1 a Marion Ikura Bax J Magn Res 84 425 420 1989 spol qpol and sfil qfil are especially used to subtract strong signals e g a water signal at the centre of the spectrum Note that sfil gfil perform a bet ter reduction at the risk of losing valuable signal For reducing off centre signal you can set the parameter COROFFS to the offset frequency In this table s ingle stands for single detection mode and g uad for quad rature detection mode be evaluates BC_mod for the function to be sub tracted but not for the detection mode The latter is evaluated from the acquisition status parameter AQ_mod This means for example it does not matter if you set BC_mod to single or quad The same counts for the P 69 1D Processing commands values spol qpol and sfil qfil Furthermore for AQ_mod DQD no base line correction is performed for BC_mod single or quad Note that the commands trf and xtrf do evaluate the detection mode from BC_mod and perform the baseline correction for BC_mod single quad when AQ_mod DQD The command bc is automatically executed as a part of the commands em gm ft or any of the composite Fourier transform commands When executed on a 2D or 3D dataset be prompts you for the row and output procno Alternatively it can be entered with up to four arguments be lt row gt lt procno gt n y proces
360. ook txt notebook text file SEE ALSO peakw TOPSPIN Interface Processes newtop NAME newtop Open a new Topspin interface DESCRIPTION The command newtop opens a new additional TOPSPIN interface The additional interface is completely equivalent to the one it was started from Entering newtop in the second or in the initial TOPSPIN interface opens another interface etc The number of TOPSPIN interfaces is only limited by the available computer memory When single dataset is displayed in multiple TOPSPIN interfaces the dis play in each interface is completely independent from the others As such you can display different regions scalings and data objects When the dataset is re processed from one interface its display is automatical ly updated in all TOPSPIN interfaces The command exit closes the current Topspin interface Interfaces that were opened from that interface remain open Entering exit in the last open TOPSPIN interface finishes the entire TOPSPIN session The position and geometry of each TOPSPIN interface is saved and re stored after restart SEE ALSO exit newwin hist P 587 TOPSPIN Interface Processes newwin nextwin close closeall NAME newwin Open a new empty data window nextwin Select the next data window close Close the current data window closeall Close all data windows DESCRIPTION The command newwin opens a new empty data window It is equivalent to clicking
361. opriate options and parameters INPUT PARAMETERS set from the pp dialog box with edp or by typing 1p mi etc F1P low field left limit of the peak picking region in F2 and F1 F2P high field left limit of the deconvolution region F2 and F1 MI minimum relative intensity cm MAXI maximum relative intensity cm P 397 Analysis commands PC peak picking sensitivity PPDIAG diagonal gap minimum distance to spectrum diagonal PPRESOL peak picking resolution PPMPNUM maximum number of picked peaks PPIPTYP interpolation type PSIGN peak sign pos neg or both INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc F2 processing parameters including peak picking parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt procs F2 processing parameters including peak picking parame ters peaklist xml 2D peak list in XML format peak txt 2D peak list in TXT format lt userhome gt lt topspin hostname prop globals prop peak picking setup USAGE IN AU PROGRAMS PP2D SEE ALSO pp3d pps ppl pph ppj P 398 Analysis commands pp3d pp NAME pp3d Perform peak picking 3D pp Open peak picking control dialog 1D 2D 3D DESCRIPTION 3D peak picking can be started from the command line or from the peak picking dialog box The latter can be opened
362. or 3 1 2 Processed data however are always stored in the order 3 2 1 For AQSEQ 321 ft3d is equivalent to the command sequence tf3 tf2 tf1 For AQSEQ 312 it is equivalent to tf3 tf1 tf2 Note however that for magnitude or power data the processing order is inde P 269 3D processing commands P 270 pendent of AQSEQ t3d then behave as follows for F1 PH_mod mc ps t 3 t 2 tf1 is executed for F2 PH_mod mc ps tf3 tf1 tf2 is executed Note that PH_mod mc ps is only allowed in either F2 or F1 not in both and also not in F3 t3d evaluates the processing parameter FCOR The first point of the FIDs is multiplied with the value of FCOR which lies between 0 0 and 2 0 For digitally filtered Avance data FCOR has no effect in F3 because the first point is part of the group delay and as such is zero In that case it only plays a role in the F2 and F1 direction However on A X data or Avance data measured with DIGMOD analog there is no group delay and FCOR also plays a role in F3 t3d evaluates the processing parameter PKNL On A X spectrometers PKNL true causes a non linear 5th order phase correction of the raw data This corrects possible errors caused by non linear behaviour of the analog filters On Avance spectrometers PKNL must always be set to TRUE For digitally filtered data it causes t3d to handle the group de lay of the FID For analog data it has no effect t3d evaluates the processing
363. or modified by the processing command input parameters Parameters which are interpreted by processing commands These can be processing parameters set by the user Most input parameters are processing parameters e acquisition status parameters set by an acquisition command An example is parameter AQ_mod processing status parameters set by the previous processing command An example is the parameter SI set by ft and then interpreted by abs This means you cannot change the size between ft and abs output parameters Parameters which are set or modified by processing commands These can be processing status parameters Examples are FT_mod and YMAX_p set by ft Most output parameters are processing sta tus parameters processing parameters Examples are PHCO and PHC1 set by apk and SR and OFFSET set by sref Processing parameters can be set with the parameter editor edp and processing status parameters can be viewed with dpp Alternatively each parameter can be set or viewed by entering its name in lowercase letters on the command line For example the parameter SI e si setthe parameter SI e ssi view the status parameter SI The dimensionality of the dataset is automatically recognized For exam ple for a 2D dataset the following dialog box is offered Although status parameters are normally not changed by the user a com TOPSPIN parameters CT Size of real spectrum F2 F1 Sl 1024 5
364. orithm Auto correct baseline shift correction region altern algo O Correct baseline using correction result from 1D rowicolumn Required parameters F2 and F1 Apply to axis F2 F1 Degree of polynomial ABSG 0 5 Left limit for correction region ABSF1 ppm Right limit for correction region ABSF2 ppm Figure 4 1 This dialog box offers several options each of which selects a certain command for execution The command further depends on the selected P 144 2D processing commands direction Here we describe the commands for the F2 direction F2 Auto correct baseline using polynomial This option selects the command abs2 for execution It performs an automatic baseline correction in the F2 direction This means it sub tracts a polynomial from the rows of the processed 2D data The de gree of the polynomial is determined by the parameter ABSG which has a value between 0 and 5 with a default of 5 It works like abs in 1D which means it only corrects the spectral region between ABSF 1 and ABSF2 F2 Auto correct baseline shift correction region This option selects the command abst2 for execution It performs an automatic selective baseline correction in the F2 direction This means it corrects the rows of the processed 2D data It works like abs2 except for the following only the rows between F1 ABSF2 and F1 ABSF1 are corrected e the part region of each row which is corrected shifts from row to row
365. ork on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary proc processing parameters lt tshome gt exp stan nmr filt 1d digital filtering file s OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS FILT 1D Processing commands fp fmc NAME fp Fourier transform phase correction 1D fmc Fourier transform magnitude calculation 1D DESCRIPTION The composite processing command p is a combination of t and pk i e it performs a 1D Fourier transform and a phase correction fmc is a combination of ft and mc i e it performs a 1D Fourier transform and a magnitude calculation fp and fmc automatically perform an FID baseline correction according to BC_mod All composite processing commands can be found under the menu Processing More Transforms Shortcuts INPUT AND OUTPUT PARAMETERS see the commands ft pk and mc INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i
366. orward single channel real fqr forward quadrature real fsc forward single channel com plex fqc forward quadrature complex isr inverse single channel real iqr inverse quadrature real isc inverse single channel complex iqc inverse quadrature complex Table 4 8 a baseline correction is performed according to BC_mod This parameter can take the value no single quad spol qpol sfil or qfil xtrf evaluates BC_mod for the baseline correction mode e g quad qpol or qfil and for the detection mode e g single or quad spol or qpol sfil or qfil Note that xfb evaluates the acquisition status parameter AQ_mod for the detection mode More details on BC_mod can be found in chapter 2 4 when all parameters mentioned above are set to no no process ing is done but the raw data are still stored as processed data and displayed on the screen This means the raw data are converted to submatrix format files 2rr 2ir 2ri and 2ii and scaled according to the vertical resolution The intensity scaling factor is stored in the processing status parameter NC_proc and can be viewed with dpp The size of these processed data and the number of raw data points which are used are determined by the parameters SI TDeff and TDoff as described for the command xfb For example if 0 lt TDeff lt TD the processed data are trun cated This allows you to create pseudo raw data with a sm
367. ow input of tm TM2 the start of the falling edge of a trapezoidal window input of tm LB Lorentzian broadening factor input of tra set by the acquisition can be viewed with dpa or s aq AQ acquisition time input of tm INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data input if they exist but are not Fourier trans formed 1 Usually a result of rsr rsc or a previous 1D processing command on that 2D or 3D data P 131 1D Processing commands P 132 proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS TM SEE ALSO em gm sinm qsin sinc qsinc 1D Processing commands NAME trf trfp trf User defined processing of raw data 1D trfp User defined processing of processed data 1D DESCRIPTION The command trf processes the raw data performing the following steps baseline correction according to BC_mod linear prediction according to ME_mod window multiplication according to WOW Fourier transform according to FT_mod phase co
368. owner as it appears in the output file enter a charac ter string The default title is the plot title as defined with edti If no plot title is de fined the data name is taken as default The default origin and owner are taken from the acquisition status parameter files acqus If you enter an character as argument the default value will be used Here are some examples are tojdx C temp mydata dx 0 2 mytitle BRUKER guest tojdx D nmr mydata dx 0 2 mytitle tojdx 1 mytitle MYORIGIN joe tojdx F users guest mydata dx INPUT FILES For 1D and 2D data lt tshome gt prog curdir lt user gt curdat current data definition For 1D data lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data li imaginary processed 1D data proc processing status parameters P 553 Conversion commands procs processing status parameters For 2D data lt dir gt data lt user gt nmr lt name gt lt expno gt ser 2D raw data acqus F2 acquisition status parameters acqu2s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data proc F2 processing parameters proc2 F1 processing parameters procs F2 processing status parameters proc2s F1 process
369. ows cols from display Required parameters Projection sum of Display projection First rowicol 1 Last row col 10 Destination PROCNO 999 1 Figure 4 8 This dialog box has several options each of which selects a certain com mand for execution P 167 2D processing commands Calculate sum of rows This option selects the command 2sum for execution It calculates the sum of all rows within a region specified by the parameters Calculate sum of columns This option selects the command 1sum for execution It calculates the sum of all columns within a region specified by the parameters The calculated sum is stored under the specified Destination procno The Required parameter Display projection can be set to on 2D to display the calculated projection with the 2D dataset The cur rent 2D dataset remains the active dataset as 1D to display the calculated projection as a 1D dataset The active dataset changes to the destination procno The required parameters can also be specified as arguments on the com mand line As an example we use the command 2sum here f2sum lt firstrow gt prompts for astrow and stores the sum under data name TEMP f2sum lt firstrow gt lt lastrow gt stores the specified sum under data name TEMP f2sum lt firstrow gt lt lastrow gt lt procno gt stores the specified sum under the specified procno of the current data name f2sum lt firstrow gt lt la
370. p and run xfbp to apply them xfbp uses but does not change the processing parameters PHCO and PHC1 edp It does however change the corresponding processing status parameters dpp by adding the applied phase values The ph command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the ph dialog box with edp or by typing phcO phc1 PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value frequency dependent OUTPUT PARAMETERS can be viewed with dpp or by typing s phc0 s phc1 P 248 2D processing commands PHCO zero order phase correction value frequency independent PHC 1 first order phase correction value frequency dependent INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr ir 2ri 2ii processed 2D data procs F2 processing status parameters proc2s F1 processing status parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr ir 2ri 2ii processed 2D data procs F2 processing status parameters proc2s F1 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS XFBP XF2P XF1P SEE ALSO xfb xf2 xfl xtrf xtrfp xtrfp2 xtrfp1 P 249 2D processing commands xht2 xht1 NAME
371. parameters proc2s F3 processing status parameters proc3s F2 processing status parameters proc4s F1 processing status parameters For 3D data the output data file is 3r rr whereas proc4s does not exist For data of dimension n where n gt 5 output data files are named nr and ni e g 5r 5i 6r 6i etc SEE ALSO abs2 abs1 tabs3 tabs2 tabs1 P 313 nD processing commands ftnd NAME ftnd nD processing including Fourier transform 3D DESCRIPTION The command ftnd processes nD data performing fid baseline correc tion linear prediction window multiplication Fourier transform and phase correction The command automatically recognizes the data di mensionality and handles data of dimension gt 3D In TOPSPIN 2 1 ftnd has been tested by Bruker on 3D 4D 5D and 6Ddata Note that 3D data can also be processed with the conventional commands t 3 tf2 tf1 and t3d As an example ftnd is described here for a 4D dataset It takes the fol lowing three arguments e lt direction gt the direction s to be processed Allowed values are 0 all directions in the order defined by AQSEQ 4321 4312 4231 4213 4132 4123 all directions in specified order 4 3 2 or 1 F4 F3 F2 or F1 respectively e lt procno gt Output procno of the processed data Optional argument normally unused In special cases however the data cannot be processed in place and must be stored in a different procno ftnd wil
372. pear in the bas dialog box They do appear in the integration dialog box Command int Data points greater than ABSL standard deviation are considered spectral information all other points are considered noise If two peaks are more than AZFW apart they are treated independently If they are less than AZFW ppm apart they are considered to be overlapping Integral regions are ex tended at both sides by AZFE ppm If this extension causes adjacent regions to overlap the centre of the overlap is used as the limit of the two regions Only regions whose integrals are larger area than the largest integral divided by ISEN are considered abs n does not store the integral ranges It is for example used in the command sequence ef mc abs efp abs n to store the integral re gions of both positive and negative peaks The command abs only stores the regions of positive peaks Auto correct spectral range ABSF1 ABSF2 only This option selects the command absf for execution It works like abs except that it only corrects the spectral region which is deter mined by the processing parameters ABSF1 and ABSF2 Auto correct baseline alternate algorithm This option selects the command absd for execution It works like P 53 1D Processing commands abs except that it uses a different algorithm It is for example used when a small peak lies on the foot of a large peak In that case absd allows you to correct the baseline around the
