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Processing Manual

1. sucrose 1 1 u guest new sucrose 2 1 u guest new fructose 1 1 v guest old Table 5 9 Example of a data set list lt NAME gt lt EXPNO gt lt PROCNO gt lt DU gt lt USER gt lt flag gt The data sets in a list are evaluated by the variable data set statement wr n in pulse programs This command uses the list whose name is defined in the acquisition parameter DSLIST The new flag indicates that the data set is to be created newly by possibly deleting an existing one The old flag will retain an existing data set 5 3 9 Miscellaneous files edmisc Miscellaneous files are text files containing information produced by various XWIN NMR operations such as integral ranges peaks for deconvolution etc which are stored on disk for later use This command allows you to create a new miscella neous file and to edit or view an existing one XWIN NMR locates miscellaneous files in the directory u exp stan nmrNists lt file type gt The command edmisc displays all files in this directory in a dialog box from where the desired one can be selected Table 5 10 shows the available file types The command edmisc may also be entered on the keyboard followed by the type of the desired file or followed by the file type and the desired list name which may contain wildcard characters see edpul and how to change the default text edi The File Menu P 90 file type contains integration regions generated by manua
2. Figure 4 1 The 3D screen layout 2 Shrink spectrum by a factor of 1 1 3 Reset the spectrum size to the default value 3D Data Processing Tutorial P 66 ddel 1 No function assigned 2 No function assigned 3 Change the assignment of colors to intensities by keeping the number of colors used constant The mapping can be observed by looking at the color bar at the right side of the XWIN NMR window Keep the left mouse button depressed while the cursor is located on this button and move the mouse t ERA 1 No function assigned 2 No function assigned 3 Normally when the spectrum contains negative peaks both negative and posi tive intensity values levels are displayed The standard colors assigned are red yellow green shadings for positive data and light blue dark blue violet shadings for negative data This button allows you to toggle through display modes where the negative or the positive data are turned off or where the whole color range from red to violet is assigned to the positive data display Calculate contours and display the spectrum as already described above If the spectrum does not fit in memory a file dsp3d is created It is stored in the current processed data directory i e the directory where the transformed spectrum file is located The name of the spectrum file real data only is 3rrr You can delete the file dsp3d before archiving if you want to save space on the archive or speed up ar
3. 0 0 0 000000 P 170 7 22 Inverse Fourier Transformation xif2 xifl 0 00 000 cee eee P 171 7 23 2D Hilbert Transformation xht2 xhtl 0 0 00 P 171 7 24 Reflection of a 2D spectrum rev1 rev2 0 cee eee ee P 172 7 25 Create a ser file from processed data genser 0000 P 172 7 26 Convert AVANCE data to AMX format convdta 000 P 173 7 27 Add and subtract 2D spectra add2d 0 0 0 eee eee eee P 173 7 28 Calculate level file levcalc 0 0 eee eens P 173 7 29 Quadrature image correction xqcl xqc2 20 0 0 P 174 The 3D Process Menu cece cee cece cece cece eee ee cee e PATS 8 1 General parameter setup edp 00 cee eee eee eee P 175 8 2 Fourier Transformation tf3 tf2 tfl 0 0 eee P 176 8 3 Phase correction tf3p tf2p tflp 0 0 0 e eee eee eee ee P 178 8 4 Baseline correction tabs3 tabs2 tabs 0 0 eee P 178 8 5 Calculate projections r23p rl3p rl2p 0 0 ee eee eee ee P 178 8 6 Hilbert transform tht3 tht2 thtl 0 0 0 eee P 179 8 7 Read Planes yess 5 sea deer eeeae ges aa E ee sigh ets ENARTAR ae aba baste she P 179 The Analysis Menu cc cece eee c cece cece eee e cee ee cece P I81 9 1 Manual calibration annaa naaa eee een teens P 181 9 2 Auto calibration sref pe a 0 ccc ccc eee a a n eens P 182 9 3 Integration and peak picking 0
4. Table 10 14 HEWLETT PACKARD DeskJet 550C A4 single sheet feeding printer 10 13 Supported printers plotters P 283 XWIN NMR plotter type hpdprop Plotter Setup Grapics Language HP GL 7595A Memory off Serial Baud Rate 9600 Handshake both Parity none Page Format Expand on Plot Scaling 01 01 Plot Management File Timout off Table 10 15 HEWLETT PACKARD DraftPro Plus A1 single sheet XWIN NMR plotter type hplj3p SIZE A4 VO SERIAL BAUDRATE 9600 ROBUST XON OFF DTRPOLAR HI PAGEPRO A4 RAM size 3072K bytes minimum total Interfacing parallel possible too Table 10 16 HEWLETT PACKARD LaserJet IIP A4 single sheet feeding The 1D Output Menu P 284 XWIN NMR plotter type hplj41 hplj3p is possible too PAPER SIZE A4 IMAGE ADAPT AUTO PAGE PROTECT AUTO AUTOCONTINUE OFF ECONOMODE OFF RAM size 1024K bytes Interfacing parallel Table 10 17 HEWLETT PACKARD LaserJet 4L A4 single sheet feeding Laser Printer XWIN NMR plotter type kyf5000 H1 RS232C baud rate 96 H2 RS232C data bits 8 H3 RS232C stop bit 1 H4 RS232C parity bit 0 H5 RS232C protocol 1 H9 FE F time out 0 P1 Default Emulation 6 GO KCGL option 4 Table 10 18 KYOCERA F 5000 A4 A3 single sheet feeding Laser Printer 10 13 Supported printers plotters P 285 XWIN NMR plotter type kyf5000 Current interface RS232C baud rate RS232C data bits RS232C
5. 00 cc cece een nee P 137 6 3 Exponential multiply em 0 000 cee eee eee eee eee P 137 6 4 Manual window adjustment 0 0 eee ee cee eee eee P 138 6 5 Real spectrum size Si 0 0 6 eee cee tenet ene nee P 138 6 6 Fourier transformi ft eaa oes Stes eis seen inden a OR watt pda aaah RACES P 138 6 7 Automatic phase correction apk 0 0 00 c cee eee eee ee P 139 6 8 Manual phase correction 0 0 c eect eee teens P 139 6 9 Phase correction with constants PHCO and PHC1 pk P 139 6 10 Magnitude spectrum mc 0 0 eee eee eee P 140 6 11 Power spectrum ps 2 0 0c eee ccc eect nets P 140 6 12 Special window functions 0 0 cece cece eee P 141 6 13 Sequential operations 2s cc seseriai noei ee eb eb ET ey atten P 143 6 14 Baseline correction operations 0 0 cece eee ee eee P 144 Old wPilealsebran ss cnt tod At ak A eR eR EAS ce A Pol tical hs Mek AE AE P 145 6 16 Special transforms 2 cee teenies P 147 6 17 Digital filtering smooth filt 00 0 00 eee eee eee P 150 6 18 Miscellaneous operations 0 eect eee P 151 6 19 Linear Prediction eii n 22 05 aseads Rieke hee ea On AO SS P 153 The Process Menu for 2D data cece e cece ee ceec cece cee P 155 7 1 General parameter setup edp 00 0 0 cee cece cee eee eee P 155 7 2 2D Transform AiO er aree a AA rE AE eta wae e
6. Simultaneous plot of a second spectrum Inside the contour window the contours of two 2D data sets may be plotted side by side CONTADD yes the current data set in the upper left triangle and a second data set in the lower right triangle The second data set is specified by the parame ters CADDU disk partition CADUSER user Owner CADNAME name CADEXP experiment number EXPNO CADPROC processed data number PROCNO As for the current data set the intensity levels for the second data set may be set interactively or with edlev The corresponding colors or line styles are specified with the parameters CALIN CADIFCL CALCOL CALTYPP CALTYPN CACOLPA and The 2D Output Menu P 294 CACOLNA which have the same meanings as the previously described parameters CPLIN CPDIFCL CPLCOL CPLTYPP CPLTYPN CPCOLPA and CPCOLNA The additional spectrum may also be plotted with reduced resolution by setting the parameter REDARES to yes default value no 11 3 6 Plotting integration regions As described in the chapter 2D Data Processing Tutorial 2D spectra are inte grated by interactively defining the integration regions and storing them in a file The integrals are then calculated with the processing command int2d For their identification in the spectrum they may be plotted as rectangles labeled with the corresponding number either in the contour plot or on a separate sheet e g transparency For this the parameter FRINT must be s
7. qk and qc are always applied to the processed data if they exist eg after em or ft Otherwise they are applied to the raw data Fid If one wants to apply the quad correction to the fid even though the processed data already exists then the proc essed data must be deleted delp In our experience quad correction works best if applied directly to the fid because the window function disturbs the algorithm If the data is acquired with AQ_mod qsim the quad correction may be applied 6 19 Linear Prediction P 153 either to the spectrum or to the fid If data acquisition is performed using AQ_mod qseq the spectrum must be corrected because the fid does not have the correct format 6 19 Linear Prediction The parameter ME_mod which is set to no by default controls whether a linear prediction is to be applied to the data Details about ME_mod are described in the chapter on 2D transforms A linear prediction of the Fid is executed if a window function or ft command is issued but only if the parameter ME_mod is not set to no Please note during a backward prediction of an fid the first n points of the fid are replaced by the predicted points Therefore if one wants to extend the fid beyond its leftmost side and keep its original first n points a rightshift of the fid by n points must be performed prior the linear prediction The Process Menu for 1D Data P 154 Chapter 7 The Process Menu for 2D data 7 1 Gene