373. pf Perform peak picking on full spectrum ppl Perform peak picking in predefined regions pph Perform peak picking and also show an intensity histogram ppj Perform peak picking and store peaks in JCAMP DX format pp Open the peak picking dialog box DESCRIPTION Peak picking commands can be started from the command line or from the peak picking dialog box see Figure 8 10 All peak picking commands open the dialog box with the corresponding option selected The command pp however selects the last used option Auto Pick peaks on displayed spectrum region This option selects the command pps for execution It determines all peaks within the displayed region Table 8 1 shows an example of its output Ber re FREQUENCY INTENSITY Hz PPM 648 7 3698 825 7 3995 0 17 2 6584 3687 649 7 3771 0 21 Table 8 1 The peak list is created according to several criteria which are deter mined by various parameters A data point is added to the peak list if e its intensity is higher than its two neighbouring points e its relative intensity is smaller than MAXI e its relative intensity is larger than MI P 387 Analysis commands P 388 PN Peak picking pps Options Auto Pick peaks on displayed spectrum region O Auto Pick peaks on full spectrum oO Define regions peaks manually adjust Ml MAXI Auto Pick peaks in predefined regions file peakrng O Like 1st option but peak
374. ples directory in data browser Fi Spectrum title Ane z i Shectrum cursor Setup users for TopSpin internal logindogoff and esign Spectrum parameters Automatic termination of TopSpin when idle time exceeded Printer Automatic locking of TopSpin when idle time exceeded Fonts Dialogs Icons a i O Window settings oTe Miscellaneous Sota Directory path names Tabbed pane layout Acquisition status bar Change spectral window color scheme pial Save spectral window colors as a new color scheme BSMS display Lock display Background color Figure 13 13 In the left part of the dialog window you find various cathegories of ob jects Click the cathegory of which you want to view change certain ob jects It will become highlighted and the corresponding objects will be displayed at the right part of the dialog box Some objects can be changed by entering a value others can be changed by clicking the Change button to the right of the object entry INPUT AND OUTPUT FILE lt home gt topspin lt hostname gt prop P 592 TOPSPIN Interface Processes globals prop ascii file containing User Interface settings view prop colors fonts etc where lt home gt is the users home directory lt hostname gt is the hostname of the computer P 593 TOPSPIN Interface Processes setdef NAME setdef Switch error message acknowledgment on off DESCRIPTION The command setdef is mainly used to switch the error message ac knowledgement fun
375. proc TOPSPIN processing parameters procs TOPSPIN processing status parameters jnm original Jeol parameter file For 2D and 3D data the raw data are stored in the file ser and the addi tional parameter files acqu2 s acqu3 s proc2 s and proc3 s are created USAGE IN AU PROGRAMS JCONV jname uxname uxexp uxdisk uxuser SEE ALSO vconv fconv conv winconv convdta P 550 Conversion commands tojdx NAME tojdx Convert dataset to JCAMP DX format 1D 2D DESCRIPTION The command todjx converts a TOPSPIN dataset to JCAMP DX format JCAMP DX is a standard ascii exchange format for spectroscopic data When tojdx is entered without argument it will open a dialog box tojdx Please specify destination Name of archive file examid_13C dx Directory of archive file Crdata_jdx Type of archive file JCAMP DIFF DUP k Include these data types RSPEC ISPEC v JCAMP version 6 0 Figure 12 5 in which you can enter the required information This includes Name of the archive file The filename should have the extension ax This allows you to open it in TOPSPIN with drop amp drag Default is the dataset name with the ex tension dx Directory of the archive file Any directory Default is the users home directory Type of archive file For JCAMP format you can choose between the following archive P 551 Conversion commands P 552 types e FIX 0 table format e PACK
376. r real processed data input if it exists but is not processed in F1 2ir second quadrant imaginary processed data input if FAMODE QF 2ii second quadrant imaginary processed data input if FAMODE QF proc F2 processing parameters proc2 F1 processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed data 2ir third quadrant imaginary processed data output if FNMODE QF 2ii fourth quadrant imaginary processed data output if FAMODE QF 2ii second quadrant imaginary processed data output if FNMODE QF procs F2 processing status parameters proc2s F1 processing status parameters P 215 2D processing commands P 216 auditp txt processing audit trail USAGE IN AU PROGRAMS XF1 SEE ALSO xf2 xfb xtrf xtrfp1 2D processing commands xfbm xf2m xf1m ph NAME xfom Calculate magnitude spectrum in F2 and F1 2D xf2m Calculate magnitude spectrum in F2 2D xf1m Calculate magnitude spectrum in F1 2D ph Open phase correction dialog box 1D 2D DESCRIPTION The magnitude spectrum commands can be started from the command line or from the phase correction dialog box The latter is started with the command ph Phase correction xfbm Options Manual phasing O Additive phasing using PHCOM Power spectrum Required parameters Apply to axis F2 F1 Figure 4 21 This dialo
377. r LPbc LPmifr or LPmifc Usu ally ME_mod no which means no prediction is done Forward prediction in F2 LPfr LPfc LPmifr or LPmifc can for example be used to extend truncated FIDs Backward prediction LPbr or LPbc is not used very often in F2 Linear prediction is only per formed for NCOEF gt 0 Furthermore LPBIN and for backward prediction TDoff play a role see these parameters in chapter 2 4 3 Window multiplication of the F2 time domain data Each column is multiplied with a window function according to WDW This parameter takes the value em gm sine qsine trap user sinc qsinc traf or trafs More details on WDW can be found in chapter 2 4 4 Fourier transform of the F2 time domain data tf2 Fourier transforms each column according to the F2 process 3D processing commands ing status parameter MC2 and stores the corresponding Fourier transform mode in the processing status parameter FT_mod see table 5 7t The status MC2 has been set by the t 3 command to F2 status MC2 Fourier transform mode status FT_mod QF forward quad real fqc QSEQ forward quad real fqr TPPI forward single real fsr States forward quad complex fqc States TPPI forward single complex fsc Echo AntiEcho forward quad complex fqc Table 5 7 the value of the F2 acquisition status parameter FNMODE 1 Note that t 2 does not evaluate the processing parameter FT_mod 5 Phase
378. r and 3iii as input and output The role of MC2 is described in detail for the 2D processing command x b INPUT PARAMETERS F2 parameters set by the user with edp or by typing be_mod bcfw etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset for BC_mod spol qpol or sfil qfil ME_mod FID linear prediction mode NCOEF number of linear prediction coefficients LPBIN number of points for linear prediction TDoff number of raw data points predicted for ME_mod LPb WDW FID window multiplication mode LB Lorentzian broadening factor for WDW em or gm GB Gaussian broadening factor for WDW gm sinc or qsinc SSB Sine bell shift for WDW sine qsine sinc or qsinc TM1 TM2 limits of the trapezoidal window for WDW trap PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk PHC first order phase correction value for PH_mod pk FCOR first FID data point multiplication factor 0 0 2 0 default 0 5 REVERSE flag indicating to reverse the spectrum F3 F2 and F1 parameters set by t 3 can be viewed with dpp or by typing s si s stsi etc SI size of the processed data STSR strip start first output point of strip transform STSI strip size number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 3D pr
379. r backward prediction TDoff play a role see these parameters in chapter 2 4 3 Window multiplication of the F1 time domain data Each tube is multiplied with a window function according to WDW This parameter takes the value em gm sine qsine trap user sinc qsinc traf or trafs More details on WDW can be found in chapter 2 4 4 Fourier transform of the F1 time domain data P 301 3D processing commands Each tube is Fourier transformed according to the F1 processing F1 MC2 Fourier transform mode status FT_mod QF forward quad real fqc QSEQ forward quad real fqr TPPI forward single real fsr States forward quad complex fqc States TPPI forward single complex fsc Echo AntiEcho forward quad complex fqc Table 5 8 status parameter MC2 as shown in table 5 7 t 1 does not evalu ate the processing parameter FT_mod Instead it evaluates the F1 processing status parameter MC2 which was set by t 3 to the value of the F1 acquisition status parameter FnMODE 1 t 1 stores the corresponding Fourier transform mode as the process ing status parameter FT_mod type dpp 5 Phase correction of the F1 frequency domain data Each column is phase corrected according to PH_mod This parameter takes the value no pk mc or ps For PH_mod pk tf1 applies the values of PHCO and PHC1 This is only useful if the phase values are known You can determine them by typing xfb on th
380. r command 569 bpan command 569 570 browse command 427 430 byte order 41 232 Cc cal command 410 calibration automatic 410 default 411 interactive 31 35 37 checksum 605 chemical shift 411 412 chpwd command 602 circular shift 200 Clipboard 416 445 close command 588 closeall command 588 l 2 cmdhist 574 cmdindex 572 compileall command 507 compiling AU programs 508 515 composite processing command 19 75 83 98 111 composite pulse decoupling 478 486 contour levels 352 conv command 444 534 convdta command 536 conversion commands 533 convertpeaklist command 538 copy command 416 correction offset 23 cosine window multiplication 120 121 CPD programs 478 486 cplbruk command 508 cpluser command 508 cron command 509 current 441 D daisy command 374 daisyguide command 375 dalias command 417 data mode 24 overflow 42 232 data window close 588 current 428 430 441 geometry 596 new 428 430 588 next 588 position 596 reopen 453 swap 596 dataset dimensionality 16 directory tree 18 dosy 3D 266 hypercomplex 2D 178 inconsistent 585 status 15 dcon command 91 156 dcon2d command 156 dconpl command 91 deconvolution Gaussian 91 Lorentzian 91 mixed Gaussian Lorentzian 91 469 deconvolution 2D 156 default calibration 411 find criteria 435 printer 364 degree of the polynomial 20 53 145 148 286 312 del command 419 del2d command 423 dela command 419 delau command 512 delcpd 486 deldat co
381. r gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS XFBM XF2M XF1M SEE ALSO xf2ps xflps xfbps P 219 2D processing commands xfbps xf2ps xf1ps ph NAME xfbps Calculate power spectrum in F2 and F1 2D xf2ps Calculate power spectrum in F2 2D xf1ps Calculate power spectrum in F1 2D ph Open phase correction dialog box 1D 2D DESCRIPTION The commands xf ps calculate the magnitude spectrum They can be started from the command line or from the phase correction dialog box The latter is started with the command ph see Figure 4 25 EN Phase correction xfbps Options Manual phasing O Additive phasing using PHCOM Magnitude spectrum Required parameters Apply to axis F2 F1 Figure 4 25 This dialog box offers several options each of which selects a certain command for execution Power spectrum in F2 This option selects the command x 2ps for execution It recalculates the real and F2 imaginary data according to P 220 2D processing commands Dif sed rr rr ir Tya ri ri ii Figure 4 26 Power spectrum F1 This option selects the command xf1ps for execution It recalculates the real and F1 imaginary data according to rr rr ri ir ir i Figure 4 27 Power spectrum F2 and F1 This option selects the command xfbps for execution I
382. r multiple of 16 Furthermore when the data are stored in subcube format see below STSI is rounded to the P 271 3D processing commands P 272 next multiple of the subcube size Type dpp to check this if XDIM is smaller than SI then the data are stored in subcube format and STSI is a multiple of XDIM t3d stores the data in subcube format It automatically calculates the subcube sizes such that one row F3 of subcubes fits in the available memory Furthermore one column F2 and one tube F1 of subcubes must fit in the available memory The calculated subcube sizes are stored in the processing status parameter XDIM type dpp The alignment of the data points subcube format is the extension of the alignment in a 2D dataset as it is shown in table 4 7 The storage handling is completely transparent to the user and is only of interest when the data are interpret ed by third party software INPUT PARAMETERS F3 F2 and F1 parameters set by the acquisition can be viewed with dpa or s td TD time domain number of raw data points set by the user with edp or by typing si stsr etc SI size of the processed data STSR strip start first output point of strip transform STSI number of output points of strip transform TDeff number of raw data points to be used for processing TDoff first point of the FID used for processing default 0 BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil
383. r set DESCRIPTION The command wpar stores the parameters of the current dataset in a pa rameter set It opens a dialog box where you can select an experiment name and then click Write to store it or click Write New to store the them under a new name see Figure 10 15 The command edpar opens an ankin dialog as rpar and wpar com mand The difference to wpar and rpar is that with edpar parameter sets can be read written written new and edited whereas rpar only of fer reading possibilities for parameter sets and wpar gives the possibility to write and create button Write New parameter sets Same possi bilities as edpar offers the command delpar P Parameter Sets wpar Source Crits21 expistaninmripar aa File Options Help Search in names AL2 ND B11ZG C13APT C13CPD C13CPD32 C13DE45S5N C13DEPT134 C13DEPT135p C13DEPT45 C13GD C13HUMP C13IG C13MULT C13PPTI C13RESOL C13SENS CBCACONHGP CBCANHGP3D CBCANHGPWYG CCACONHGP2 CCACONHGP3D CCANHGP2H3D CCANHGP3D CCANHGP3D 2 CCCONHGP2H CD111ZG CD113ZG CL35ZG CL3 ZG cosys0svy COSYCWPHPS COSYDCPHWT COSYDQFPHSW OOM ES DRA Ole raiat rarat Figure 10 15 P 493 Parameters lists AU programs The following buttons are available Write Write the parameters of the current dataset to the selected param
384. r sets P Parameter Sets rpar File Options Help Source Cits 21 expistaninmripar v an C13APT C13DEPT135 C13HUMP Search in names AL27 ND C13CPDSN C13DEPT90 B11ZG C13DE455N C13G6D C13CPD C13DEPT135p C13IG C13CPD32 C13DEPT45 C13MULT C130FF C13PPTI C13RESOL C13SENS CBCACONHGP CBCACONHGP CBCANHGP3D CBCANHGPWG CCACONHGP2 CCACONHGP3D CCACONHGPS CCANHGP2H3D CCANHGP3D CCANHGP3D 2 CCCONHGP2H CCCONHGP3D Ccosy45svy CD111ZG cosys0svy CD113ZG COSYCWPHPS CL35ZG COSYDCPHWT CL37 ZG COSYDQFPHSW Figure 10 13 Here you can select a Source directory at the upper right of the dialog then select a parameter set and click Read to read it to the current data set for detailed information please refer to paragraphe 1 9 This will open the dialog shown in Figure 10 14 In this dialog you can select the file types to be read or just click OK to read all types The following buttons are available Read P 488 Parameters lists AU programs Read the parameters of the selected parameter set to the current da taset Close Close the rpar dialog Source Parameter Set C its21 expistaninmripanc1 3CPDSN Destination Data Set test 1 1 Cibio guest 1 Select the desired file types of the source parameter set 2 Press OK to copy them to the destination data set Figure 10 14
385. r transform phase correction referencing baseline correction and plotting Processing steps can be switched on or off and two parameters line broadening and plot layout can be set The command takes one argument procld y will process the current dataset without opening the dialog using the last settings SEE ALSO prguide P 115 1D Processing commands ps NAME ps Calculate power spectrum 1D DESCRIPTION The command ps calculates the power spectrum of the 1D current data set replacing the intensity of each data point i according to the formula PS i R i Mi Figure 3 16 where R and are the real and imaginary part of the spectrum respec tively If no processed input data exist ps works on the raw data The re sult is always stored as the real processed data ps can also be started from the phase correction dialog box which is opened with ph INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if no processed data exist lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt lr 1i processed 1D data real imaginary auditp txt processing audit trail P 116 1D Processing commands USAGE IN AU PROGRAMS PS SEE ALSO mc pk apk trf trfp P 117 1D Proce
386. rals which are larger area than the largest integral divided by ISEN are stored LB Lorentzian broadening factor for exponential window multiplication e used in 1D 2D and 3D datasets in all directions e takes a float value e interpreted by em gm e interpreted by trf xfb xf2 xf1 xtrf tf if WOW EM or GM LB must be positive for an exponential and negative for Gaussian window multiplication LPBIN number of points for linear prediction e used in 1D 2D and 3D datasets in all directions e takes a positive integer value interpreted by ft trf xfb xf2 xf1 xtrf tf P 27 TOPSPIN parameters P 28 e also interpreted by em gm sin tm traf For backward prediction LPBIN represents the number of input points with a maximum of TD abs TDoff The default value of LPBIN is zero which means all data points are used as input The status parameter LP BIN dpp shows how many input points were actually used For forward prediction LPBIN can be used to reduce the number of prediction output points as specified in table 2 4 Note LPBIN only has an effect in the last two cases If LPBIN is smaller than TD or greater than 2 SI this has the same effect as LPBIN 0 parameter values normal predicted l zeroes points points LPBIN 0 2 SI lt TD 2 Sl LPBIN 0 TD lt 2 SI lt 5 TD TD 2 SI TD LPBIN 0 2 TD lt 2 SI TD TD 2 SI 2 TD TD lt LPBIN lt 2 SI lt 2 TD TD LPBIN
387. resolved spectrum O Tit along rows Tit along columns Required parameters 0 Figure 4 18 This dialog box offers several options each of which selects a certain command for execution Auto tilt along rows This option selects the command tilt for execution It tilts the 2D spectrum shifting each row of the 2D spectrum by the value P 199 2D processing commands P 200 n tiltfactor nsrow 2 row The variables in this equation are defined as tiltfactor SW_p1 SI1 SW_p2 SI2 nsrow total number of rows row the row number where SW_p1 SI1 SW_p2 and SI2 represent the processing status parameters SW_p and SI in F1 and F2 respectively The upper half of the spectrum is shifted to the right the lower half to the left Furthermore this is a circular shift i e the data points which are cut off at the right edge of the spectrum are appended at the left edge and vice versa Tilt along rows This option selects the command ptilt for execution It tilts the 2D spectrum about a user defined angle by shifting the data points in the F2 direction It is typically used to correct possible magnet field drifts during long term 2D experiments The tilt factor is determined by the F2 processing parameter ALPHA which can take a value between 2 and 2 Each row of the 2D matrix is shifted by n points where n is de fined by n tiltfactor nsrow 2 row The variables in this equation are de
388. result in the current dataset You have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that The adsu command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the adsu dialog box with edp or by typing de datmod etc DC multiplication factor DATMOD data mode work on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid current raw data input of add addc if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i current processed data input of add addce if DATMOD proc 1D Processing commands proc processing parameters curdat2 definition of the second dataset lt dir2 gt data lt user2 gt nmr lt name2 gt lt expno2 gt fid second raw data input of add if DATMOD raw addfid lt dir2 gt data lt user2 gt nmr lt name2 gt lt expno2 gt pdata lt procno2 gt 1r 1i second processed data input of add if DATMOD proc OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid current raw data output of addfid audita txt acquisition audit trail output of addfid lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i current processed data output o
389. rhome gt lt mydata dx gt TOPSPIN data in JCAMP DX format lt userhome gt lt mydata bnmr zip gt TOPSPIN data in ZIP format SEE ALSO tojdx tozip P 456 Dataset handling wrpa wra wrp Wraparam wrpparam NAME wrpa Copy a dataset raw and processed data nD wra Copy raw data nD wrp Copy processed data nD wraparam Copy acquisition dataset parameters only wrpparam Copy processing dataset parameters only DESCRIPTION The command wrpa writes copies a dataset It opens a dialog box where you can specify the destination dataset EN wrpa Please specify destination data set NAME examid_13C EXPNO 1 PROCNO 1 DIR C Bio USER guest igure 9 16 When you click OK the entire expno directory is copied including raw da ta acquisition parameters processed data and processing parameters wrpa takes six arguments lt name gt the dataset name lt expno gt the experiment number lt procno gt the processed data number lt dir gt the disk unit data directory lt user gt the user y overwrite the destination dataset if it already exists All arguments are parts of the destination data path except for the last one which is a flag You can but do not have to specify all of these ar P 457 guments If the first argument is a character string it is interpreted as the destination data name If the first argument is an integer value it is inter preted a
390. riority for TopSpin when search ing for a file Please note that changes will not become effective before TopSpin re start Introduction amp Source Directories Please enter the source directories for the various types of parameter files Use 1 line per directory The order of the directories defines the priority for TopSpin when searching for a file NOTE Changes will not become effective before TopSpin restart e ABruke TOPSPIN exp staninmrlists ppiuser CABruker TOPSPIN exp staninmrilists pp Pulse Programs CABruker TOPSPIN exp stan nmrlists cpd user CABruker T OPSPIN expistan nmrvlists cpd CPD Programs C A Bruker T OPSPIN exp stan nmrilists wave user CABrukern TOPSPIN exp stan nmrilists wave Shape Files C Bruker T OPSPIN exp stan nmrilists gp user CABruken TOPSPIN exp stan nmrilists gp Gradient Files C Bruker TOPSPIN exp stan nmripariuser CABruken TOPSPIN exp stan inmripar Parameter Sets CABruker TOPSPIN exp stan nmrilists mac user CABruken TOPSPIN exp stan nmrilists imac Macras C A Bruker TOPSPIN exp stan nmripy user CABruker TOPSPIN exp stan nmripy Python Programs Qk Browse Reset Cancer Figure 1 1 1 9 6 How to define userspecific directories with commands Userspecific directories can also be configured from the corresponding reading writing and editing commands for the respective information like pulse programs parameter sets AU programs lis
391. rocess the data in F2 only s si to check the F1 size of the 2D data click Cancel s mc2 to check status MC2 QF click Cancel rvpp to store the F1 projection in TEMP and change to that dataset s si to check the size of the resulting 1D dataset click Cancel You will see that the size of the 1D data is only half the F1 size of the 2D data The reason is that rvpp unshuffles the input data file 2rr As such rvpp behaves like the command rsc If you want to prevent the unshuffling of the input data file 2 rr you can use the following trick Set the status parameter MC2 to QF before you run rvpp s mc2 click QF Then the size of the 1D data will be the same as the F1 size of the 2D data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 178 2D processing commands 1r 1D spectrum containing the projection auditp txt processing audit trail If the commands are used without arguments the files are stored in lt dir gt data lt user gt nmr TEMP 1 pdata 1 USAGE IN AU PROGRAMS RHPP procno RHNP procno RVPP procno RVNP procno For all these macros counts that if procno 1 the projection is written to the dataset TEMP SEE ALSO f2projn f2sum f2disco P 179 2D processing commands rsc NAME rsc Read
392. rocessing In F2 the data are acquired phase sensitive in F1 non phase sensitive In the example below the following parameter settings are used In F2 TD 8 Sl is 4 In F1 TD 2 Sl 2 Furthermore the following notation is used for individual data points rnem point n of FID m This point is real in F2 and complex in F1 inem point n of FID m This point is imaginary in F2 and complex P 235 2D processing commands in F1 Input F2 processing raw data F2 r c1 r2c1 i2c1 r3c1i3c1 r4c1 i4c1 Fl i1c1 r14c2 i1c2 r2c2i2c2 r3c2i3c2 r4c2 i4c2 For F2 processing r1c1 i1c1 is the first complex input point r2c1 i2c1 the second etc Output F2 processing Input F1 processing F2 rict r2c1 r3c4 r4c1 i1dc1 i2c1 i3c1 i4c1 FI r4c2 r2c2 r3c2 r4c2 i1c2 i2c2 i3c2 i4c2 2rr file ee 244 file Below the F1 input data are simply redisplayed in vertical order with the first complex input point in bold Input F1 processing F2 rict r2c1 r3c1 r4ct f Fl 2rr file r4c2 r2c2 r3c2 r4c2 i1c1 i2c1 i3c1 i4c1 i1c2 i2c2 i3c2 i4c2 2ii file P 236 2D processing commands Output F1 processing F2 rict r2c1 r3c1 r4ct FI 2rr file r4c2 r2c2 r3c2 r4c2 i1ce1 i2c1 i3c41 i4c1 ee 2ii file i1c2 i2c2 i3c2 i4c2 FnMODE QF xfb performs hypercomplex four quadrant processing Both in F2 and F1 the data are acquired phase sensitive In the example below t
393. rocessing parameter NC_ proc i e the value set by the previous processing step on this dataset raw proc xfb works on raw data if no processed data exist or if processed data exist and have been Fourier transformed in F2 and or F1 One of them is usually true i e the data have not been processed yet or they have been processed for example with x b If however the data have been processed with xtrf with FT_mod no they are not Fourier transformed and a subsequent xfb will work on the processed data The raw option causes xfb to work on the raw data no matter what The proc option causes xfb to work on the processed data If these do not exist or are Fourier transformed the command stops and dis plays an error message In other words the option proc prevents xfb to work on raw data big little xfb Stores the data in the data byte order big or little endian of the computer it runs on e g little endian on Windows PCs Note that TOP SPIN S predecessor XWIN NMR on SGI UNIX workstations stores data in big endian The byte order is stored in the processing status param eter BYTORDP which can be viewed with s bytordp The option big or little allows you to predefine the byte order This for example is used to read processed data with third party software which can not interpret BYTORDP This option is only evaluated when x b works on the raw data xdim Large 2D spectra are stored in the so called submatrix format The si
394. rogram DESCRIPTION The command xpy opens a dialog where you can select the desired Py thon Program see Figure 10 17 Please enter the complete path of your Python module Path Se MESAN LOCALS 1 Tempiexam Execute Browse Browse in data base Cancel Figure 10 17 This dialog offer the following functions Path Field where you can enter the full pathname of the Python program Click Execute to run it Browse Button to open a file browser where you can enter or select the Python program Click Execute to run it Browse in data base Button to open a dialog showing the available Python programs in the database see Figure 10 1 Just select the desired macro and click the Execute button to run it In TOPSPIN 2 0 and newer Python programs can be stored in a database xpy opens the same dialog as the cor responding commands edpy For more details see the description of this command ty Macros File Options Help Search in names 7 search Ov ner Bruker exam efapk exam_efp Figure 10 18 Python programs can also be executed from the command line by enter ing the macro name e g ExamCmd4 py or xpy ExamCmd4 py The difference is that using the xpy command searches for Python pro grams only whereas only entering just the name searches for a TOPSPIN command AU program Python program or macro of that name SEE ALSO edpy delpy xmac Parameters lists AU programs P 500
395. rogramming Manuals Python programming INPUT AND OUTPUT FILES In TopSpin 2 1 and newer the default directories for pulse programs CPD programs Macros and Python programs are listed below just like Bruker default directories lt tshome gt exp stan nmr lists pp Bruker pulse programs lt tshome gt exp stan nmr lists pp user User defined pulse programs lt tshome gt exp stan nmr lists cpd Bruker CPD programs Parameters lists AU programs lt tshome gt exp stan nmr lists cpd user User CPD programs lt tshome gt exp stan nmr lists mac Bruker TOPSPIN macros lt tshome gt exp stan nmr lists mac user User TOPSPIN macros lt tshome gt exp stan nmr py Bruker Python programs lt tshome gt exp stan nmr py user User Python programs SEE ALSO edlist delpul delcpd delpy delmac xmac xpy P 485 Parameters lists AU programs delpul delcpd delpy delmac NAME delpul Delete pulse programs delcpd Delete composite pulse decoupling CPD programs delmac Delete macros delpy Delete Python programs DESCRIPTION The commands delpul delcpd delpy and delmac open a dialog from which you can delete pulse programs CPD programs Python pro grams and macros respectively In TOPSPIN 2 0 and newer these pro grams are stored in a database The commands open the same dialog as the corresponding commands edpul edcpd etc see the descrip tion of these commands and Figure 10 12
396. rom each column retain sign O Subtract a 1D spectrum from each row Subtract a 1D spectrum from each column O Multiply with another 2D spectrum Required parameters 0 1 NAME 2nd spectrum examid_1 H EXPNO 1 PROCNO 4 USER guest DIR C Bio Figure 4 16 Subtract a 1D spectrum from each column This option selects the command sub1d1 for execution It subtracts a 1D dataset from each column of the current 2D spectrum Unlike sub1 it does not compare intensities The sub commands only work on the real data After using them the imaginary data no longer match the real data and cannot be used for phase correction If the second dataset has not been defined yet the sub commands open the add subtract adsu dialog box The adsu command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options P 193 2D processing commands and parameters INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data lt dir2 gt data lt user2 gt nmr lt name2 gt lt expno2 gt pdata lt procno2 gt 1r real processed 1D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS SUB2 SUB1 SUB1D2 SUB1D1 SEE ALSO add2d P 194 2D processing commands s
397. rom real absorption to imagi nary dispersion or vice versa Note that his only plays a role for DATMOD proc INPUT PARAMETERS set by the user with edp or by typing nsp datmod etc NSP number of points to be shifted DATMOD data mode work on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if DATMOD proc proc processing parameters P 102 1D Processing commands OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS LS RS SEE ALSO pk P 103 1D Processing commands mc NAME mc Magnitude calculation 1D DESCRIPTION The command me calculates the magnitude spectrum of a 1D dataset The intensity of each point i is replaced by its absolute value according to the formula ABS i A R i Hi Figure 3 10 where R and are the real and imaginary part of the spectrum respec tively If no processed input data exist mc works on the raw data mc can also be started from the phase correction dialog box which is opened with ph INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt
398. rpar can be used with arguments rpar lt name gt opens a dialog box where you can select individual parameter files of the parameter set lt name gt Upon clicking OK this file is copied to the current dataset rpar lt name gt acqu reads the acquisition parameters file acqu of the parameter set lt name gt to the current dataset rpar lt name gt proc reads the processing parameters file proc of the parameter set lt name gt to the current dataset rpar lt name gt acqu proc reads the acquisition and processing parameters files acqu and proc of the parameter set lt name gt to the current dataset P 489 Parameters lists AU programs P 490 e rpar lt name gt all reads all parameter files of the parameter set lt name gt to the cur rent dataset e rpar lt name gt all remove yes reads all parameter files of the parameter set lt name gt to the cur rent dataset deleting all data files and all status parameters The first argument may contain wildcards e g rpar C shows all parameter sets beginning with the letter C The remove yes argument can be used together with any other argu ment After reading a parameter set with rpar you can modify parameters of the various types with the commands e eda acqu parameters edp processing parameters Note that Bruker parameter sets contain all parameter types but user de fined parameter sets contain only those parameter types that were stored wh
399. rrection according to PH_mod trf offers the following features when all parameters mentioned above are set to no the raw data file id are simply stored as processed data files 1r 1i The even points are stored as real data file 11 and the odd points as imaginary data file 1i The size of these processed data and the number of input FID points are determined by the parameters Sl and TDeff as described for the command ft For example if 0 lt TDeff lt TD the processed data are truncated This allows you to create an FID with a smaller size than the original one see also the command genfid trf evaluates BC_mod for the baseline correction mode e g quad qpol or qfil and detection mode e g single or quad spol or qpol sfil or qfil Note that the command be evaluates the acquisi tion status parameter AQ_mod for the detection mode and ignores the BC_mod detection mode see parameter BC_mod trf evaluates WDW for the window multiplication mode em gm sine qsine trap user sinc qsinc traf or trafs This allows you to vary the window multiplication by varying the value of WDW rather than the window multiplication command This can be useful in AU programs P 133 1D Processing commands P 134 e the Fourier transform is performed according to FT_mod Nor mally the Fourier transform is done with the command ft which determines the Fourier transform mode from acquisition status parameter AQ_mod Howev
400. rs Title PulseProg Peaks Integrals Sample Structure Fid Acqu z 4 vM 2 a a Reference F Reference A Window Phase SI 32768 Size of real spec Baseline SF MHz 500 1300000 Spectrometer fre Fourier OFFSET ppm 11 008 Low field limit of Integration SR Hz oo 8 Spectrum referel Peak HZpPT Hz 0 183399 Spectral resolutic Automation F B VVindow function Miscellaneous User Phase correction PHCO degree 111 456 Figure 10 8 Oth order correci y Entering edp on the command line is equivalent to clicking ProcPars in the tab bar of the data window The following buttons are available Undo the last modification Can be used repeatedly M Switch to Maxent parameters S Switch to processing status parameters P 475 Parameters lists AU programs 12 Change raw dataset dimensionality parameter PPARMOD 4 Search for the parameter specified in the search field Inside the parameter editor you can do the following actions e click a processing step e g Window at the left of the dialog box The step becomes highlighted and the corresponding parameters will appear in the right part of the dialog box e click in a parameter field e g SI to set the parameter value It is automatically stored e hit the Tab key to jump to the next parameter field e hit Shift Tab to jump to the previous parameter field e use the scroll bar at the right of the di