8. 11 7 Plot to queue plots plots plot suspend outputs the contour layout into a queue rather than sending it to the plotter Please refer to the chapter The 1D Output Menu for more details about plots Output queue on separate sheet fiplot flplot outputs the contents of a queue filled by one or more plots commands to the current plotter Remove all plots from queue rmplot All plots issued with the plots command are deleted if they were not sent yet to the plotter with fiplot Stacked plot plotw The command plotw outputs the stacked plot layout set up with edgw or rpar on the current plotter CURPLOT defined with edo CURPLOT does not play a role if the Plotter system variable is set which has priority over CURPLOT use the command setres of the chapter The Display Menu As soon as the layout has been plotted the next paper sheet is fed into the plotter Other commands The remaining commands in the 2D Output Menu are identical to the correspond ing commands in the D Output Menu Please refer to that chapter The 2D Output Menu P 300 Chapter 12 The Display Menu Figure 12 1 shows the Display menu The following sections describe the various Active commands Status amp history Dual display Figure 12 1 The Display menu menu entries 12 1 Active Commands In the Active Commands submenu the following commands are available Show Show and allow for killing Show and update table on
9. Important note If you omit five spectral ranges there are six left 9 10 2 2 Programs DSYMPLOT and DCYMPLOT The input parameters for DSYMPLOT and DCYMPLOT are very similar Any differences will be pointed out e Miscellaneous parameters Title individual title for this simulation Output experiment name Output experiment number Output experiment processing number The last three variables are automatically taken from the main menu page If you modify them the simulators will store their results in a different data set from the one you are currently editing This is useful if you want to simulate several spectra which differ only with respect to the chemical shifts for instance Spectrometer frequency is read from the XWIN NMR data set Usually you will not change this value since it reflects the status of your exper iment You should not change the value unless you want to simulate fictitious data Low frequency limit right end of the simulated spectrum High frequency limit left end of the simulated spectrum Minimum intensity weaker lines are suppressed Halfwidth of the lines in the simulated spectrum Number of Points in the simulated spectrum Number of Nuclei The low and high frequency limits are interpreted as Hz values If a value is followed by p or P it is accepted as a ppm value and immediately con The Analysis Menu P 222 verted to Hz In
10. The File Menu P 124 Aspect file format 11122333 XWIN NMR file format 11113333222 2 get aspect filename Aspect filename CSYEC104 3 process filename attempting to match entries in the tokens file Tokens file entries CSY cosy EC ehc 104 chcel 4 generate new filename XWIN NMR filename cosychclehc Filename Protocols When defining a file format the following points should be noted e Digits 0 9 must be used to specify a file format All other characters includ ing spaces are illegal The characters 1 to 8 may be used to define a single or group of characters The digits 0 and 9 have a special meaning described below e The same digit may not be used to define two different sets of characters i e the format 11122111 is ILLEGAL e The digits 0 and 9 have a special meaning O is only meaningful in the X32 file format and reserves a character space for the date stamp 9 is used in the Aspect file format to define a USER name For example if the Aspect file format is defined as 11229994 the characters 5 6 and 7 are extracted and stored in the Destination User Directory string WARNING Files will only be copied to this user s directory if the user exists on the system AND already has a valid user data directory structure i e DU data USER nmr e The number of characters substituted into the XWIN NMR filename depends on how many characters were allocated in the XWIN NMR file format For example for the fol
11. The parameter CPCOLNA CPLTYPN is responsible for the plotting of negative intensities just as CPCOLPA CPLTYPP is for positive levels If CPDIFCL is set to no but negative levels are to be plotted nonetheless the colors line styles contained in CPCOLPA CPLTYPP are transferred to both 11 3 Page layout contour plot edg P 293 11 3 5 positive and negative contours where the first color line style is assigned to the lowest negative level CPCOLNA CPLTYPN will be ignored If line styles are to be used instead of colors they are entered into the parameters CPLTYPP and CPLTYPN as A B where A is the code for the line style and B is the length of a dash or pattern in decimeters 1 dm 10 cm A may be one of the following 0 continuous line B has no effect 1 dotted line B is the distance between dots 2 short dash B is the distance between the starting point of one dash and the starting point of the next 3 long dash see above 4 dot dash B is the distance between dots 5 long dash short dash B is the distance between the starting points of the long dashes 6 long dash short dash short dash B is the length of one pattern repetition Example The value 2 05 i e A 2 B 0 05 causes a short dashed line with a rep etition length of 0 05 dm 0 5 cm to be drawn The contour window will be framed if FRAME yes instead of no The color of the frame is determined by the parameter FRCOLOR
12. the program will ask for the following two values once asymmetrical an asymmetrical lineshape will be generated the program will ask for the following two values twice one value for each half of the PSF 3 Lorentz Gauss Winged You have to enter the Gauss Lorentz Winged contribution to the lineshape With the following numbers these lineshapes are generated The Analysis Menu P 228 100 Gaussian 100 Lorentzian 100 Winged 6 60 Lorentz 40 Gauss 4 60 Lorentz 40 Winged ON Half width at half height Enter the half width at half height of the lineshape here because the lineshape is split into two halves When designing a PSF for a certain region of the NMR spectrum you should measure the half width of a peak in the spectrum in Hz using the mouse cursor The selected peak should be a single peak not overlapping with other peaks and the peak should be representative for the region you want to deconvolve Write PSF or 1r or both You can store the lineshape in three different ways p will write the lineshape into the file mem psf fora MEMSYSS5 run r will write the lineshape to the file Zr as if it would be a spectrum b will write the lineshape into the file mem psf and 1r To check the generated PSF it is sometimes useful to compare it with the original NMR spectrum If you want to do this proceed as follows 1 2 3 Switch to a new processed data set number Proc
13. 9 12 Bayesian Analysis P 237 the data but it tends to lead to too many noise peaks which need to be tested in the model selection process thus making the calculations much slower VERBOSE The parameter VERBOSE determines the amount of information written to the protocol file bay_prot during the analysis BAYSTO2 With this parameter the resulting model can be stored as the data set defined as data set 2 set up via edc2 either after each new model has been optimized BAYSTO2 intermediate or only after the whole Bayesian analysis has been completed BAYSTO2 final BAYSTO3 This parameter works exactly like the parameter BAY STO2 except that the resid ual FID i e the difference between original FID and model FID is stored in the data set defined as data set 3 set up via edc2 BAYCMD If an intermediate model or residual is to be stored in data set 2 or 3 then a com mand can also be executed on this data set e g ft or efp Any command that can be typed in from the keyboard can be used here BAY VARP This parameter only takes effect for the coherent phase model and determines whether the phase parameters defined by the processing parameters PHCO and PHC1 in XWIN NMR should be held fixed at their specified values BAY VARP no or whether they should be optimized together with the frequencies and decay rates BAY VARA In the parameter optimization routine the decay rates can be treated in three differ ent
14. Contents Chapter 1 Mntroduction sesse sunra Seale a ven lon A E oo sible E wate tare oreo P 1 1 1 Hardware software requirements 00 cee eee cee eens P 2 1 2 Notatione 3 6 facie Landed th eek dae Leek bes Ree dale ibs eh Sed Al Geen P 3 1 3 Versions 3 03 skh dete eal ae tet Sot aoe de haa Pee ed a P 3 1 4 SUPPOMt n caer waes s Se celal a hia dees e cup ewes on Wee whee Gaol P 3 1 5 Installation of XWIN NMR 1 teen e teenies P 3 1 6 XWIN NMR screen layout 0 eee cee eee es P 4 1 7 Manipulation of the XWIN NMR window 0 0 eee e eee e neces P 6 Chapter 2 1D Data Processing Tutorial 4 34 Gewese E EE PAO 2 1 Getting the data set 3 fei a eg ee aM a in Gea dee ees P 9 2 2 Manipulating fid or spectrum on the screen 0 000 c eee eee P 10 23 Setting the size of the real spectrum 0 0 00 eee eee eee eee P 14 2 4 Applying a window function to the fid 0 0 0 eee eee eee P 15 2 5 Applying the Fourier Transform usseesee eee cece eee P 18 2 6 Phase correctos pecs gegesin degree aS COs ida dele ee eG NG AGE P 18 2 7 Spectrum calibration see can y i r EE i e cence eee e E P 20 2 8 Baseline Correction s serciceon i aaee ee bela tba EE E aes P 21 2 9 Spectrum integration osre sereni natae ey des Eep ERDRE EA REE P 24 210 Peak Picking res ee e i ip ee a eS EE a E R RA P 30 DU Plotting oes sh sas eyed a TE are AA A oa utan a He P 34 Chapter 3 2D Data Pro