401. rst NZP points of the dataset to zero OFFSET the ppm value of the first data point of the spectrum PC used in 1D 2D and 3D datasets in all directions takes a float value ppm set by sref or interactive calibration also set by accumulate The value is calculated according to the relation OFFSET SFO1 SF 1 1 0e6 0 5 SW SFO1 SF where SW and SFO1 are acquisition status parameters In fact the re lation for OFFSET depends on the acquisition mode When the acqui sition status parameter AQ_mod is qsim gseq or DOD which is usually the case the above relation counts When AQ_mod is gf the equa tion OFFSET SFO1 SF 1 1 0e6 is used peak picking sensitivity used in 1D datasets takes a float value interpreted by pp 1i lipp a spectral point is only a considered peak if it is a maximum which is greater than the previous minimum plus 4 PC noise In addition to P 31 TOPSPIN parameters MI PC provides an extra way of controlling the peak picking sensitiv ity It allows you for instance to detect a shoulder on a large peak PHCO zero order phase correction value frequency independent used in 1D 2D and 3D datasets in all directions takes a float value degrees set by apk apks apkf apk0 on 1D datasets set interactively in Phase correction mode on 1D and 2D datasets interpreted by pk xfbp xf2p xflp tf p interpreted by trf xfb xf2 xf1 xtrf tf3 tf2 t 1 when PH_mod pk PHC
402. ruker NMR Soft ware Support the logfiles can be loaded up automatically to the Bruker FTP server but only if the user assertively affirms This tool is also available in the menu bar e Click Options Administration Execution protocols e Click Execute savelogs e The following window will appear amp Execute Savelogs This tool will collect support information about your TOPSPIN installation and send it to Bruker Use this tool only if you have been instructed to do so Please enter your support token Send result of savelogs command to Bruker FTP server Output of savelogs Help Execute Close Figure 7 6 The recommended token will be told by Bruker support If the possibility Send the result of savelogs command to Bruker FTP server is not chosen the collected logfiles will be saved on user PC P 367 Print Export commands e Click execute to save the output files The output files and information about the ftp upload if selected will be shown in the same window below the line Output of savelogs See Figure 7 6 e Please note that if ftp upload doesn t work the tar gz file can be send manually to Bruker NMR Software Support under the following address nmr software support bruker de If you cannot start TopSpin but want and are instructed by Bruker NMR Software Support to transfer your log data to Bruker FTP server do the following Under Windows e C
403. s peak list containing all peaks in the entire spectrum peaklist xml peak list created by pp and pps for the Plot Editor TOPSPIN 2 1 and newer peak txt peak list created by pp and pps TOPSPIN 2 0 and older or by convertpeaklist TOPSPIN 2 1 and newer peakhist txt peak list with histogram created by pph pp dx peak list in JCAMP DX format created by ppj USAGE IN AU PROGRAMS PP PPL PPH PPJ SEE ALSO peakw ppp lipp lippf P 392 Analysis commands ppd NAME ppd Perform peak picking with derivative based algorithm DESCRIPTION The command ppd performs t can be usefull to pick peak shoulders which are not found by other peak picking commands INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt peaklist xml peak list created for the Plot Editor SEE ALSO pps ppf ppl pph ppj pp P 393 Analysis commands P 394 pp2d pp NAME pp2d Perform peak picking 2D pp Open peak picking control dialog 1D 2D 3D DESCRIPTION 2D peak picking can be started from the command line or from the peak picking dialog box The latter can be opened with the command pp see Figure 8 11 In this dialog window you can set the following options Append peaks to list When it is checked the
404. s Furthermore you will find commands that are used to read or edit lists like pulse programs gradient programs frequency lists etc Note that several commands in this chapter are acquisition related rather than processing related Nevertheless they play a role in the processing part of TOPSPIN P 461 Parameters lists AU programs dpp NAME dpp Display processing status parameters 1D 2D 3D DESCRIPTION The command dpp displays the processing status parameters Entering dpp is equivalent to clicking the ProcPars tab in the data window and clicking the button examid_13C 1 1 C ibio guest SEE Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid gt EAEN Reference window Phase A Reference Sl 262144 Size of real spe __ Baseline SF MHz 75 4677490 Spectrometer fr Fourier OFFSET ppm 219 161 Low field limit o Integration SR Hz 0 00 Spectrum refere Peak S_p Hz 17985 6 Processing Sp PREE HZpPT Hz 0 068610 Spectral resolut ja sh a PPARMOD 1D Dimension of pr NC_proc a Intensity scalinc amp Window function Phase correction lt Figure 10 1 The processing status parameters are set by processing commands and represent the status of the processed data As such they can only be viewed in the dpp window The following buttons are available P 462 Parameters lists AU programs Undo t
405. s is typically done on a 1D dataset which is a trace extracted by a previous rtr command which was entered on the source 3D dataset In that case rtr requires only one argument the trace number By de fault the same axis orientation and source 3D dataset procno are used as with the previous rtr command as defined in the used_from file of the 1D dataset You can however use two or three arguments to specify a different axis orientation and or 3D source procno On a regular 1D dataset not a trace from a 3D rtr requires three arguments Here are some examples of rtr executed on a 1D dataset which is a trace from a 3D dataset rtr Prompt the user for the trace number use the axis orientation and source 3D procno as defined in the current 1D dataset and read the trace accordingly rtr 11 Read trace 11 Use the axis orientation and source 3D procno as de fined in current 1D dataset rtr 3 11 2 Read F3 trace 11 from the 3D dataset under procno 2 Note that on 2D data the command rtr works like rsr and rsc except that the trace direction can be freely chosen Furthermore rtr always stores the 1D output data in a different procno of the same dataset whereas rsr and rsc can store data in the dataset TEMP On 4D or higher dimensional datasets rtr works the same as on a 3D P 339 nD processing commands P 340 dataset except that there are more axis orientations INPUT FILES lt dir gt data lt user gt nmr lt n
406. s option selects the command apk1 for execution It works like apk except that it only performs the first order phase correction Automatic zero order phasing selected region order only This option selects the command apkO f for execution It works like apkf except that it only performs the zero order phase correction If you run a command like apkOf from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that If automatic phase correction does not give satisfactory results you can perform interactive phase correction This can be started with the entry Manual phasing in the ph dialog box by clicking the 4 button in the toolbar or by entering ph on the command line The ph command can be used on 1D 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the ph dialog box with edp or by typing absf1 absf2 etc ABSF 1 low field left limit of the region used by apkof ABSF2 high field right limit of the region used by apkO OUTPUT PARAMETERS can be viewed with edp dpp or by typing phcO s phco etc PHCO zero order phase correction value output of apk0 and apkOf PHC 1 first order phase correction value output of apk1 Note that this is one of the rare cases where the output parameters of a P 63 1D Processing commands command are store
407. s properties file SEE ALSO logoff uadmin esign chpwd lockgui P 608 TOPSPIN User Management logoff NAME logoff Exit TOPSPIN DESCRIPTION The command logoff allows you to logoff the internal user It opens the following dialog Please identify yourself UserID jos Password Figure 14 8 Enter the current user name and enter the password The command can also be started as follows click Options Administration Log Off From Internal User INPUT FILES lt tshome gt conf topspin users prop TOPSPIN users properties file SEE ALSO login uadmin esign chpwd lockgui P 609 uadmin NAME uadmin TOPSPIN internal user administration DESCRIPTION The command uadmin allows you to administer TOPSPIN internal users It opens the dialog shown in Figure 14 9 tj User Administration uadmin C Enforce login for working with TopSpin User ID User Name Allowed Signature Meanings Diane Lopez all James Evans review Larry Hill approval Add User Change Meanings Passwd Length Figure 14 9 To add a new user click the button Add User which will open the following dialog shown in Figure 14 10 Here you can enter the User ld full user name and Signature meaning The Signature meaning can be chosen userspecifically This freedom is offered by Bruker TopSpin Software because normally the Signature meaning is acted in accordance to the guidelines of your concern e g ISO 9001
408. s tab of the data window toolbar The peak picking dialog window has two extra buttons Reset all to allows you to reset all parameters to the stored parameters or to the most recent values stored in the peak list Note that the stored param eters and the parameters in the peak list can be different since param eters can also be set with edp or from the command line However right after peak picking they are the same Start manual picker To switch to interactive peak picking mode equivalent to clicking the button in the TOPSPIN upper toolbar P 401 Analysis commands The options specified in square brackets in the dialog window and further options can also be specified on the command line For example pp append open peak picking dialog with the Append option checked pp noduplicates open peak picking dialog with the Discard new peaks option checked pp silent perform peak picking on the displayed region with the last stored op tions no dialog Equivalent to the command pps pp nodia perform peak picking on the last stored region with the last stored op tions no dialog pp append noduplicates nodia perform peak picking on the last stored region with the specified op tions The pp command can be used on 1D 2D or 3D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the pp dialog box with edp or by typing
409. s the command 2projn for execution It calculates the negative partial 1D projection of the 2D dataset in the F2 direction Calculate negative projection of columns This option selects the command 1projn for execution It calculates the negative partial 1D projection of the 2D dataset in the F1 direction The calculated projection is stored under the specified Destination procno The Required parameter Display projection can be set to on 2D to display the calculated projection with the 2D dataset The cur rent 2D dataset remains the active dataset as 1D to display the calculated projection as a 1D dataset The active dataset changes to the destination PRONCNO The required parameters can also be specified as arguments on the com mand line As an example we use the command 2projn here f2projn lt firstrow gt prompts for astrow and stores the projection under data name TEMP f2projn lt firstrow gt lt lastrow gt stores the specified projection under data name TEMP f2projn lt firstrow gt lt lastrow gt lt procno gt stores the specified projection under the specified procno of the cur rent data name f2projn lt firstrow gt lt lastrow gt lt procno gt n 2D processing commands stores the specified projection under the specified procno of the cur rent data name but does not change the display to this procno A projection is a 1D trace where every point has the highest intensity of all points of the corr
410. s the destination experiment number Examples of using wrpa are wrpa lt name gt wrpa lt expno gt wrpa lt name gt lt expno gt wrpa lt name gt lt expno gt lt procno gt wrpa lt name gt lt expno gt lt procno gt lt dir gt lt user gt y wra makes a copy of the current expno directory including raw data ac quisition parameters and processing parameters The command takes two arguments and can be used as follows wra prompts you for the destination experiment number wra lt expno gt copies the raw data to lt expno gt wra lt expno gt y overwrites existing raw data in lt expno gt wrp makes a copy of the current procno directory including the proc essed data and processing parameters The command takes two argu ments and can be used as follows wrp prompts you for the destination processed data number wrp lt procno gt copies processed data to lt procno gt wrp lt procno gt y overwrites existing processed data in lt procno gt wrpparam works like wrp except that it does not copy the processed data files and auditp txt file wraparam works like wra except that it does not copy the raw data files and audita txt file Note that the wr commands only work if user who started TOPSPIN has the permission to create the destination dataset INPUT AND OUTPUT FILES For wrpa wra and wraparam lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data 1 The data path of
411. s the specified row and store it under the specified procno The last two arguments are optional n prevents changing the display to the output 1D data y causes a possibly existing data to be overwritten without warning When executed on a dataset with 2D or 3D raw data but 1D processed data1 be takes one argument be lt row gt process the specified row and store it under the current procno bc same process the same row as the previous processing command and store it under the current procno The same option is automatically used by the AU program macro BC When used on a regular 1D dataset i e with 1D raw data it has no effect bc can also be started from the baseline dialog box which is opened with the command bas INPUT PARAMETERS set from the bas dialog box with edp or by typing be_mod bcfw etc BC_mod FID baseline correction mode BCFW filter width for BC_mod sfil or qfil COROFFS correction offset in Hz for BC_mod spol or qpol and 1 Usually a result of rsr rsc ora 1D processing command on that 2D or 3D dataset P 70 1D Processing commands sfil qfil INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data time domain lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data time dom
412. sd data in uncom pressed zip format If the graphical user interface should be used simply enter the com mand tozip as described above Zipfile from within an AU Program In AU Programs both commands tozip and tozip d can be used with the command sendgui The following two examples show the entering procedure XCMD sendgui tozip d C mydata zip QUIT XCMD sendgui tozip C Bruker ts21pl1 data guest nmr exam1d_1H 1 pdata 1 C testdata zip FID_ RE_IM NO_COMPRESS QUIT INPUT FILES If Data type includes FID lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data ser 2D or 3D raw data P 559 Conversion commands P 560 If Data type includes RSPEC lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data 2rr real processed 2D data 3rrr real processed 3D data If Data type includes ISPEC lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt li imaginary processed 1D data 2ir 2ri 2ii imaginary processed 2D data 3irr 3rir 3iii imaginary processed 3D data The parameter files acqu and proc are stored for all data types OUTPUT FILES lt pathname gt lt mydata topspin zip gt TOPSPIN data in ZIP format SEE ALSO fromzip tojdx totxt Conversion commands vconv NAME vconv Convert Varian type data to TOPSPIN data 1D 2D 3D DESCRIPTION The command vconv converts
413. selected all will be searched 4 Click OK to start the search A list of data that fulfil the defined criteria will appear see Figure 9 7 P 435 Dataset handling i EEE Searching will be performed in all data directories marked in the data directories list below The checkboxes at the right will enforce exact matching if enabled NAME EXPNO PROCNO USER Title Pulse Prog Dimension Data type Date from mm dd yy Date til mmddyy Data directories Figure 9 6 ie Search result Found 6 Data Sets Please right click in a list for more options 2004 03 30 10 43 33 1 1 1 1 1 examid_13C 2 1 Clbio guest jmod 2004 03 30 11 01 05 exam1d_13C 3 1 C ibio guest dept135 2004 03 30 11 18 36 examid_13C 4 1 C ibio guest dept45 2004 03 30 11 53 06 examid_13C 5 1 C bio guest deptg0 2004 03 30 12 27 39 examid_13C 6 1 Clbio guest zgig30 2004 03 30 13 35 54 Figure 9 7 Note that on exiting TOPSPIN the search criteria will be rest to default P 436 Dataset handling How to Display one of the Found Datasets In the search result window see Figure 9 7 1 Click one or more datasets to select them 2 Click Display to display the selected dataset s in the current data window If multi ple datasets are selected they are displayed in the new data window in multiple display mode The search result window offers a right click context menu with various op tions see Figure 9
414. ser part of the data path of the currently selected dataset Please distinguish e the user part of the data path the owner of the dataset P 421 Dataset handling e the user who runs TOPSPIN Usually these three things are the same i e a user works on his own da ta However the user part of the data path can be any character string and does not have to correspond to a user account on the computer Fur thermore the user who runs TOPSPIN might work on someone else s data In this case he she may or may not have the permission to delete this dataset In the latter case the de 1 commands will not delete the dataset but show an error message instead OUTPUT FILES For dela Delete raw data files of the selected EXPNOs lt dir gt data lt user gt nmr lt name gt lt expno gt audita txt acquisition audit trail For delp Delete processed data files of the selected PROCNOs lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt auditp txt processing audit trail SEE ALSO delf dels delser del2d deli P 422 Dataset handling delf dels delser del2d deli delete NAME delf Delete raw data 1D dels Delete processed data 1D delser Delete raw data 2D 3D del2d Delete processed data 2D 3D deli Delete imaginary processed nD delete Open delete dialog box nD SYNTAX del lt name gt DESCRIPTION Delete commands can be started from the command
415. ser specific directories for Source Directories as described below will appear see Figure 1 1 Please note that in the following chapters where the respective com mands for pulse programs parameter sets AU programs lists and files are described we will always refer to this chapter and the function Op tions Manage Source Directories P 13 2 1 Chapter 2 TOPSPIN parameters About TOPSPIN parameters TOPSPIN parameters are divided in acquisition and processing parameters In this manual we will mainly concern ourselves with processing parame ters The following terms are used processing parameters Parameters which must be set for example by entering edp or clicking the Procpars tab and are interpreted by processing commands acquisition status parameters Parameters which are set by acquisition commands like zg They repre sent the acquisition status of a dataset and can be viewed for example by entering dpa or clicking the Acgupars tab Some acquisition status pa rameters are used as input by processing commands processing status parameters Parameters which are set by processing commands They represent the processing status of a dataset and can be viewed for example by dpp TOPSPIN parameters P 16 or by clicking the Procpars tab Most processing status parameters get the value of the corresponding processing parameter as it was set by the user edp Some parameters however are explicitly set
416. set the parameters WDW and in F2 and F1 ME_mod and NCOEF to ap propriate values If you use the command ftnd 0 the following happens 1 Processing in F4 WM FT 2 Processing in F3 WM FT 3 Processing in F2 LP WM FT 4 Processing in F1 LP WM FT So when linear prediction is done in F2 data have not been Fourier trans formed yet in F1 which can cause distortions If however you use the command ftnd 0 dip for delayed linear predic tion the following happens 1 Processing in F4 WM FT 2 Processing in F3 WM FT 3 FT 4 Processing in F1 LP WM FT 5 Processing in F2 IFT 1 6 Processing in F2 LP WM FT Now when linear prediction is done in F2 the data are Fourier trans formed in F1 and all other directions For the F1 direction linear predic tion does not have to be delayed because F1 is the last direction being processed Note that ftnd also performs fid baseline correction and spectrum phase correction if the parameters BC_mod and PH_mod re spectively are set Processing in F2 Delayed linear prediction can also be performed in two steps The com mand ftnd 0 dip with F2 ME_mod 0 and NCOEF 0 1 Inverse Fourier transform including Hilbert Transform to create temporary imaginary data P 317 nD processing commands P 318 is equivalent with the command sequence 1 ftnd 0 with F2 ME_mod 0 and WDW 0 2 Ipnd 2 with F2 ME_mod 0 NCOEF 0 and WD
417. sform in F2 only rsc 17 2 to read column 17 to procno 2 and switch to that dataset ft to Fourier transform the resulting 1D data according to Fn MODE Explanation the 1D data shares the expno and the acquisition pa rameters in it with the source 2D dataset 1D processing commands automatically recognize that this 1D dataset is a column from a 2D da taset The command ft interprets the F1 acquisition parameter Fn MODE to determine the Fourier transform mode Example 2 A 2D dataset with F1 acquisition mode States is Fourier transformed in F2 Column 17 time domain is extracted and stored under data name TEMP The resulting 1D dataset is Fourier transformed On the 2D dataset enter the following commands s nmode check the FnMODE value States click Cancel xf2 to Fourier transform in F2 only s mc2 check the MC2 value States click Cancel rsc 17 read column 17 to TEMP and switch to that dataset s aq_mod check the AQ_mod value qsim click Cancel ft Fourier transform the resulting 1D data according to AQ_mod Explanation the source 2D and the destination 1D have a separate a set of acquisition parameters rsc reads the F1 status parameter MC2 of the 2D data and translates that to the corresponding AQ_mod of the 1D data 1D processing commands recognizes this 1D dataset as regular 1D data This means for example that ft interprets the AQ_mod to determine the Fourier transform mode Example 3 2D proc
418. shift will be set to exactly 10 5 ppm On 2D spectra sref calibrates the F2 and F1 direction and this involves the same steps as described above for 1D spectra INPUT PARAMETERS set by the acquisition can be viewed with dpa or by typing s solvent P 412 etc SOLVENT the solvent of the sample INSTRUM configuration name entered during c of the spectrom eter LOCNUC lock nucleus SFO1 spectral frequency NUC1 measured nucleus SW sweep width OUTPUT PARAMETERS processing parameters which can be viewed with edp processing status parameters which can be viewed with dpp SF spectral reference frequency OFFSET the ppm value of the first data point of the spectrum SR spectral reference INPUT FILES lt tshome gt conf instr lt instrum gt 2H1lock edlock table for 2H locked samples 19Flock edlock table for 19F locked samples OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters USAGE IN AU PROGRAMS SREF Analysis commands P 414 t1guide NAME t1guide Open the relaxation analysis guide 2D DESCRIPTION The command tiguide opens a dialog box with a workflow for relaxa tion analysis including T1 T2 This procedure is completely described in the TOPSPIN Users Guide To open this click Help Manuals General User Manual Dataset handling Chapter 9 Dataset hand
419. small peak which can then be integrated Usually absd is followed by abs To display the integral regions determined by one of the above com mands 1 Right click inside the data window and select Display Properties 2 Check the entry Integrals and click OK The integral regions are also used by various commands which calculate spectral integrals like 1i lipp and plot If you run a command like abs from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that If automatic baseline correction does not give satisfactory results you can apply an interactively determined polynomial exponential sine or spline baseline correction This can be started with the first entry of the bas dialog box by clicking the s button in the toolbar or by entering bas1 on the command line The bas command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the bas dialog box with edp or by typing absg absf1 etc ABSG degree of the polynomial input of abs absf absd ABSF 1 low field left limit of the region corrected by abs ABSF2 high field right limit of the region corrected by abs set from the int dialog box with edp or by typing abs1 azfw etc ABSL integral sensitivity factor with reference to the noise AZFW minimum distance betwe
420. ssing commands peakw NAME peakw Calculate width of highest peak in displayed region 1D DESCRIPTION The command peakw calculates the peak width at half height of the high est peak in the displayed region The result is stored in the notebook and displayed on the screen x Peak ppm 77 4304 Width ppm 110 8054 at 0 50 El Save Clear Cancel Figure 3 17 The command can also be used with one argument the height at which the width must be calculated peakw lt height gt For example peakw 0 66 calculates the width of the highest peak in the displayed region at 66 of the height OUTPUT FILES lt userprop gt notebook txt notebook text file SEE ALSO nbook P 118 1D Processing commands sinm qsin sinc qsinc wm NAME sinm Sine window multiplication of the FID 1D qsin Sine squared window multiplication of the FID 1D sinc Sinc window multiplication of the FID 1D qsinc Sinc squared window multiplication of the FID 1D wm Open window multiplication dialog box 1D 2D DESCRIPTION Window multiplication commands can be started from the command line or from the window function dialog box The latter is opened with the command wm see Figure 3 18 Window function sinm Options Manual window adjustment Required parameters Window function type WD v Sine bell shift SSB 0 1 2 Figure 3 18 This dialog box offers several window
421. ssing status parameters proc2s F1 processing status parameters In a 3D dataset lt dir gt data lt user gt nmr lt name gt lt expno gt acqu F3 acquisition parameters acqu2 F2 acquisition parameters acqu3 F1 acquisition parameters acqus F3 acquisition status parameters acqu2s F2 acquisition status parameters acqu3s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc F3 processing parameters proc2 F2 processing parameters proc3 F1 processing parameters procs F3 processing status parameters proc2s F2 processing status parameters proc3s F1 processing status parameters 2 4 List of processing parameters This paragraph contains a list of all processing parameters with a descrip tion of their function and the commands they are interpreted by Please note that composite processing commands like efp which combines em ft and pk are not mentioned here Nevertheless they interpret all param eters which are interpreted by the single commands they combine Processing parameters can be set from the parameter editor which can be opened by entering edp or clicking Procpars Alternatively you can set parameters by entering their names in lowercase letters on the command line ABSF 1 low field limit of the region which is baseline corrected e used in 1D 2D and 3D datasets in all directions P 19 TOPSPIN parameters takes a floa
422. status Fourier transform mode status FT_mod AQ_mod qf forward single real fsr qsim forward quad complex fqc qseq forward quad real fqr DQD forward quad complex fqc Table 5 1 In F2 and F1 they are Fourier transformed according to the acqui sition status parameter FnMODE see table 5 2 FnMODE Fourier transform mode status FT_mod undefined according to MC2 QF forward quad real fqc QSEQ forward quad real fqr TPPI forward single real fsr States forward quad complex fqc States TPPI forward single complex fsc Echo AntiEcho forward quad complex fqc Table 5 2 The Fourier transform mode is stored in the processing status pa rameter FT_mod Note that t3d does not evaluate the processing parameter FT_mod 5 Phase correction The frequency domain data are phase corrected according to PH_mod This parameter takes the value no pk mc or ps For PH_mod pk t3d applies the values of PHCO and PHC1 This is only useful if the phase values are known You can determine them by typing xfb on the 3D data to process a 23 or 13 plane do 1 If FnMODE undefined t3d evaluates the processing parameter MC2 P 268 3D processing commands a phase correction on the resulting the 2D dataset and store the phase values to 3D The size of the processed data is determined by the processing param eter SI SI real and SI imaginary points are created A
423. strow gt lt procno gt n stores the specified sum under the specified procno of the current data name but does not change the display to this procno INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt P 168 2D processing commands 1r 1i 1D spectrum containing the sum auditp txt processing audit trail USAGE IN AU PROGRAMS F2SUM firstrow lastrow procno F1SUM firstcol lastcol procno For both macros counts that if procno 1 the sum is written to the da taset TEMP SEE ALSO f2projn f2disco rhpp P 169 2D processing commands P 170 genser NAME genser Generate pseudo raw data 2D DESCRIPTION The command genser generates pseudo raw data from processed 2D data When entered without arguments genser opens the following di alog box EN genser Please specify destination NAME exam2d_Hc EXPNO 99 Figure 4 9 Here you specify the output dataset and click OK to actually execute the command genser is normally used in combination with xi f2 and xi f1 These commands perform an inverse Fourier transform converting proc essed frequency domain data into processed time domain data genser converts these processed time domain data into pseudo raw time do main data and stores them under a new name or
424. t process the specified row and store it under the current procno em same process the same row as the previous processing command and store it under the current procno The same option is automatically used by the AU program macros EM and GM When used on a regular 1D da taset i e with 1D raw data it has no effect If you run a command like em from the command line you have to make sure that the required parameters are already set Click the Procpars tab or enter edp to do that The wm command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the wm dialog box with edp or by typing 1b bc_mod etc LB Lorentzian broadening factor GB Gaussian broadening factor BC_mod FID baseline correction mode set by the acquisition can be viewed with dpa or s swh SWH spectral width 1 Usually a result of rsr rsc or a previous 1D processing command on that 2D or 3D data P 79 1D Processing commands INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data input if they exist but are not Fourier trans formed proc processing parameters OUTPUT FILES lt dir gt d
425. t 2p 3rri F1 imaginary processed data input of t 1p OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 3rrr real processed 3D data 3irr F3 imaginary processed data output of t 3p 3rir F2 imaginary processed data output of t 2p 3rri F1 imaginary processed data output of t 1p auditp txt processing audit trail USAGE IN AU PROGRAMS TF3P store_imag where store_image can be y orn TF2P store_imag where store_image can be yorn TF1P store_imag where store_image can be y orn SEE ALSO tf3 tf2 tfl xf2p xflp pk P 307 3D processing commands tht3 tht2 tht1 NAME tht3 Hilbert transform in F3 3D tht2 Hilbert transform in F2 3D tht1 Hilbert transform in F1 3D DESCRIPTION tht3 performs a Hilbert transform in the F3 direction creating imaginary data from the real data The resulting imaginary data can then be used for phase correction with t 3p tht2 performs a Hilbert transform in the F2 direction creating imaginary data from the real data The resulting imaginary data can then be used for phase correction with t 2p tht1 performs a Hilbert transform in the F1 direction creating imaginary data from the real data The resulting imaginary data can then be used for phase correction with t 1p Note that Hilbert Transform is only useful when the real data have been created from zero filled raw data with SI gt TD Normally the
426. t 5 output data files are named nr and ni e g 5r 5i 6r 6i etc SEE ALSO ftnd tf3p tf2p tflp xf2p xflp xht2 xht1 P 327 nD processing commands P 328 projcbp projcbn sumcb NAME projcbp Calculate positive 3D projection projcbn Calculate negative 3D projection sumcb Calculate sum 3D projection DESCRIPTION The commands projcbp projcbn and sumcb calculate the positive negative and sum 3D projection respectively from a dataset of dimen sion gt 4 They require take up to 5 arguments lt cube orientation gt 234 134 124 432 321 etc lt first cube gt the first cube included in the calculation lt last cube gt the last cube included in the calculation lt dest procno gt the procno where the 3D output data are stored xdim sets the subcube sizes according to XDIM optional n prevents the destination dataset from being displayed activated optional Here is an example of the usage of a 3D projection command projcbp 234 1 32 999 n calculates the positive F2 F3 F4 3D projection of cube 1 to 32 along the F1 direction stores it under PROCNO 999 but does not change the display to the output data Instead of specifying the first and last cube you can also use the argu ment a11 for all cubes For example projcbp 234 all 10 calculates the positive F2 F3 F4 3D projection of all cubes along F1 and stores it under PROCNO 10 Missing arguments except for the optional ones wi
427. t SI only the processed data between STSR and STSR STSI are stored if STSI 0 STSR is ignored and SI points are stored 0 lt STSI lt SI only the processed data between STSR and STSR STSI are stored Note that only in the first case the processed data contain the total infor mation of the raw data In all other cases information is lost xfb performs a quad spike correction which means that the central data point of the spectrum is replaced by the average of the neighbouring data points in the F1 direction Note that the quad spike correction is skipped 2D processing commands if you process the data with the sequence xf2 xf1 xfb evaluates the parameter FCOR The first point of the FIDs is multi plied with the value of FCOR which lies between 0 0 and 2 0 For digitally filtered Avance data FCOR is only used in the F1 direction In F2 it has no effect because the first point is part of the group delay and as such is zero However A X data or Avance data measured with DIGMOD analog FCOR is used in F1 and F2 xfb evaluates the F2 parameter PKNL On A X spectrometers PKNL true causes a non linear 5th order phase correction of the raw data This corrects possible errors caused by non linear behaviour of the analog fil ters On Avance spectrometers PKNL must always be set to TRUE For digitally filtered data it causes xfb to handle the group delay of the FID For analog data it has no effect xfb evaluates