15. Example wrd v where v specifies another disk or disk partition Processed data only wrp This command creates a copy of the processed data files Zr Ji 2rr 2ii and parameter files of the current data set under a new PROCNO which is prompted for by the program If the command is entered at the keyboard additional argu 5 6 Copy P 101 ments may be specified wrp PROCNO y The destination PROCNO is typed in explicitely The y argument tells the pro gram to overwrite any processed data with the same PROCNO If y is omitted the user will be prompted for a confirmation if such data exist Example wrp 2 5 6 4 Acquisition data only wra 5 6 5 This command creates a copy of the acquisition data files fid or ser and parame ter files of the current data set under a new EXPNO which is prompted for by the program If the command is entered at the keyboard additional arguments may be specified wra EXPNO y The destination EXPNO is typed in explicitely The y argument tells the program to overwrite any processed data with the same EXPNO If y is omitted the user will be prompted for a confirmation if such data do exist Example wra 5 Copying acquisition data requires that the program creates a new EXPNO direc tory under the same NAME as the current data set Since PROCNO directories are subdirectories of EXPNO directories the copied data set will also have a PROCNO identical to
16. If you have picked the points with the command pft2 then all available data points are displayed on the screen because they all belong to one series In this case the command nxtp is not applicable ctl dati ct2 dat2 You can use these commands if the following two conditions apply a The data points were picked with the commands pft2 pd or pdO b The intensities of the data points originate from a single component The commands ctl datl ct2 and dt2 do not require a specific parameter setup Nevertheless these commands update certain parameters If you want to use the command simfit after you have used ctl dat1 ct2 or dat2 make certain to set the parameter FCTTYPE properly and check other parameters as necessary for the simfit run see Section 9 6 4 4 The commands ctl and ct2 will fit the data points currently displayed on the screen If there is another series of data points you can switch to it with the com mand nxtp see Section 9 6 4 2 You can now type again ctl or ct2 to fit this series of data points If you want to switch to a specific peak number enter edt1 and set the parameter CURSOR to the desired peak number Leave the editor with SAVE and type ctl or ct2 The display will be updated with this peak and its fit curve If you want to fit all peaks then use the command dat1 or dat2 If you have defined integral ranges then toggle the parameter FITTYPE from intensity to area if you want to fit the pea
17. XWIN NMR locates CPD programs in the directory u exp stan nmrNists cpd The File Menu P 84 5 3 5 The command edcpd displays all CPD programs in this directory in a dialog box from where the desired one can be selected On XWIN NMR release media a number of sample CPD programs are delivered After installation of XWIN NMR they are stored in the directory u exp stan nmr lists cpd rexam for A X systems u exp stan nmr ists cpd dexam for Avance type systems The command expinstall see menu Acquire which must be executed after instal lation of XWIN NMR will copy the contents of the respective directory to the work ing directory u exp stan numrllists cpd The command edcpd may also be entered on the keyboard followed by the name of the desired CPD program or followed by an argument containing wildcard characters see edpul and how to change the default text editor for details Gradient programs edgp Gradient programs are text files containing statements in the Bruker gradient pro gram language described elsewhere in this manual This command allows you to create a new gradient program and to edit or view an existing one XWIN NMR locates gradient programs in the directory u exp stan nmrNists gp The command edgp displays all gradient programs in this directory in a dialog box from where the desired one can be selected The phase read and slice gradients are contained in three different files with
18. conv and btran convert data sets which were acquired or processed with the A2000 3000 computer series into the XWIN NMR format bconv converts an XWIN NMR data set into the A2000 3000 format tojdx converts XWIN NMR data sets into JCAMP DX data format which is a man ufacturer independent data format fromjdx reads JCAMP DX data sets and converts them into the XWIN NMR format vconv converts Varian VNMR data sets into the XWIN NMR data format Conversion between Aspect 2000 3000 and XWIN NMR format In principle there are two ways of transferring data from a spectrometer equipped with an Aspect 2000 3000 to a workstation running XWIN NMR You can get them directly for instance via Ethernet using the BRUKNET program Or you get them 5 11 Conversion P 111 indirectly for instance via a PC using NMRLINK Other transfer programs will work in a way similar to BRUKNET or NMRLINK On the Aspect 2000 3000 data files are stored in a 24 bit per word format Each word consists of three bytes in the order high middle low A parameter sector is stored together with the data files This parameter sector is called the 1 sector BRUKNET can run in four different modes which determine how the data are stored on the receiving computer The file SPEC 00 transferred by the user guest from a spectrometer called am400 will have a different name and size on the receiving computer depending on which transfer mode of BRUKNET is used e Binary mode
19. using the predefined variables The first argument is an arbitrary text which is printed before the user is asked to enter the requested string or number The second argument is a variable which must have the correct type 15 13 Ordering a screen refresh If your AU program manipulates data you might want to refresh the screen with the modfied data to observe the result The function Show_meta will serve this purpose if the data set manipulated in the AU program is identical to the data set currently visible on the screen Otherwise this function has no effect The com mand viewdata in contrast makes the data set currently being processed by the AU program the current screen data set and displays the data viewdata should therefore not be used if you want to interactively manipulate data on the screen while the AU program is in progress 15 14 Executing several AU programs simultaneously Since XWIN NMR is a multi tasking program you may start an arbitrary number of AU programs They will execute in parallel This feature is in fact used during automatic spectrometer operation with a sample changer where an AU program controlling acquisition and another one performing data processing and plotting Writing AU Programs P 332 are started up by the AU program stan_sx 15 15 Continue execution at a specified time The command wait_until hour minute day month included in an AU program suspends its execution until the
20. 0 eee cee eee P 183 9 4 Calculate signal to noise ratio Sino 0 eee eee eee P 183 9 5 Deconvolutiones 3 60 4 04 53 3 0 Sass Hed SAPO EE E Ln E S P 185 9 6 The T1 T2 relaxation menu 0 0 0 P 187 9 7 Quantitative NMR nmrquant 00 eee P 208 9 8 The Simulation submenu nna 00 0 n eee P 213 9 9 INMR SIM Esso oni2 hese ines en As Gee OHTA ois ded RO lee Fgh Peas P 213 9 10 DATS Ys fess sles eigen dee Bak nts copes Bec haat ae a a r ates ss P 214 9110 MAXENT MEMSY SS rreren eon d ea ee ead ond bed EREA n P 226 9 12 Bayesian Analysis es os cc Naku ip fe ges ee A P 232 The 1D Output Menu cc ccc ce ccc cece eee reece eee P 241 10 1 Printer plotter installation cfpp 00 cee ee eee P 242 Chapter 11 Chapter 12 Chapter 13 Chapter 14 Chapter 15 10 2 Pen setup edpp eissi oeeyieleatiien decked ad E E way eas we ae oe yale dle P 246 10 3 Pag layout edg 25 3 3h ek kee ee ae Sas ee ee eae P 248 10 4 Page layout for auto expansions edgx 0 0 0 cee ee eee ee P 262 10 5 Using a prepared page layout rpar 2 0 0 0 eee eee eee P 268 10 6 Define show plot region 0 2 0 ec nenene P 268 10 7 Plot Commands 0 cee ccc eee eens P 269 10 8 Plot print status 0 cc cece eect eens P 270 TO 9 Scree dump ecean g s praveeh a a Son E verti ance exits den Seventies pence P 271 10 10 Print status parameters 0 2 cee eee P 2
21. 12 4 Options P 307 toggle through a number of spectra while you are in dual display mode Assume the spectrum specifications only differ either in their EXPNO or in their PROCNO Then you can load the spectrum corresponding to the next or previous EXPNO or PROCNO by just clicking on one of the commands Incr EXPNO of 2nd Decr EXPNO of 2nd Incr PROCNO of 2nd Decr PROCNO of 2nd If you have another series of data differing from the previous series not only in EXPNO or PROCNO but also in its name user and disk location you may define the data as third data set with edc2 Then you may rapidly switch between the sec ond and third data set in dual display mode by invoking the commands 2nd data set and 3rd data set from the Display menu To toggle through the spectrum series of the 3rd data set you may apply the commands Incr EXPNO of 3rd Decr EXPNO of 3rd Incr PROCNO of 3rd Decr PROCNO of 3rd In order to leave dual display mode select the command Return from the File menu or from the menu which pops up when the return button is cliccked 12 4 Options The Options submenu contains a number of commands influencing the data dis play on screen If the current data set is a 1D data set XWIN NMR displays the file Ir of the processed data directory of the current data set This file contains the real spectrum if a Fourier transform was already executed If Zr does not exist the file fid from the acquisit
22. 2 SI TD zeroes before the transformation 6 7 Automatic phase correction apk P 139 The processing parameter TDeff effective TD defines the number of points of the FID that will contribute to the transform The default value of TDeff is zero which means that all TD data points of the fid will be taken into account but maximum 2 SD The command ft can transform data which have been acquired in one channel mode or two channel mode quad There are two cases in quad mode Sequen tial acquisition is where the data points from the two channels are sampled one after the other with a time interval set by the dwell time The second case is a simultaneous acquisition where data points from the two channels are sampled at the same time The type of acquisition used is recognized by the transform soft ware from the value of the status acquisition parameter AQ_mod The first data point is multiplied by the parameter FCOR immediately before the transform is executed Values from 0 to 2 are allowed with the default being 0 5 After the transform a non linear 5th order phase correction is applied automatically if the processing parameter PKNL is set to true This correction removes phase errors introduced by the butterworth filters If the processing parameter REVERSE is set to true both the real and the imagi nary part of the spectrum are reflected by a vertical line through the center of the spectrum In other words the spectrum is reverse
23. 7 6 Linear Prediction P 161 7 6 with the option n e g xfb n The effect is that the imaginary parts 2ri 2ir 2ii will not be stored on disk This option can be useful if disk space is restricted or to improve processing time if phase constants are already known e g after delp All 2D processing commands which do baseline correction linear prediction win dow multiplication or Fourier transform evaluate the option nc_proc followed by a decimal value If possible data are scaled such that the resulting processing status parameter NC_proc equals the preset check status parameters for success Instead of a numeric value the keyword last may be specified to use the value of the cur rent status parameter NC_proc as a preset Commands working on acquisition data can be forced to generate big or little endian processed data by the options big and little This option should only be used when processed data are exported to 3rd party programs that do not evaluate the processing status parameter BYTORDP The only commands always using raw data ser file are xtrf and xtrf2 The com mands xf2 xfl xfb work either on raw or processed data all other commands work on processed data Processed data is used with xf2 xfl and xfb unless 1 there is no 2rr file or procs or proc2s are not readable missing 2 a negative number is found in the file dsp hdr entry LOC indicating last processing command was killed 3 a Fourier tra
24. Click on the large dot at right side of the window manager bar The window will automatically be resized so as to utilize the whole screen Another click on the same button will restore the last size before maximizing Restore default size When you exit from XWIN NMR and restart the program it will come up with the window size of the last session In order to obtain the default size as proposed by Bruker start the program with the command xwinnmr d Move to another position While the mouse pointer is located in the window manager bar of the XWIN NMR window depress the left mouse button and move the mouse Release the button when the desired position is reached Shuffle into foreground The XWIN NMR window may be invisible because it is hidden behind other windows If at least part of its border is still accessible click on the border to get the entire window into foreground Otherwise start iconifying other windows until XWIN NMR appears Open a pull down menu Command execution Click onto the name of the desired menu in the top menu bar The menu remains open until you click on a command which is then executed Clicking outside the 1 7 Manipulation of the XWIN NMR window P 7 menu on an insensitve window area will close the menu without action You can also open a menu by pressing the left mouse button when the cursor points to a menu name Now keeping the button depressed you can move the mouse to point to a command which will
25. The baslpnts file is stored in the current data directory of the processed data where the spectrum file is also located Please refer to the command edmisc for its struc ture You can copy it using the commands wmisc and rmisc from the File gt Copy menu and use it for similar spectra Spectrum integration This section presents the standard integration procedures In the chapter The Anal ysis Menu we will explain the command nmrquant which was designed for the quantitative analysis of spectra comprising complex overlapping signals XWIN NMR provides two modes of integration automatic and manual 2 9 Spectrum integration P 25 2 9 1 Automatic integration abs Select this command from the Analysis menu or enter abs on the keyboard abs first executes a baseline correction of the spectrum by fitting a polynomial see previous section Automatic baseline correction Then it searches for spectral regions containing signals integration regions and stores them in the file intrng in the same directory where the spectrum file is located see command edmisc in the File gt Open menu for the description of the structure of this file If you want to get the integral traces and values displayed you must enter Manual integration mode see page 26 open the File menu and execute the command Read intrng In order to print the integral values refer to the command li below abs always applies the polynomial baseline correction t
26. and will initially be a zero line as all coeffi 2 8 Baseline Correction P 23 2 8 3 cients are zero Adjust the coefficients such that the displayed curve fits best to the baseline of the spectrum Then click on the diff button to subtract the baseline curve from the spectrum The program now displays the result You may further adjust the coeffi cients and the effect on the spectrum will be seen in real time The button undo lets you return from the difference display and the original spectrum with the cal culated baseline reappear The reset button resets all coefficient to zero and lets you restart baseline adjustment You exit from baseline correction mode by clicking the return button or by openening the File menu The program lets you select a normal return leaving the spectrum file on disk unchanged or a save amp return which applies the baseline correction to the spectrum file If you have expanded the spectrum on the screen to display only a selected region save amp return will apply the correction only to that region This procedure can generate discontinuities at the region edges but the effect is not important if only that region is to be plotted or integrated Correcting special regions in a spectrum is often more successful than correcting the entire spectrum at once XWIN NMR stores the function type and the coefficients in the text file base_info whose structure is described in the chapter The File Menu under
27. edinfo The purpose of this command is to setup or change the so called information file info a text file stored in the directory DU data USER nmr NAME EXPNO that is in the same directory as the acquisition data files fid or ser The info file enables the user to store additional text information along with each acquisition data set or experiment The info file has the following internal structure It consists of up to 20 two line entries with up to 80 characters per line Figure 5 11 shows an example The info file is displayed on the screen via the command edinfo Only the second line of each entry may be edited by positioning the mouse cursor accordingly The first line of each entry cannot be edited Instead these lines are predefined in a template which is a text file called info_item and which must be stored in the directory u exp stan nmr lists 5 3 Open Other Files P 95 COMPANY Bruker Instruments Inc DEPARTMENT NMR Applications ACCOUNT 3D 2576 ORDER NO 372 SAMPLE P 2740 Sucrose EXPERIMENT cosy Figure 5 11 Info file example The template file must be set up by the system administrator via a text editor The template corresponding to the example in Figure Figure 5 11 is shown in Figure 5 12 COMPANY DEPARTMENT ACCOUNT ORDER NO SAMPLE EXPERIMENT Figure 5 12 Template of an Info file The info file can be plotted along with the data set For this purpose the pl
28. the integral is plotted inside the spectral window The zero line of the integral is defined relative to the zero line of the spectrum by placing it IZERO cm above this line Since the spectrum s zero line is drawn SZERO cm above the lower edge of the data window the integral s zero line is plotted SZERO cm above this lower edge The color of the integral is determined by the parame ter ICOLOR The vertical scaling is done by the parameter HEI cm which affects the integral in the same way as CY affects the spectrum cf the previous section THEI The biggest integral contained in the file intrng is plotted with height THEI cm If one prefers to use the second largest integral for scaling the parame ter ASSFACI must be set appopriately if h2 lt hmax ASSFACI where h2 is the value of the second largest and hmax that of the largest integral the second largest is taken otherwise the largest THEI 0 The integral is plotted with the height set up by the operator on the screen THEI 1 The integral is plotted such that it may be compared with the previous inte gral plot The vertical scaling factor is taken from the file u prog lt version gt curdir lt userloginid gt scale where the last scaling factor with IHEI gt 0 was stored Peak lists The top window within the spectral window contains a list of peak positions with vertical lines simplifying their identification in the spectrum The listed maxima and minima ar