428. t depending on the processing status of the data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt For FnMODE z QF 2rr real processed 2D data 2ir second quadrant imaginary processed data 2ri third quadrant imaginary processed data 2ii fourth quadrant imaginary processed data For FnMODE QF 2rr real processed 2D data 2ii second quadrant imaginary processed data For all values of FnMODE procs F2 processing status parameters proc2s F1 processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS XFB If you want to use XFB with an option you can do that with XCMD e g XCMD xfb raw P 245 2D processing commands SEE ALSO xf2 xfl xfbp xfbm xfbps xtrf P 246 2D processing commands xfbp xf2p xf1p ph NAME xfbp Phase correction in F2 and F1 direction 2D xf2p Phase correction in F2 2D xf1p Phase correction in F1 2D ph Open phase correction dialog box 1D 2D DESCRIPTION 2D phase correction can be started from the command line or from the phase correction dialog box The latter is opened with the command ph PY Phase correction xfbp Options Manual phasing Magnitude spectrum Power spectrum Required parameters Apply to axis F2 F1 Oth order correction PHCO deg 0 7 0 a 1st order correction PHC1 deg 0 0 Figure 4 30 This dialog box offers severa
429. t pdata lt procno gt 3rrr 3irr 3rir 3rri 3iii processed data wp1 on 3D data A4rrrr 4iiii processed data wp1 on 4D data auditp txt processing audit trail SEE ALSO rpl rtr wtr rcb rser wser wserp P 343 nD processing commands wtr NAME wtr Write 1D data to a trace of data gt 2D DESCRIPTION The command wtr replaces a trace of processed data with dimension gt 2D with a 1D processed dataset It is usually but not necessarily used to write back a trace that was extracted with rtr This trace can be modified and or written back to a different trace number wtr takes up to three arguments As an example we take a trace written to a 3D dataset lt axis orientation gt 1 2o0r3 The digit refer to the F3 F2 and F1 axes of the 3D data lt trace number gt 1 MAX where MAX is the product of the SI value in the directions orthogo nal to the trace orientation lt procno gt destination 3D procno source 1D procno if wtr is entered on the destination 3D dataset wtr can be entered on the 1D source dataset or on the destination 3D dataset The number of required arguments is different see below wtr entered on the source 1D dataset In this case wtr prompts the user for two arguments only the trace number and the D destination procno The axis orientation is taken from the 3D dataset used_f rom file The two arguments can also be spec ified on the command line If however you sp
430. t of xht1 created from 2rr 2ii fourth quadrant imaginary data auditp txt processing audit trail USAGE IN AU PROGRAMS XHT2 XHT 1 SEE ALSO xfb xf2 xfl P 251 2D processing commands xif2 xif1 NAME xif2 Inverse Fourier transform in F2 2D xif1 Inverse Fourier transform in F1 2D DESCRIPTION The command xif2 performs an inverse Fourier transform in the F2 di rection This means frequency domain data spectrum are transformed into time domain data FID xif1 performs an inverse Fourier transform in the F1 direction Note that after xi f2 or xif1 or both the data are still stored as proc essed data i e the raw data are not overwritten You can however cre ate pseudo raw data with the command genser which creates a new dataset Inverse Fourier transform can also be done with the commands xtrfp xtrfp2 and xtrfp1 To do that 1 Type dpp and check the status FT_mod 2 Type edp to set the processing parameters set BC_mod WDW ME_mod and PH_mod to no and FT_mod to the inverse equiva lent of the status FT_mod 3 Perform xtrfp xtrfp2 or xtrfpl INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr ir 2ri 2ii processed 2D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr ir 2ri 2ii processed 2D data auditp txt processing audit trail P 252 2D processing commands
431. t recalculates the real according to Dr Dee chere tA rry r rr Tir TrYL Til Figure 4 28 where rr real data 2rr file ir F2 imaginary data 2i r file ri F1 imaginary data 2ri file ii F2 F1 imaginary data 2ii file The commands x ps is for example used in special cases to convert a phase sensitive spectrum to a power spectrum This is useful for data which cannot be phased properly or data which are not phase sensitive but have been acquired as such The ph command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters P 221 2D processing commands P 222 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS XFBPS XF2PS XF1PS SEE ALSO xfbm xf2m xflm 2D processing commands xf2 NAME xf2 Process data including FT in F2 2D DESCRIPTION The command x 2 processes a 2D dataset in the F2 direction It can be started from the command line or from the Fourier transform dialog box The latter is opened with the command ftf xf2 Fourier transforms time domain data FID into frequency domain data spectrum Depending
432. t value ppm and must be greater than ABSF2 interpreted by absf apkf abs1 abs2 abst absot zert tabs The 1D commands abs and absd do not interpret ABSF1 because they work on the entire spectrum The command apkf for automatic phase correction uses ABSF1 as the left limit of the region on which it calculates the phase values ABSF2 high field limit of the region which is baseline corrected used in 1D 2D and 3D datasets in all directions takes a float value ppm must be smaller than ABSF1 interpreted by absf apkf abs2 abs1 abst absot zert tabs The 1D commands abs and absd do not interpret ABSF2 because they work on the entire spectrum The command apkf for automatic phase correction uses ABSF2 as the right limit of the region on which it calculates the phase values ABSG degree of the polynomial which is subtracted in baseline correction used in 1D 2D and 3D datasets in all directions takes an integer value between 0 and 5 default is 5 interpreted by abs absd absf abs2 abs1 abst absot tabs A polynomial of degree ABSG is calculated by the baseline correc tion commands and then subtracted from the spectrum ABSL integral sensitivity factor with reference to the noise used in 1D datasets takes a float value between 0 and 100 default is 3 interpreted by abs absd absf Data points greater than ABSL standard deviation are considered spectral information all other points are co
433. ta edp to set the processing parameters xfb to process the pseudo raw data If the input data are processed but not Fourier transformed you can skip the first two steps INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr 2ir 2ri 2ii processed time domain data OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt ser pseudo raw time domain data P 171 2D processing commands P 172 audita txt acquisition audit trail USAGE IN AU PROGRAMS GENSER expno SEE ALSO xif2 xifl genfid 2D processing commands projd NAME projd Display projections along with the 2D spectrum 2D DESCRIPTION The projd commands opens a dialog box see Figure 4 10 where you can specify the projections to be displayed along with the 2D spectrum PN Projection display Options Display 1D spectra along with the 2D spectrum O Display projections along with the 2D spectrum O Turn projection display off Define 1D data sets for F2 F1 Apply to axis F2 F1 NAME exam1d_1H exarn1d_13C EXPNO PROCNO DIR USER Figure 4 10 This dialog box offers the following tree options Display 1D spectra along with the 2D spectrum Displays the specified 1D dataset s as external projections Display projections along with the 2D spectrum Displays the internal projections Turn projection display off P 173 2D processing commands
434. ta storage order INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if 1r 1i do not exist or are Fourier transformed acqus acquisition status parameters P 89 1D Processing commands P 90 lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data input if they exist but are not Fourier trans formed proc processing parameters OUTPUT FILES 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail USAGE IN AU PROGRAMS FT SEE ALSO trf trfp ift ht 1D Processing commands gdcon Idcon mdcon ppp dconpl dcon NAME gdcon Gaussian deconvolution 1D Idcon Lorentzian deconvolution 1D mdcon Mixed Gaussian Lorentzian deconvolution 1D ppp Generate peak list for deconvolution 1D dconpl Show result of last deconvolution 1D dcon Open deconvolution dialog box 1D 2D DESCRIPTION Deconvolution commands can be entered on the command line or start ed from the deconvolution dialog box see Figure 3 8 The latter is opened with the command dcon This offers several options each of which selects a certain command for execution Use Lorentzian shape This option selects the command 1dcon for execution It deconvolves the spectrum fitting a Lorentzian function to the peaks It is typically used for overlapping peaks with a Lorentz
435. tains several EXPNO PROCNO pairs corresponding to several ravv processed data files Open Display the selected data set Print Print the data set list Type set and navigate to Printer gt Printer Font in order to change the fort EXPNO PROCNO dim pulsprog title T 1d zgpg30 13C 1H AV 300 Automation Cholesterylacetate ari 1d jmod 13C APT AY 300 Automation Cholesterylacetate se 1d depti35 13C DEPT135 AVY 300 Automation Cholesterylacetate 4i4 id dept45 13C DEPT45 A 300 Automation Cholesterylacetate Si id dept90 13C DEPT9S0 AY 300 Automation Cholesterylacetate 6 4 id zgigs0 13CIG AY 300 Automation Cholesterylacetate Show dimipulsprogttitle next time Figure 9 14 If the current dataset contains only one expno procno combination it is automatically opened The dialog offers the following buttons Open open the highlighted dataset equivalent to pressing the Enter key Print print the dialog contents P 451 Dataset handling Save print the dialog contents to a text file Cancel Close the dialog The command rep works like rel except that it lists the available proc nos under the current expno If no dataset is open re refers to the last active dataset If no dataset has been open yet during the current TOPSPIN session it shows an error message SEE ALSO repl re rep rew repw new P 452 Dataset handling reopen NAME reopen Reopen current dataset in new
436. take a value between 0 and the size of the FID or spectrum The value of NZP is the number of the real plus imaginary data points that are zeroed As such the first NZP 1 2 real points and the first NSP 2 imaginary data points are zeroed INPUT PARAMETERS set by the user with edp or by typing nzp datmod etc NZP number of data points set to zero intensity DATMOD data mode work on raw or proc essed data INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data input if DATMOD raw lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data input if DATMOD proc proc processing parameters OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data real imaginary procs processing status parameters auditp txt processing audit trail P 140 1D Processing commands USAGE IN AU PROGRAMS ZP SEE ALSO zf P 141 Chapter 4 2D processing commands This chapter describes all TOPSPIN 2D processing commands Most of them only work on 2D data but some e g xfb can also be used to process a plane of 3D data They store their output in processed data files and do not change the raw data We will often refer to the two directions of a 2D dataset as the F2 and F1 direction F2 is the acquisition direction which is displayed horizontally and F1 the orthogona
437. taset rcb takes up to five arguments lt cube axis orientation gt 234 134 124 432 321 etc The digits refer to the F4 F3 F2 and F1 axes of the 4D data Note that the order of the three digits is relevant e the first digit is the 4D axis that corresponds to the 3D F1 axis e the second digit is the 4D axis that corresponds to the 3D F2 axis e the last digit is the 4D axis that corresponds to the 3D F3 axis This means that for values like 234 134 124 etc the axis order or the 3D cube and the 4D dataset are the same For values like 432 423 143 etc they are different lt cube number gt 1 Sl SI is the 4D size in the direction orthogonal to the cube orientation lt procno gt destination 3D procno source 4D procno if reb is entered on the destination 3D dataset xdim optional argument sets the subcube sizes according to the processing parameter XDIM in the respective directions This parameter must be set in the source 4D dataset before reb is executed n optional argument prevents the destination dataset from being displayed activated P 330 nD processing commands Arguments which are not specified on the command line will be prompted for except for xdim and n argument rcb can be entered on the source 4D dataset or if this already exists on the destination 3D dataset The number of required arguments is differ ent see below rcb entered on a source 4D dataset In this case
438. tches the baseline of the spectrum Click to save the baseline correction to the 2D dataset and leave baseline mode Select the 2D data window Then you can enter bem2 to perform the baseline correction Correct baseline using correction result from 1D row column F1 This option selects the command bem1 for execution It works like bem2 except that it performs a baseline correction in the F1 direction columns Before you can use bem1 you must read a column with rsc and define the baseline on it see above bem commands only works on the real data After applying them the im aginary data no longer match the real data and cannot be used for phase correction INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data base_ info baseline correction coefficients P 154 2D processing commands OUTPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data auditp txt processing audit trail USAGE IN AU PROGRAMS BCM2 BCM1 SEE ALSO abs2 abs1 P 155 2D processing commands P 156 dcon2d dcon NAME dcon2d Gaussian Lorentzian or mixed deconvolution 2D dcon Open deconvolution dialog box 1D 2D DESCRIPTION The command dcon2d performs deconvolution fitting a Gaussian Lorentzian or mixed function to the peaks in the displayed region Before you start this com
439. ters proc2s F3 processing status parameters proc3s F2 processing status parameters proc4s F1 processing status parameters For 3D data the output data file is 3r rr whereas proc4s does not exist For data of dimension n where n 5 processed data files are named nr and ni e g 5r 5i 6r 6i etc and the additional files proc5s etc ex ist SEE ALSO absnd pknd Ipnd projcbp projcbn sumcb projplp projpln sumpl P 322 nD processing commands Ipnd NAME Ipnd nD linear prediction DESCRIPTION The command Ipnd performs a linear prediction of data with dimension gt 3D It takes one argument the direction to be processed If no argument is specified on the command line it is requested see Figure 6 1 Enter direction 4 3 2 1 for F4 F3 F2 F1 H Figure 6 3 1pnd works on data that have already been Fourier transformed in the specified direction e g with ftnd Since linear prediction is normally performed on a unfiltered FID the data should first be processed with ftnd with WDW no and then with 1pnd while WDW is set to the de sired window function 1pnd performs the following steps in the specified direction 1 Inverse Fourier transform 2 Regular processing including e Linear prediction according to ME_mod NCOEF e Window multiplication according to WOW e Fourier transform Linear prediction is a valuable method for improving the resolution of nD data with small TD values and oft
440. the FID of digitally filtered data starts with a group delay of which the first points are zero so that the value of FCOR is irrelevant On A X data FCOR allows you to control the DC offset of the spectrum ft evaluates the parameter PKNL On A X spectrometers PKNL true causes a non linear 5th order phase correction of the raw data This cor rects possible errors caused by non linear behaviour of the analog filters On Avance spectrometers PKNL must always be set to TRUE For dig itally filtered data it causes t to handle the group delay of the FID For analog data it has no effect ft evaluates the parameter REVERSE If REVERSE TRUE the spec trum will be reversed i e the first output data point becomes the last and the last point becomes the first The same effect is attained by using the command rv after ft t automatically performs an FID baseline correction according to BC_mod ft performs linear prediction according to ME_mod This parameter can take the following values no no linear prediction P 87 1D Processing commands P 88 LPfr forward LP on real data LPfc forward LP on complex data LPbr backward LP on real data LPbc backward LP on complex data LPmifr mirror image forward LP on real data LPmifc mirror image forward LP on complex data Forward prediction can for example be used to extend truncated FIDs Backward prediction can be used to improve the initial data points of the FID
441. the foreground dataset is displayed above the TOPSPIN data field ser 2D or 3D raw data acqu acquisition parameters acqus acquisition status parameters For wrpa and wra lt dir gt data lt user gt nmr lt name gt lt expno gt fid raw data 1D ser raw data nD audita txt acquisition audit trail For wrpa wra wrp and wrpparam lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt proc processing parameters procs processing status parameters For wrpa wra and wrp lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed data 1D 2rr 2ir 2ri 2ii processed data 2D 3rrr 3irr 3rir 3rri 3iii processed data 3D 4rrrr 4iiii processed 4D data auditp txt processing audit trail For 2D data the additional parameter files acqu2 acqu2s proc2 and proc2s will be created For 3D 4D etc data the respective additional parameter files will be created Note that apart from data and parameters several other files are copied USAGE IN AU PROGRAMS WRPA name expno procno diskunit user WRA expno WRP procno Note that these macros overwrite possibly existing data SEE ALSO new open re rep rew repw reb dir Dataset handling P 460 Parameters lists AU programs Chapter 10 Parameters lists AU programs This chapter describes all TOPSPIN commands which handle parameters and parameter set