29. tiff gif xwd etc The screen dump command puts the bitmap in a file of your home directory with the extension j LaserJet II format or ps PostScript format according to your choice You may either dump the entire XWIN NMR window or the data area only 10 10 Print status parameters XWIN NMR maintains two sets of acquisition and processing parameters for any data set The first set contains the parameters set up with the commands eda and edp the second one contains the so called status parameters A status parameter has the same name as its corresponding set up parameter e g NS or PHCO It is written into a status parameter file upon completion of an operation For example at the end of an acquisition the last scan acquired is stored as parameter NS in the acquisition status parameter file of the current data set NS need not be equal to the set up parameter NS you might have entered NS 16 with eda but halted acquisi tion after 8 scans This is the reason for the two sets Table 10 4 shows the file names of the status parameter files They are stored in the acquisition or processed The 1D Output Menu P 272 acqus acquisition status parameter file acquisition status parameter file for 2nd acqu2s dimension if 2D parameter set procs processing status parameter file processing status parameter file for 2nd proras dimension if 2D parameter set Table 10 4 Status parameter file names
30. tion Hz cm ppm cm as defined by the user previously will be retained The plot length CX of the plot will be adjusted accordingly new CX F1 F2 resolution The new CX is printed on the status line Retain CX and Hz cm Auto adjust F2 F1 and FIP will be set according to the display limits The frequency resolution Hz cm ppm cm and the plot length CX as defined by the user previously will be retained The right plot limit F2 of the plot will be adjusted accordingly new F2 F1 resolution CX The new F2 is printed on the status line Show plot region Invoking this command will set the display such that it shows the range defined by the plot limits F1 F2 FIP F2P Plot Commands 10 7 1 10 7 2 Before sending a plot to a pen plotter or printer it is advisable to preview it using the command view or viewx described in the chapter The Windows Menu Plot plot The command plot outputs the layout set up with edg or rpar on the current plotter CURPLOT to be defined with edo CURPLOT does not play a role if the Plotter system variable is set which has priority over CURPLOT use the command setres of the chapter The Display Menu As soon as the layout has been plotted the next paper sheet is fed into the plotter Plot to queue plots plots plot suspend outputs the layout into a queue rather than sending it to the plotter This allows you to set up more plots of the same or a different data set and send those to t
31. with an ASPECTstation In this case SW1 03 is to be set to off and the Centronics printer cable part no HZ03318 is to be used The pen thickness is realized in steps of 0 14 mm 1 180 with the minimum of 0 07 mm 1 360 All other pen parameters have no meaning and are ignored Table 10 9 Canon BJ 330 bubble jet printer 14 endless paper 10 13 Supported printers plotters P 279 XWIN NMR plotter type bjc800 Configuration original factory settings NVRAM INITIALIZE Interfacing parallel When using a seriell parallel converter set it to 38 400 baud When using the newer Wiesemann amp Theis Interface 82008 S2 is to be set to on all other settings are the same as in the general part The logical XWIN NMR colors are realized in the following way black black ink blue CMY blue violet CMY blue magenta CMY magenta red CMY red orange CMY red yellow CMY yellow green CMY green turquoise CMY cyan brown CMY black The pen thickness is realized in steps of 0 14 mm 1 180 with the minimum of 0 07 mm 1 360 All other pen parameters have no meaning and are ignored Table 10 10 Canon BJC 800 A3 single sheet feeding bubble jet printer The 1D Output Menu P 280 XWIN NMR plotter type _hp7475a B1 0 B2 1 B3 0 B4 1 A3 A4 depending on paper MET S1 S2 Table 10 11 HEWLETT PACKARD 7475A A3 single shee XWIN NMR plotter type hp7550A Configu
32. 1D tutorial Like 1D plots 2D plots may be obtained either using xwinplot or parameter driven plot Please refer to the 2D Data Processing Tutorial P 54 3 13 1 XWIN PLOT manual if you prefer the interactive plot editor This introduction to 2D plotting using the older parameter driven plot system assumes that you are familiar with 1D plotting Like in 1D you can set up all plot parameters from the edg plot parameter editor which will now show the settings for 2D spectra You can also preview 2D plots with view The spectral region to be plotted and the contour levels are often set up interactively from the screen We shall describe this in the following paragraph Defining the spectrum region and the contour levels to be plotted 1 Zoom the part of the spectrum you want to plot 2 Adjust the contour levels as desired using the 2 2 8 8 buttons In intensity display mode not in contour mode you may also use the online adjust button 2 Open the Output gt Define show region levels menu 3 Select the command According to current screen limits Before the program stores the expanded region as plot region it asks you whether to change the contour levels If your answer is yes the levels to be plotted will be those currently visible on the display You can also enter the number of levels to be plotted at this time Switch to contour mode to see the intensity values of the levels at the right side of the screen If your answe
33. 7 3 Typical automated execution nmrquant can be easily incorporated into AU programs thus making automated analysis of a range of similar samples possible To run the program in automation mode the user must enter the command nmrquant lt filename gt The program then searches for the files u exp stan nmr lists intrng lt filename gt u exp stan nmr lists basereg lt filename gt u exp stan nmr lists nmrquant lt filename gt for the integral region baseline region and proton matrix information The integral region and proton matrix files must be readable but the baseline region file need not exist for the analysis to proceed 9 7 4 Input specification The basic information required by nmrgant is stored in 2 files the intrng file and the nmrquant file which must be stored in the processed data directory where the spectrum is stored 9 7 Quantitative NMR nmrquant P 211 The intrng file must contain at least two entries and may be of the A P H type A W type intrng file is invalid as it contains no explicitly defined integral regions See the section on integration in the chapter The File Menu for more information about intrng file formats The nmrquant file contains the proton contribution to each integral region from a given named component This file is set up automatically when running the nmr quant command and the user need not worry about the file format which is defined according to Table 9 3 n nu
34. Correction 2 8 1 2 8 2 Certain spectra may show a baseline distortion i e the noise in the signal free por tions of the spectrum is not scattered around the zero line but around a polynomial or some other curve If this effect is large enough to prevent accurate integration of the spectrum the baseline correction routines of XWIN NMR should be applied XWIN NMR provides automatic and user interactive baseline correction routines and a semi automatic mode using spline functions Automatic baseline correction abs absf absd These commands assume that the baseline distortion can be removed by subtract ing a polynomial from the spectrum They try to find the suitable polynomial auto matically The only parameter you have to submit is the degree of the polynomial ABSG Type in the command absg or set this parameter via the processing param eter editor edp 5 is usually a reasonable value the allowed maximum is 6 If you want to correct the entire spectrum enter the command abs on the keyboard or select it from the menu Process gt Special processing gt Baseline correction There are cases where the baseline distortion cannot be be described by a polynomial over the whole spectrum and it is more appropriate to apply the correction only to a particular region The region can be specified by setting the parameter ABSF1 to its left limit in ppm and ABSF 2 to its right limit The command absf will execute the correction between
35. EDCONTP EDCONTA EDAXIS EDPROJ1 EDPROJ2 EDTITLE EDPARAM EDFRAME contour parameters parameters for additional contour plot axis parameters spectrum or projections along F1 F2 title parameters parameter window definitions parameters for frame and integration regions 11 3 Page layout contour plot edg P 291 11 3 3 Axes The axes along F1 and F2 are plotted inside the axes windows at a distance X1ZERO and X2ZERO cm from the contour window Scale tics units color and labeling are specified through the parameters XITICL X1UNIT X1TICD XICHAR X1COLOR and X2TICL X2UNIT X2TICD X2CHAR X2COLOR Their meanings are analogous to those of the corresponding parameters for the x axis of a 1D spectrum plot For contour plots it is sometimes useful to overlay the plot with a grid of vertical or horizontal or both lines A set of horizontal lines is obtained if the parameter XI1GRID is set to yes instead of no They correspond to the labeled scale tics on the F1 axis Likewise a set of vertical lines is obtained with X2GRID yes If an axis has been suppressed see parameters X1AXIS and X2AXIS below the corre sponding set of lines will not be plotted either The color of a set of lines always equals that of the corresponding axis 11 3 4 Contours In order to plot the contours of a 2D spectrum the program must perform a con tour search which may require significant time particularly for large spectra For this re