442. the layout not available in Windows version 1 N Remove N data sets from the portfolio and print again n Don t reset before printing f Force all 1D and or 2D objects in the layout to use axis limits as used in TOPSPIN uses the F1P F2P parameter for each direction e output ps Create e g a Postscript file instead of printer output Use the option to see a complete list of supported file formats V Show autoplot version number h Show help text Same as h For a extended description of autoplot please refer to the Plot Editor P 348 Print Export commands online help INPUT PARAMETERS set with edp or by typing layout etc LAYOUT Plot Editor layout CURPLOT Default plotter for Plot Editor INPUT FILES lt tshome gt plot layouts xwp Bruker library Plot Editor layouts lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r real processed 1D data procs processing status parameters intrng integral regions parm txt ascii file containing parameters which appear on the plot title default title file outd output device parameters portfolio por Plot Editor portfolio input file is it exists For a 2D dataset the files 2rr proc2s and clevels are also input USAGE IN AU PROGRAMS AUTOPLOT AUTOPLOT_WITH_PORTFOLIO AUTOPLOT_TO_FILE outputtfile AUTOPLOT_WITH_PORTFOLIO_TO_FILE outputfile SEE ALSO plot print prnt P 349 Print
443. the screen Before printing starts the operating system print dialog box will appear where you can for example select the printer and printer properties P 363 Print Export commands Print with layout start Plot Editor plot If you select this option and click OK the Plot Editor will be started This option is equivalent to entering plot on the TOPSPIN command line Print with layout plot directly autoplot Selecting this option activates the Plot Editor layout list box Select the desired layout and click OK to print Standard layouts are deliv ered with TOPSPIN They use the Windows default printer User defined layouts use the printer defined in the Plot Editor On a 1D dataset only 1D layouts are listed on a 2D dataset only 2D layouts are listed etc For the last two options the following Required Parameters are availa ble Use plot limits from screen CY the plot limits and maximum intensity are used as they are on the screen processing parameter F1P F2P and CY respectively from Plot Editor Reset Actions the plot limits and maximum intensity are set according to the Plot Editor Reset Actions right click inside the Plot Editor data field and choose Automation to set the Reset Actions as saved in Plot Editor the plot limits and maximum intensity are set in the specified lay out Fill dataset list from your default portfolio the portfolio contains the current TOPSPIN dataset plus the
444. the table see figure 10 4 All items shown in the table can be edited read written or new written This also corresponds to the commands edmisc rmisc and wmisc Parameters lists AU programs For detailed information about user specific definition of Source Directo ries and the functionalities of Manage Source Directories please refer to the information given in chapter 1 9 Types of Miscellaneous Files The lists which can be edited are shown in Table 10 1 list type contains intrng integral regions created by interactive integration or automatic baseline correction abs Used for spectrum display print and integral listing base _ info polynomial sine or exponential baseline function created from the baseline mode bas1 Used by the baseline correction command bem baslpnts baseline points created by def pts from the base line mode bas1 Used by the spline baseline correction command sab peaklist peak information created by the command ppp and mdcon auto Used by the mixed deconvolu tion command mdcon reg plot regions created in interactive integration mode command int Used by pp lipp when PSCAL ireg or pireg When entered on the command line rmisc takes two arguments and Table 10 1 Miscellaneous list types can be used as follows rmisc lt type gt Shows all entries of the type lt type gt If you select an entry the corre sponding
445. tion em x Options Manual window adjustment E Required parameters Window function type WDY exponential Line broadening LB Hz fi Gaussian max position 0 lt GB 1 bo Sine bell shift SSB 0 1 2 lo Left trapezoid limit O Th1 lt 1 Dee Right trapezoid limit 0sTM2 1 fo i Cancel Help Figure 3 5 The parameter section of this dialog box offers several window functions each of which selects a certain command for execution Exponential multiplication This function selects the command em for execution It performs an exponential window multiplication of the FID It is the most used win dow function for NMR spectra em multiplies each data point i with the P 77 1D Processing commands factor N ees POZ SWH where LB the line broadening factor is a processing parameter and SWH the spectral width an acquisition status parameter Gaussian multiplication This function selects the command gm for execution It performs a Gaussian window multiplication of the FID The result is a Gaussian lineshape after Fourier transform This lineshape has sharper edges than the lineshape caused by em gm multiplies the FID with the func tion exp at br where is the acquisition time in seconds and a and b are defined by a a n7 LB and ah AG In this equation LB and GB are processing parameters which repre sent the exponential broadening factor and the Gaussian broadening fa
446. toPspiN Bruker BioSpin Processing e Commands and References TopSpin 2 1 Version 2 1 2 NMR Spectroscopy think forward Copyright C by Bruker BiosSpin GmbH All rights reserved No part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means without prior consent of the publisher Product names used are trademarks or reg isteresd trademarks of their respective holders This document was written by NMR C Bruker BioSpin GmbH printed in Federal Republic of Germany 03 07 2008 Part No Variant H9776SA2 10 Document No SM Proc2 1 2 Document Part No 02 Contents Chapter 1 Chapter 2 Chapter 3 Chapter 4 Chapter 5 Chapter 6 Chapter 7 Chapter 8 Chapter 9 Chapter 10 Chapter 11 Chapter 12 Chapter 13 Chapter 14 INtrOdUCtION oe ea Ea ee SAS eee eee ee EY P 3 1 1 About this manual 1 6 0 0 00 eae P 3 1 27 Conventions 3 40826 va eed a n ee oe hana Binh Pied eed a P 3 1 3 About directions as ee a 5 eee teens tee rege oat ee tle Db eet ae P 4 1 4 About time and frequency domain data 2 5 P 5 1 5 About raw and processed data 20000e eee ee eeee P 6 1 6 About digitally filtered Avance data 0 0 eee eee P 8 1 7 Usage of processing commands in AU programs P 8 1 Clicking commands from the TOPSPIN menu 2 00 P 9 1 9 Userspecific handling of Source Directories
447. top with an error message On 1D data abs absf absd apk apk0 apk1 apks bcm sab trfp ift ht genfid filt On 2D data P 7 Introduction P 8 1 7 abs2 abs1 abst2 abst1 sub2 sub1 subl1d2 sublid1 bcm2 bem1 xf2p xf1p xfbp xf2m xf1m xfbm xf2ps xflps xfbps sym syma symj tilt ptilt ptiltl1 rev2 rev1 xif2 xif1 xht2 xht1 xtrfp xtrfp2 xtrfp1 add2d genser On 3D data tf2 tf1 tht3 tht2 tht1 tf3p tf2p tflp tabs3 tabs2 tabs1 1 6 About digitally filtered Avance data The first points of the raw data measured on an Avance spectrometer are called group delay These points represent the delay caused by the digital filter and do not contain spectral information The first points of the group delay are always zero The group delay only exists if digital filtering is actu ally used i e if the acquisition parameter DIGMOD is set to digital Usage of processing commands in AU programs Many processing commands described in this manual can also be used in AU programs The description of these commands contains an entry USAGE IN AU PROGRAMS This means an AU macro is available which is usually the name of the command in capitalized letters If the entry USAGE IN AU PROGRAMS is missing no AU macro is available Usually such a command requires user interaction and it would not make sense to put it in an AU program However if you still want to use such a command in AU you can use the XCMD
448. tracted wsc lt column gt the specified column of the destination 2D data is replaced by the cur rent 1D data The 2D dataset is the one from which the current 1D da taset was extracted wsc lt column gt lt procno gt the specified column of the destination 2D data is replaced by the cur rent 1D data The 2D dataset must reside under the current data name 1 the current expno and the specified procno Examples of usage of wsc on the destination 2D dataset P 203 2D processing commands wsc lt column gt the specified column of the current 2D processed data is replaced The source 1D data must reside under the data name TEMP wsc lt column gt lt procno gt the specified column of the current 2D processed data is replaced The source 1D data must reside under the current data name the cur rent expno and the specified procno Although wsc is normally used as described above it allows you to spec ify a full dataset path in the following way wsc lt column gt lt procno gt lt expno gt lt name gt lt user gt lt dir gt When entered on a 1D dataset the arguments specify the destination 2D dataset When entered on a 2D dataset the arguments specify the source 1D dataset If only certain parts of the destination 2D data path are specified e g the expno and name the remaining parts are the same as in the current 1D data path In AU programs wsc must always have 6 arguments see USAGE IN AU PROGAMS below
449. trap FT_mod Fourier transform mode STSR strip start first output point of strip transform STSI strip size number of output points of strip transform REVERSE flag indicating to reverse the spectrum PKNL group delay compensation Avance or filter correction A X PH_mod phase correction mode PHC zero order phase correction value for PH_mod pk 2D processing commands PHC first order phase correction value for PH_mod pk set by the acquisition can be viewed with dpa or by typing s td TD time domain number of raw data points F2 direction set by the acquisition can be viewed with dpa or by typing s bytorda BYTORDA byteorder or the raw data NC normalization constant F1 direction set by the acquisition can be viewed with dpa or by typing s fnmode FnMODE Acquisition mode OUTPUT PARAMETERS F2 and F1 parameters can be viewed with dpp or by typing s si etc SI size of the processed data TDeff number of raw data points that were used for processing STSR strip start first output point of strip transform STSI strip size number of output points of strip transform XDIM submatrix size F2 parameters can be viewed with dpp or by typing s ymax_p s ymin _petc YMAX_p maximum intensity of the processed data YMIN_p minimum intensity of the processed data S_DEV standard deviation of the processed data NC_proc intensity scaling factor BYTORDP byte order of the processed data IN
450. try for each processed data number procno Each entry shows the dataset NAME EXPNO PROCNO PROC DA P 420 Dataset handling TA and SIZE Datasets which do not contain processed data are dis played with PROC DATA none To delete data mark one or more datasets and click one of the following buttons Delete selected PROCNOs to delete the procno directories Delete processed data files of the selected PROCNOs Data acquired at certain dates This option selects the command de1dat for execution It prompts the user for a time range as specified in table 9 1 Depending on the time all all data acquired by the current user between data acquired between two specified dates day data acquired on the specified date earlier data acquired before the specified date later data acquired later than the specified date Table 9 1 range you select you are further prompted for one or two specific dates A list of datasets that were measured within the specified time range is displayed with a separate entry for each experiment number expno When started from the command line de1 commands can take one ar gument which may contain wild cards Examples dela examid list all datasets whose name starts with exam ld dela exam1ld list all datasets whose name is exam d plus three extra characters de1 commands only list and delete the datasets of current user The current user here refers to the u
451. ts and files For defining special lists please enter the corresponding command in the command line Pulse Programs edpu1 CPD Programs edepd Shape Files edshape Parameter Sets edpar Macros edmac Python programs edpy Introduction e AU Prgrams edau e VD VP VC VA VT F1 DS Solvent Region Files Phases edlist e intrng Files peakrng Files etc edmisc After entering the respective command in the command line TopSpin will open the corresponding window in appearance like the following window Here the example for the command edlist see Figure 1 2 amp Miscellaneous Files edmisc File Options Help Source C My_intrng_files X Search in names Search Misc type inttng 1D integral FANGS ea intrng 1D integral ranges peakrng 1D peak ranges examid 1H tt intrng test txt basipnts baseline points for abs base_info baseline function for pcm peaklist peak file for dcon clevels 2D contour levels reg reference regions for pp int2drng 2D integral ranges _Eoit Read write write new Close Figure 1 2 On the topright of this window the sources are listed in the pull down menu and below the file types are shown also in a pull down menu All shown items can be edited read written or written new depending on user wishes By clicking Options Manage Source Directories the window for defining u
452. ts from TOPSPIN r Apply Reset Actions on all objects after loading the layout n Do not change anything after loading the layout p myfile por Load the portfolio file myfile por i Ignore a portfolio por file found in the data set The main window of the Plot Editor consists of a drawing area a menu bar and a toolbar which offers various graphical objects Here you can display objects like FIDs one or two dimensional NMR spectra Stacked Plots parameter lists and titles You can add integral curves and peak lists to a spectrum combine several spectra to a stacked plot draw pro jections around a 2D spectrum Furthermore the Plot Editor offers a set of so called graphic primitives like lines text rectangles and bezier curves You can place these objects anywhere on the screen and change their appearance They can be su perimposed on NMR related graphics All objects can be moved and re sized interactively and for each object a range of editing modes is available The TOPSPIN command autoplot allows you to plot a spectrum using a Plot Editor layout For a full description please click click Help Manuals Automation and Plotting TopSpin Plotting P 361 Print Export commands INPUT PARAMETERS set with edp or by typing layout etc LAYOUT Plot Editor layout CURPLOT Default plotter for Plot Editor INPUT AND OUTPUT FILES lt tshome gt plot layouts xwp Bruker library Plot Editor layouts portfolio por Plot
453. ty datasets which only contain parameter files You can mark one or more entries in the list and click e Display to display the data in the current data window or e Display in new window to display the data in a new data window When multiple entries were marked they will be shown in one data win dow in multi display mode An entire dataset with all EXPNOs PROCNOs This option selects the command dir for execution It lists datasets showing the data names only Acquisition data This option selects the command dira for execution It lists datasets showing a separate entry for each expno Each entry shows the data set NAME EXPNO ACQU DATA and SIZE The entry file refers to the data files and can be fid 1D raw data ser 2D or 3D raw data or no raw data Processed data This option selects the command dirp for execution It lists datasets showing a separate entry for each processed data number procno Each entry shows the dataset NAME EXPNO PROCNO PROC DA TA and SIZE The type refers to the name of the data files and can be Ir li processed 1D data 2rr 2ir 2ri 2ii 2D raw data 3rrr 3rri proc essed 3D data or no processed data Data acquired at certain dates This option selects the command dirdat for execution It prompts the Dataset handling user for a time range as specified in table 9 2 Depending on the time all all data acquired by the current user between data acquired between two spe
454. typical value for SI is TD 2 in which case all raw data points are used and no zero filling is done In fact several parameters control the number of input and output data points for example 1 SI gt TD 2 the raw data are zero filled before the Fourier transform 2 SI lt TD 2 only the first 2 SI raw data points are used 3 0 lt TDeff lt TD only the first TDeff raw data points are used 4 0 lt TDoff lt TD the first TDoff raw data points are cut off and TDoff zeroes are appended at the end 5 TDoff lt 0 TDoff zeroes are prepended at the beginning Note that e for SI lt TD TDoff 2 raw data are cut off at the end for DIGMOD digital the zeroes would be prepended to the group delay which does not make sense You can avoid that by converting the raw data with convdta before you process them 6 0 lt STSR lt SI only the processed data between STSR and STSR STSI are stored if STSI 0 STSR is ignored and SI points are stored 7 0 lt STSI lt SI only the processed data between STSR and STSR STSI are stored Note that only in the first case the processed data contain the total infor mation of the raw data In all other cases information is lost Before you run t3d you must set the processing parameter SI in all three direc tions F3 F2 and F1 ft3d evaluates the acquisition status parameter AQSEQ which defines the storage order of the raw data Raw data can be stored in the order 3 2 1