36. Eliminated points are either marked with in the output listing commands ctl dat1 ct2 and dat2 or do not appear command simfit 9 6 6 Supplementary commands prxy prints the list of x y pairs currently displayed on the screen CURPRIN is used stp lists the complete information for the points of the currently displayed peak CURPRIN is used elim eliminates a point from the currently displayed peak Irstp restores all eliminated points of the currently displayed peak 9 6 7 Files The following files are used by the T1 T2 commands They all reside in the processing directory PROCNO of the data set Depending on the fit function and the point picking command used some files might not exist The Analysis Menu P 208 baslpnts Contains the positions from where points are picked if you work with a 2D data file baslpnts is an ASCII file and can be edited with the command edmisc baslpnts see XWIN NMR Manual Chapter 5 3 9 intmng Contains the left and right limit of the range around the position defi ned in the basipnts file Every position must have a corresponding range in the intrng file Between the limits all data points are added up for area fitting intrng is an ASCII file and can be edited with the command edmisc intrng see XWIN NMR Manual Chapter 5 3 9 tlascii Contains data points in ASCII format for fitting with the command simfit asc ctlt2 out Out
37. FW sw SW_h dof O2 spin RO Table 5 12 Parameters converted from VNMR to XWIN NMR The File Menu P 130 s status parameter f foreground parameter 2D a parameter which is only set in 2D data files 5 11 3 3 Running vconv vconv has five arguments The command syntax is vconv lt VNMR name gt lt NAME gt lt EXPNO gt lt DU gt lt USER gt You can enter these arguments on the command line and they are interpreted in this order If an argument is missing vconv will ask for it If all arguments are specified on the command line and the VNMR data set is found vconv will do the conver sion silently The meaning of the arguments is as follows e VNMR name The directory name under which the VNMR data set is stored e NAME The XWIN NMR directory name under which the converted data set is stored e EXPNO The experiment number under which the converted data set is stored e DU The disk on which the converted data set is stored e USER The user name under which the converted data set is stored vconv can also be used in automation The command is VCONV and it must be called with the five arguments decribed above Example VCONV eva fid eva fid 7 u guest This would convert the VNMR data set eva fid into an XWIN NMR data set called u data guest nmr eva fid 7 pdata 1 All arguments are of type string except for the EXPNO which is of type integer Foreground and automatic conversion w
38. NMR filename for each entry in the Preview table Auto mated renaming useful when Aspect file formats are consistent involves defining both the Aspect and the XWIN NMR filename format and possibly defining entries in the tokens file Filename Formats Filenames are often represented by a string comprising one or more sets of charac ters For example you may identify a file by assigning the first 3 characters to mean one thing the next 2 characters to mean another thing and the last 3 charac ters to mean something else The filename format may be represented as follows Aspect file format 11122333 Supposing you wish to rename the Aspect file In this case you have to decide on a format for the renamed file One possibility is to expand 1 the first 3 characters in the Aspect filename to 5 characters 2 the next 2 characters in the Aspect filename to 3 characters 3 the last 3 characters in the Aspect filename to 5 characters The XWIN NMR file format is 1111122233333 Automatic renaming is then performed by extracting groups of characters from the Aspect filename according to the Aspect file format attempting to match these characters with an entry in the tokens file and then replacing these characters with the replacement string in the XWIN NMR filename If no match is found in the tokens file then the original set of characters is used in the XWIN NMR possibly padded out with _ characters Example 1 determine formats
39. STKSCAL This parameter defines the y scaling spectrum height global the global maximum of the spectrum will be plotted with height CY preg the maximum of the plot region will be plotted with height CY pscal check the processing parameter PSCAL if PSCAL preg perform accord ingly otherwise assume global WHIWA Enable disable whitewashing whitewash do not plot those parts of a spectrum row hidden behind previously plotted rows ZAXIS ZHEI ZTICLEN ZUNIT ZTICDIS ZCHAR ZCOLOR These parameters define how the z axis is plotted they are analogous to the x axis parameters described earlier Please remember that ZAXIS must be disabled no if STKINC 1 If STKINC gt 0 and ZUNIT sec the numbers along the axis are calculated from the acquisition parameters This allows one plot reasonable z units if the second dimension of a 2rr file is e g obtained from an LC run 11 5 Use prepared page layout rpar Please refer to the chapter The 1D Output Menu 11 6 Plot commands 11 6 1 Plot plot The command plot outputs the contour plot layout set up with edg or rpar on the current plotter CURPLOT to be defined with edo CURPLOT does not play a role if the Plotter system variable is set which has priority over CURPLOT use the command setres of the chapter The Display Menu As soon as the layout has been plotted the next paper sheet is fed into the plotter 11 7 Other commands P 299 11 6 2 11 6 3 11 6 4 11 6 5
40. Section 9 6 4 4 The Analysis Menu P 202 5e 08 2 0e 08 5 0e 07 Figure 9 6 The display after executing simfit Three components contribute to the peak intensities COMPNO 3 The command simfit asc will do the following a It will read the file t ascii b It will create all auxiliary files t _disp tlelim tlints and tlpeaks which are otherwise created by the commands pd pdO or pft2 But these com mands are not applicable if you want to fit from the ASCH file t ascii c It will update the display with the points of the peak specified by the param eter CURSOR 9 6 The T1 T2 relaxation menu P 203 2 4 0e 08 aB 7 Ses 3 04408 2 5 2 00408 y k 1 5e 08 m 1 0e 08 5 0e 07 bkt Xx PE AKK K ex y XKX K k k x ee Ox Figure 9 7 The display after executing simfit Three components contribute to the peak intensities but only one was specified in edt COMPNO 1 This serves basically also as an example for a bad guess d It will fit the data and display the fit curve You can use simfit asc all to fit all peaks with one command The command simfit asc works exactly like the command simfit After you have typed simfit asc once you can switch to the next peak with the command nxtp The new peak can now be fitted by typing simfit or simfit asc You can also switch to a specific peak by setting the parameter CURSOR Again you can fit this peak The Anal
41. TITNAM The following rules apply e A name starting with a slash is interpreted as a full path name to the title file Example TITNAM u guest title 1 If TITNAM starts with a Dollar sign then XWIN NMR expects the name of an environment variable immediately after the The current value of that environment variable is then substituted for the title file name perhaps followed by additional path specifications Example TITNAM XYZ title2 would cause the title text to be taken from the file u guest title2 if the environment variable is set to XYZ u guest If the environment variable is 10 3 Page layout edg P 257 undefined no title will be plotted A special case is TITNAM STAN Then the title text is taken from the file u exp lt ExpLoc gt nmr where ExpLoc is selected by the setres command or from th menu Display gt Options gt User interface However if this one is undefined stan will be sub stituted for it Example TITNAM STAN titledir title3 with ExpLoc guest is resolved to At exp guest nmr titledir title3 e Ifthe name does not start with one of the above special characters then the specified file name or path is searched for in the current data directory Example TITNAM title4 is resolved to DU data USER nmr NAME EXPNO pdata PROCNO title4 where DU USER NAME EXPNO PROCNO refers to the parameters describing the current data set e If the name starts with the characters dot d
42. Table 10 3 rotated by 90 degrees at the left of each expansion user name expno procno dddd dd Hz to dddd dd Hz Y exp factor ddd dd ddd Hz cm changed Int plot exp factor ddd Table 10 3 Text plotted along with an auto expansion Character size and color can be specified with the parameters PCHAR and PCOLOR respectively The first line gives the data set description and the plotted frequency range The second line shows the applied vertical expansion fac tor integer referring to the overview spectrum s scaling which allows for the comparison of intensities in different regions The horizontal scaling factor changed only appears if the program had to change the value set by the user with edgx because the region would not have fit onto the sheet otherwise The third line shows the vertical expansion factors of integrals and is omitted if no integrals were to be plotted The 1D Output Menu P 266 10 4 6 Plot Layout There are four possible layouts for auto expanded plots The three including the overview spectrum are shown schematically in Figure 10 7 For normal plots the position of the spectral window on the paper is specified by the parameters SXLLEFT and SYLLEFT As these parameters are not available for expansion plots the parameter LAYOUT takes their place and can take on the following val ues Figure 10 7 separat In this case only the regions listed in the file reg are plotted The plots start at the b
43. a horizontal or vertical line depending on the cho sen dimension You may now move the cross hairs to a different place and click the middle button again to fix the second region limit The program will then invite you to enter a PROCNO under which the partial projection is to be stored as a 1D spectrum As soon as you have entered the number the calculation will start and then the result will be displayed If you want to redisplay the partial projection at a later time you need not recalculate it provided the PROCNO was not overridden by other data in the mean time Just click on part to get it on screen You may ver tically scale partial projections using the 2 and 2 buttons located below the row col buttons The calculation of partial projections can also be initiated with the commands specified in Table 3 4 type them in or call them from the Process gt Calculate pro Axis Projection typ Command Fl positive flprojp Fl negative flprojn F2 positive f2projp F2 negative f2projn Table 3 4 Commands to calulate projections jections menu As you can see from this table the program allows you to obtain positive and neg ative partial projections After startup these commands invite you to enter the row or column numbers defining the spectral range for the calcuation Please note that the buttons calc for F1 or F2 dimensions calls the commands flprojp and f2projp respectively and will display the positive
44. a new EXPNO requested by the program or specified on the command line e g r23p 5 8 6 Hilbert transform tht3 tht2 tht1 The commands tht3 tht2 thtl calculate the imaginary parts of a 3D spectrum required for the phase correction commands tf3p tf2p tflp respectively from its real part 3rrr 8 7 Read planes 8 7 1 Orthogonal planes r23 r13 r12 The commands r23 r13 r12 store a 2 dimensional plane of the current 3D spec trum parallel to the F2 F3 F1 F3 and F1 F2 respectively as a regular 2D spec trum under a new EXPNO with PROCNO 1 They may be invoked in one of the following three forms 123 r23 lt plane no gt lt EXPNO gt 123 lt plane no gt lt EXPNO gt no In the first form the arguments are requested by the program The second form creates a 2D spectrum including the imaginary part while in the third form only the real part is stored If MC2 is equal to gf the imaginary part of the 2D spectrum 2ii is taken from the 2D file 3iii If MC2 is not equal to gf the generated 2D imag inary files depend on the transformation sequence The resulting 2D files and the 3D files from which they originate are given in Table 8 4 In AU programs the commands for extracting planes must always be given with the described arguments e g r23 5 2 pu Here the F2 F3 plane with number 5 including its imaginary part is extracted and stored as 2D spectrum under EXPNO 2 on disk partition u 8 7 2 3D
45. acquisition time of the fid given by the acquisition parameter AQ You can find additional display options in the menu Display gt Options 2 3 Setting the size of the real spectrum The main processing steps to calculate a spectrum from the fid are window multi plication and fourier transformation The most important parameter common to all processing commands is the size of the real spectrum SI You must set it before any processing begins 1 Open the Process menu and select the command Real spectrum size si Enter the desired value followed by Return This is the number of real data points your spectrum should finally contain More convenient is to type for exam d 32k followed by Return The unit k amounts to 1024 points In most cases SI is set equal to TD the time domain size or number of points of the fid If TD doesn t happen to be a power of 2 SI should still be a power of 2 normally the next power of 2 larger than TD Otherwise the fast fourier transform algorithm cannot be applied resulting in a significantly increased processing time When ever SI is larger than TD zero filling is applied the fid is supplemented with SI minus TD zeroes 2 Alternately you can enter the command si on keyboard followed by Return It is also possible to type e g si 32k followed by Return The SI parameter value is here specified as an argument 3 A third method of setting SI is to call the processing parameter edit
46. addition to Tcl Tk scripts a tool for adding own functionality to XWIN NMR An AU program can be considered as a new XWIN NMR command introduced by the user AU programs are set up with the command edau and executed with the command xau cf chapter The File Menu for details The purpose of this chapter is to describe the AU language which is basi cally C extended by extra functions for NMR data acquisition and processing Please note that AU programs may also be combined with the Tcl Tk script lan guage to generate fancy user interfaces cf command xwish in The File Menu 15 2 Bruker standard AU programs Every XWIN NMR release includes a number of ready to use AU programs pro vided by the Bruker software or application groups or by customers These pro grams are delivered in source text format and are automatically compiled when they are to be executed Their usage is decribed in the program header which can be viewed with the edau command This is a list of just a few Bruker AU pro grams P 321 Writing AU Programs P 322 e convtold Converts a 2D spectrum file which can be considered as a matrix into a 1D spectrum file in which the 2D rows are linearly ordered and can be viewed in 1D display mode e fidtoser Converts a series of fids to a ser file e paropt Frequently used AU program to optimize parameters such as the pulse width by repeating an experiment several changing with different parameter values e parray Sim
47. allow ing you to check the single steps e Spectral limits The frequency limits and the sweep width of the spectrum cannot be changed because they are read from the experimental data They are only displayed to guide you when you set the next parameters The different ranges are Frequency range of iteration FSTRUN and FETRUN The region for calculating the noise FSNOIS and FENOIS this region must not contain any peak The range where the baseline should be smoothed FSFL und FEFL Select the limits FSTRUN and FETRUN in such a way that only the relevant part of the spectrum is covered In this way you reduce the total number of points used for the iteration and therefore speed up the calculations If the Number of points used for noise reduction was set you must enter the region limits for the calculation of the statistical noise Otherwise you can ignore this option If a Baseline correction mode was selected you must enter the region limits for determination of the baseline Otherwise you can ignore this option e Cut outs The number of the cut out segments CUT The following line will be repeated ICUT times The limits of the cut out segments FSCUT and FECUT D 9 10 DAISY P 221 Cut outs allow you to reduce the number of points used for the iteration even further You can cut out up to five ranges without interesting signals because the iterators can handle six different spectral segments
48. around the part of the spectrum that you want to zoom in on Click on the button Position the cursor to the desired screen position Now keep the left mouse button pressed while moving the mouse A rectangle will be drawn until you release the mouse button Then the rectangle will remain on screen with small squares at the edges and in the center The center square allows you to move the rectangle to another screen position and the other squares serve to resize the area of the rectangle In order to resize the rectangle function move the cursor into a square and move the mouse while its left button is pressed Click the right button to zoom the region defined by the rectangle The following describes a second method to expand an arbitrary area Click the left mouse button while the cursor is located in the data area of the XWIN NMR window Position the cross hair to the upper left corner of the area to be expanded Fix the position by clicking the middle mouse button Position the second cross hair to the lower right corner of the region and click the middle button to fix it Release the cursor from the spectral window by clicking the left button Click on the rightmost icon as shown above to zoom the area 1 No function assigned 2 Display a grid 3 Normally when the spectrum contains negative peaks both negative and posi tive intensity values levels are displayed The standard colors assigned are red yellow green shadings for positive da
49. available for expansion plots Using a prepared page layout rpar XWIN NMR is delivered with many prepared parameter sets suitable for different experiments They also include plot parameter i e layouts suitable to plot these experiments The command rpar allows you to copy a selected plot layout to your current data set thereby overwriting the current plot parameters After rpar you can call edg or edgx to apply modifications rpar is described in the chapter The File Menu Define show plot region 10 6 1 As described in the previous sections the frequency limits of a plot are defined by the parameters F1 F2 in Hz or F1P F2P in ppm They can be set in edg or by typing f1 f2 flp f2p on the keyboard An alternate frequently used way to define the plot region is the interactive setting from the display Expand the spectrum to show the region you want to plot then select one of the following commands from this submenu Retain CX Auto adjust Hz cm F1 F2 FIP F2P will be set according to the display limits The plot length CX as defined by the user previously will be retained and the frequency resolution Hz cm ppm cm of the plot will be adjusted accordingly new resolution F1 F2 CX The new resolution is printed on the status line 10 7 Plot Commands P 269 10 6 2 10 6 3 10 6 4 10 7 Retain Hz cm Auto adjust CX F1 F2 F1P F2P will be set according to the display limits The frequency resolu