455. u can set AZFW to ten times the width at half height of the signal The result of deconvolution is e the quality of the fit expressed by the minimized chi square value e alist of peaks within the plot region and for each peak its fre quency width intensity and area This list is displayed on the screen e the fitted lineshape which is shown together with the original spec trum in multi display mode e individually fitted peaks and their sum as shown by dconpl v All deconvolution commands can be started from the command line In this case they use the current values of the required parameters Tailor Mixed Shape Deconvolution Use peak list created by regular peak picking Mixed deconvolution creates and uses its own peaklist You can how ever force it use the peaklist created with regular peak picking with the command convertpeaklist To do that P 93 1D Processing commands P 94 1 Perform peak picking e g with pps 2 Enter convertpeaklist peaklist 3 Enter mdcon Select fit parameters for each individual peaks The deconvolution fit parameters can be enabled disabled for each in dividual peak To do that Edit the file peak1ist in the PROCNO directory of the dataset At the end of a peak entry you can specify three flags for the three parame ters to be optimized chemical shift half width and amplitude 0 optimize this parameter 1 do not optimize this parameter Here is an example of a peaklist
456. ue frequency dependent used in 1D 2D and 3D datasets in all directions takes a float value degrees set by apk apks apkf apk1 apkmin 1D datasets set interactively in Phase correction mode in 1D and 2D datasets also exists as processing parameter edp PHC1 is one of the few examples where a processing parameter is set by a processing command For example apk sets both the processing and processing status parameter PHC1 pk reads the processing parameter and updates the processing status parameter For multiple phase corrections the processing status parameter PHC1 shows the total first order phase correction SINO signal to noise ratio used in 1D datasets takes a float value set by sino also exists as processing parameter The signal is determined in the region between SIGF2 and SIGF1 The noise is determined in the region between NOISF2 and NOISF1 Note that SINO also exists as a processing parameter edp which has a different purpose see chapter 2 4 SW_ p spectral width of the processed data used in 1D 2D and 3D datasets in all directions takes a double value set by all processing commands only exists as processing status parameter Normally SW_p will be the same as the acquisition status parameter SW However in case of stripped data see processing commands STSR and STSI the processing spectral width differs from the acquired spectral width SYMM 2D symmetrization type done P 44 used in 2
457. uest nmr N 2 w wo wT N o onl T T T T 200 150 100 50 ppm Figure 8 1 For more information on daisy click Help Manuals Analysis and Simulation Daisy SEE ALSO daisyguide Analysis commands daisyguide NAME daisyguide Daisy tutorial DESCRIPTION The command daisyguide opens the Daisy tutorial see Figure 8 2 This guides you through the Daisy program Note that this can also be started with the command daisy DAISY Tutorial Enter DAISY module m N Run iteration Open spin system tt View sim iteration log Edit spin system Export spin systern Run simulation Figure 8 2 For more information on daisyguide click Help Manuals Analysis and Simulation Daisy SEE ALSO daisy P 375 Analysis commands edstruc NAME edstruc Open the 2D Molecule Structure Editor DESCRIPTION The command edstruc opens the 2D Molecule Structure Editor Enter ing this command is equivalent to clicking the Structure tab in the 2D data window and the clicking the button 2D Editor examid_1H 1 1 Ciibio guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample MevrsSoQgagaQgagQgy 4Ivysoo8 ar a x a eji cyclosporina pdb Figure 8 3 A full description of the 2D Structure Editor package can be found under Help Manuals Analysis and Simulation Structure Analysis Tools SEE ALSO jmol P 376 Analysis commands
458. ution It lists 2D and 3D datasets which contain raw data showing a separate entry for each experiment number expno Each entry shows the dataset NAME EX PNO ACQU DATA and SIZE 2D processed data This option selects the command dir2d for execution It lists 2D da tasets which contain processed data showing a separate entry for each processed data number procno Each entry shows the dataset NAME EXPNO PROCNO PROC DATA and SIZE P 431 Dataset handling P 432 INPUT FILES lt dir gt data lt user gt nmr lt name gt lt expno gt fid 1D raw data ser 2D or 3D raw data lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 1r 1i processed 1D data 2rr 2ir 2ri 2ii processed 2D data Brrr Birr 3rir 3iir processed 3D data SEE ALSO dir dira dirp dirdat browse find re rep rew repw reb Dataset handling edc2 NAME edc2 Define second and third dataset DESCRIPTION The command ede2 opens a dialog box in which you can define the sec ond and third dataset see Figure 9 5 ty edc2 Please specify data sets 2 and 3 NAME examid_13C examid_13C EXPNO 1 1 PROCNO 2 3 DIR C Bio USER guest Figure 9 5 You can define the NAME EXPNO PROCNO DIR disk unit and US ER Note that these are all parts of the data pathname lt dir gt data nmr lt user gt lt name gt lt expno gt pdata lt procno gt The second dataset is
459. ver if you click Save as and store it under a different name the stored file is automatically opened in edit mode When you edit a User defined AU program it is opened in edit mode and can be modified When edau is entered on the command line with an argument the cor responding AU program will be opened If it does not exist it will be cre ated If the argument contains wildcards the AU dialog box is opened showing the matching AU programs For example edau a displays all AU programs which start with a Bruker AU programs must be installed once with expinsta11 before they can be opened with edau The installation must be repeated when a new version of TOPSPIN is installed edau uses the editor which is defined in the TOPSPIN User Preferences To change it enter set click Miscellaneous and select or change the ed itor AU programs are usually executed simply by entering their names The command xau is only needed in three cases e the AU program has not been compiled yet a TOPSPIN command with the same name exists e to call an Au program from another AU program using the macro XAU AU programs run in background and several of them can run simultane ously The command kill can be used to stop a running or hanging P 515 Automation P 516 AU program For details on writing compiling and executing AU programs please re fer to the AU reference manual click Help Manuals Programming Manuals AU progra
460. ward prediction with TDoff lt 0 The number of raw data points that were actually used is stored in the processing status parameter TDeff TILT flag indicating whether a tilt command has been performed used in 2D datasets in the F2 direction takes the value TRUE or FALSE set by ptilt ptiltlor tilt only exists as processing status parameter dpp P 45 TOPSPIN parameters XDIM submatrix or subcube size used in 2D and 3D datasets in all directions takes an integer value set by xfb xf2 xf1 xtrf xtrf2 tf3 also exists as processing parameter Although XDIM is normally calculated by processing commands 2D and 3D processing also allow you to predefine the submatrix sizes using the argument xdim On a 2D dataset the command xfb xdim interprets the processing parameter XDIM in both F2 and F1 On a 3D dataset the command tf3 xdim interprets the processing parameter XDIM in F3 F2 and F1 FTSIZE Fourier transform size used in 1D 2D and 3D datasets in all directions takes an integer value set by all processing command that perform Fourier transform Normally the status parameter FSIZE has the same value as the sta tus parameter SI Only in case of strip transform STSR gt 0 and or STSI gt 0 they are different FTSIZE then represents the size with which the raw data were Fourier transformed whereas SI represents the size with which the processed data are stored YMAX_p maximum intensity of the pro
461. where h2 is the intensity of the second highest peak and max the intensity of the highest peak If this condition is false the highest peak is used as reference Other values of ASSFAC have no effect on the plot scaling P 21 TOPSPIN parameters P 22 ASSWID region excluded from second highest peak search used in 1D datasets takes a float value Hz default is 0 interpreted by pp lipp ASSWID is interpreted as follows If abs ASSFAC gt 1 a region of width ASSWID around the highest peak is excluded from the search for the second highest peak AUNMP processing AU program name used in 1D 2D and 3D datasets in the first direction takes a character string value interpreted by xaup In all Bruker standard parameter sets the parameter AUNMP is set to a suitable processing AU program AZFE integral extension factor used in 1D datasets takes a float value ppm default 0 1 interpreted by abs Integral regions are extended at both sides by AZFE ppm If this extension causes adjacent regions to overlap the centre of the over lap is used as the limit of the two regions AZFW minimum distance between peaks for independent integration used in 1D datasets takes a float value ppm interpreted by abs 1dcon gdcon mdcon If peaks are more than AZFW apart they are treated independently If peaks are less than AZFW ppm apart they are considered to be overlapping BCFW filter width for FID baseline corre
462. with the command pp see Figure 8 12 In this dialog window you can set the following options Append peaks to list When it is checked the found peaks are appended to a possibly existing list When it is unchecked a new list is created pp3d append e Discard new peak s if already in list Check this option to avoid duplicate peaks pp3d nodupli cates Export results as XwinNmr peak list In addition to TOPSPIN XML format the result is also stored in XWIN NMR format file peak txt pp3d txt This file is typi cally used with XWIN NMR AU programs Furthermore you can set the following peak picking parameters Region parameters Here you can set the region limits for the F3 F2 and F1 direction Only peaks within this region will be picked Note that the limits can be specified in the text fields or set with the button Set to to Full range full spectrum Displayed range range displayed in the data window Range defined by stored parameters range stored in parameters F1P F2P 1 Most recent range stored in peak list range on which last automatic P 399 Analysis commands EJ Peak picking _pp3d append noduplicates Append peaks to list Discard new peak s if already in list d Export results as XVVinNMR peak list Parameters Region From F1P To F2P F3 ppr 5 1196 0 1126 F2 ppm 96 9122 17 0878 F1 ppm 51196 01126 Sensitivity Minimum intensity rel MI
463. y perform a baseline correction of the FID according to the processing parameter BC_mod Furthermore they per form linear prediction according to the parameters ME_mod NCOEF and LPBIN When executed on 2D or 3D data tm and traf take up to four argu ments e g tm lt row gt lt procno gt n y process the specified row and store it under the specified procno The last two arguments are optional n prevents changing the display to the output 1D data y causes a possibly existing data to be overwritten without warning If you run a command like tm from the command line you have to make sure that the required parameters are already set Click the Procpars tab 1D Processing commands or enter edp to do that When executed on a dataset with 2D or 3D raw data but 1D processed data tm and traf take one argument e g tm lt row gt process the specified row and store it under the current procno tm same process the same row as the previous processing command and store it under the current procno The same option is automatically used by the AU program macro TM When used on a regular 1D dataset i e with 1D raw data it has no effect The wm command can be used on 1D or 2D data It recognizes the data dimensionality and opens a dialog box with the appropriate options and parameters INPUT PARAMETERS set from the wm dialog box with edp or by typing tm1 1b etc TM1 the end of the rising edge of a trapeziodal wind
464. y processed 1D data if input file contains 1D imaginary data proc processing parameters procs processing status parameters For 2D data lt dir gt data lt user gt nmr lt name gt lt expno gt ser 2D raw data input if Output Data raw acqu F2 acquisition parameters acqu2 F1 acquisition parameters acqus F2 acquisition status parameters acqu2s F1 acquisition status parameters lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt 2rr real processed 2D data if input file contains 2D real processed data proc F2 processing parameters proc2 F1 processing parameters procs F2 processing status parameters proc2s F1 processing status parameters clevels 2D contour levels P 543 Conversion commands USAGE IN AU PROGRAMS FROMJDX name for example FROMJDX tmp mydata dx SEE ALSO tojdx totxt tozip fromzip P 544 Conversion commands fromzip NAME fromzip Unzip display a zipped TOPSPIN dataset nD SYNTAX fromzip lt pathname gt lt dir gt lt user gt DESCRIPTION The command fromzip opens a dialog box to unzip a ZIP TOPSPIN da taset amp fromzip Please enter zip file and destination The data set will be unpacked into specified DIR Zip file DIR USER Figure 12 3 Here you can enter the ZIP file pathname and the DIR and USER part of the output data path fromzip takes up to three arguments and c
465. ym syma symj symt NAME sym Symmetrize spectrum about the diagonal 2D syma Symmetrize spectrum about the diagonal keep sign 2D symj Symmetrize spectrum about central horizontal line 2D symt Open symmetrization and tilt dialog box 2D DESCRIPTION All sym commands open the symmetrize tilt dialog box S Symmetrize tilt sym Options O Symmetrize phase sensitive spectrum Symmetrize J resolved spectrum Auto titt along rows oO Tit along rows Tit along columns Required parameters oO 0 Figure 4 17 This dialog box offers several options each of which selects a certain command for execution Symmetrize COSY type spectrum This option selects the command sym for execution It symmetrizes a 2D spectrum about a diagonal from the lower left corner data point 1 1 to the upper right corner data point F2 SI F1 Sl It compares P 195 2D processing commands each data point with the corresponding data point on the other side of the diagonal and determines which one has the lowest most nega tive intensity Then both data points are set to that intensity Table 4 1 shows the intensities of four pairs of data points before and after sym before sym after sym 370000 370000 370000 12000 1000 700 700 700 18000 6000 6000 6000 13000 8000 13000 13000 Table 4 1 sym is typically used on magnitude cosy spectra Symmetriz
466. you run pd both the integral ranges and peak positions INC should be determined see rspc and ppt1 pd then picks the points storing both their integrals and intensities but it only displays one curve the one defined by FITTYP ct1 or simfit then calculate the relaxation value for one peak according to FITTYPE You can change FITTYP and recalculate the relaxation value without running pd again The same counts for the commands dati and simfit all which fit all peaks point 1D or row 2D increment used in 1D and pseudo 2D relaxation datasets takes an integer value default is 1 interpreted by pft2 1D data P 49 TOPSPIN parameters P 50 interpreted by pd pseudo 2D data Starting with START every INC point 1D or row pseudo 2D is used for relaxation analysis NUMPNTS number of data points used for relaxation analysis used in 1D and pseudo 2D relaxation datasets takes an integer value default is TD interpreted by p t2 1D interpreted by pd pseudo 2D The default value of NUMPNTS is the number of available points i e TD 1D or F1 TD pseudo 2D TD is the acquisition status parame ter which can be viewed with dpa or s td Note that if you increase INC you must reduce NUMPNTS such that INC NUMPNTS does not exceed TD START first point 1D or row 2D used for relaxation analysis used in 1D and pseudo 2D relaxation datasets takes an integer value default is 1 interpreted by p t2 1D dat
467. ze of the submatrices are calculated by xfb and depend on the size of the spectrum and the available memory The option xdim allows you to use predefined submatrix sizes It causes x b to interpret the F2 and F1 processing parameter XDIM which can be set by entering xdimon the command line The actually used submatrix sizes wheth er predefined or calculated are stored as the F2 and F1 processing status parameter XDIM and can be viewed with dpp Predefining sub 2D processing commands matrix sizes is for example used to read the processed data with third party software which can not interpret the processing status parame ter XDIM This option is only evaluated when x b works on the raw data Normally xf b stores the entire spectral region as determined by the spectral width You can however do a so called strip transform which means that only a certain region of the spectrum is stored This can be done by setting the parameters STSR and STSI which represent the strip start and strip size respectively They both can take a value between 0 and SI The values which are actually used can be a little different STSI is always rounded to the next multiple of 16 Furthermore when the data are stored in submatrix format see below STSI is rounded to the next higher multiple of the submatrix size Type dpp to check this if XDIM is smaller than Sl then the data are stored in submatrix format and STSI is a multiple of XDIM Depending on

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