50. be executed on button release If you release the button when the cursor is outside the menu no action is performed and the menu is closed Tearing off a pull down menu One or several pull down menus may be torn off the top menu bar and placed at an arbitrary position on the screen where it remains open until closed explicitely This feature gives you quick access to frequently used commands Move the cursor to the dashed line at the top of each menu Press the middle mouse button and drag the menu while holding down the button After releasing it the menu will be redrawn with a window frame that includes the menu s name You can now reposi tion the menu like any other window Tear off menus are not supported on Aspect Stations and may cause problems with some window managers Changing the window color The color of the main XWIN NMR window is controlled by the contents of the text file u prog lt XWIN NMR version gt app defaults XWinNmr This file has 4 entries XwinNmr foreground black XwinNmr background a3a3a3 XwinNmr XmText background b98e8e XwinNmr XmTextField background b98e8e describing the colors for the menu text the menus and the backround colors for the data set bar and the command line respectively A 6 digit color code starting with a character is given in RGB format For example a3a3a3 gives the same intensity a3 to the RGB components resulting in some sort of grey In order to find out which color na
51. chapter on 2DFT for details Table 6 6 For multidimensional spectra it can be advantageous to only store the real part on disk in order to save disk space and recalculate an imaginary part via the Hilbert transformation when needed The Process Menu for 1D Data P 150 6 16 4 Make fid from 1r 1i files genfid If an Fid obtained by ift is to be treated like an actually acquired Fid it must be stored under a suitable experiment number as the file fid This can be done with the command genfid Syntax of genfid genfid The new EXPNO is prompted for by the program If it exists already the user is asked whether the data can be deleted genfid EXPNO The new EXPNO is specified directly If it exists already the user is asked whether the data can be deleted genfid EXPNO y The new EXPNO is specified directly If it exists already the data are overridden without further warning The processed data number of this new data set will be set to 1 6 17 Digital filtering smooth filt filt smoothes the data by replacing each point with a weighted average of it s sur roundings The coefficients must be in a text file in the directory u exp stan nmr filt Id and have for example the following format 3 l 2 I The first number must be odd and gives the number of coefficients followed by the coefficients themselves In the above example the data point p i is replaced by 1 p i 1 2 pi 1 pit 1 The c
52. chapters 1D 2D Processing Tutorial is not possible sref may be invoked to calibrate 1D or 2D data sets In order for sref to work as expected the lock nucleus parameter LOCNUC and the solvent parameter SOL VENT must be set in either dimension The lock nucleus determines which table is used for the lock command containing parameters such as lock power field value and frequency shift for the solvent The table is located in the directory u conf instr INSTRUM Its file name is built by appending Jock to the lock nucleus name e g 2Hlock INSTRUM is the parameter where the configuration name of the spectrometer is stored You may examine it by entering the command instrum on the keyboard or by calling the dpa parameter display The lock table may be edited with the command edlock SOLVENT is usually defined with the lock command During lock in the lock power field value and frequeny shift for the solvent are set according to the values in the lock table The lock in procedure sets the frequeny shift to the exact fre quency shift value for the given solvent as listed in the table and then adjusts this slightly to achieve lock in As a result the absolute magnetic field is now nearly the same no matter what lock solvent is used This has the advantage that offsets can now be defined in ppm since the absolute frequency corresponding to a given ppm value no longer depends on the lock solvent i e SF BF1 where SF is the 9 3 Integrati
53. command sref A data set converted by conv will be stored as the following XWIN NMR data set e DU is set to the disk partition on which the foreground XWIN NMR data set is stored If you want to store the converted data on a different disk you must change to a data set on that disk Alternatively you can use the command btran for conversion e USER is set to the USER name of the foreground data set Only files which were transferred by that user can be converted btran allows you to convert data sets into a different USER directory e NAME is set to the file name of the Aspect 2000 3000 file without the file name extension e EXPNO is set to the file name extension of the Aspect 2000 3000 file e PROCNO is set to 1 Example A file APO OF 104 was transferred from the spectrometer am400 by the user guest It will be stored on the workstation in u bruknet am400 guest APOLOF 104 For the conversion the user guest must run XWIN NMR from one of his data sets e g DU z USER guest NAME test EXPNO PROCNO The converted file will be stored as DU z USER guest NAME APOJOF EXPNO 104 PROCNO 1 conv is capable of converting different types of data sets by trying to determine the data type from the name of the transferred file e g SER SMX IMAG I001 P001 If the type of data set cannot be determined the programs will display a list of known data set types and you have to select the type from the list 5 11
54. comprising the 3D acquisition data are stored in the ser file There are two possible orders depending on the pulse program used called 321 and 312 cf the chapter on 3D processing for details MC2 determines the phase type of the trans form and also depends on the performed experiment You will find a detailed description of these parameters in the chapter The 3D Process Menu XWIN NMR also allows you to modify the parameters by typing the parameter names in lower case letters on the keyboard For example the command si allows you to enter the SI parameter for the F3 dimension the command 1 si for the F dimension and 2 si for F2 The command wdw allows you to enter the WDW 4 4 Applying the 3D Fourier Tranform P 71 parameter for the F2 dimension the command 1 wdw for the F7 dimension The command lb allows you to enter the LB parameter for the F2 dimension the com mand 1 lb for the F dimension etc Please note 3D processing commands do not overwrite the measured 3D fid with the processed values Instead they create new files containing the result The 3D fid in our example is stored in the first file of Table 4 1 while the processing u data guest nmr exam3d 1 ser u data guest nmr exam3d I pdata 1 3rrr Table 4 1 Acquisition and processed data files of exam3d result is stored in the other files pdata is the processed data subdirectory The file 3rrr contains the real data points after the fourier transfor
55. conf plotter init u conf printer init depending on the device type Choose the type matching the connected plotter The program will then ask if it should be given an individual name by printing Enter identification name RET for no name q quit This is only necessary if several plotters of the same type are connected Otherwise this question can be answered with Return so that the individual name of the plotter will be set equal to its type specifier e g hpdj550c The plotter will then always be referred to by that name In the case of several plotters the chosen name max 6 characters will be appended to the plotter type by the program If for example two plotters of type hpdj550c have been assigned the names 1 and 2 they will be referred to as hpdj550c_I and hpdj550c_2 The next question Do you want to specify a class y n allows you to specify the plotter class which is most often answered with n Next the interface to which the plotter is connected must be entered Please enter output device On AspectStations enter p for the parallel channel or tty tty2 tty3 tty4 tty17 tty18 to select the appropriate serial channel On Silicon Graphics systems enter 10 1 Printer plotter installation cfpp P 245 plp for the parallel channel or ttyf1 ttyf2 to select the appropriate serial channel The program will then make the necessary calls to the line printer scheduler of the operating system which will make the n
56. data directory of the current data set The command lpa and lpp print the acquisition and processing status parameters on the current printer CURPRIN to be set up with edo In addition lpg and lpgx print the plot parameters i e the frequency range of a plot and the resolution Hz ppm lpc lists the data set parameters DU USER NAME EXPNO PROCNO lp is identical to the sequence Ipc lpa lpp lpg CURPRIN must contain a valid printer name made known to XWIN NMR with cfpp The printer name must be pre ceded by a sign otherwise the name is interpreted as a file name in the current processed data directory and the parameter output is stored there A special command is Ippl It stores a parameter list called param txt in the current processed data directory From this file the parameter list of a plot is generated For this reason Ippl is called by any plot command that is to output parameters The format of a parameter printout is taken from a format file It contains the parameters to be included in the list and their numerical format and physical units Format files are stored in the directory u exp stan nmr form Table 10 5 shows the Ipc curd l normlp Ipa acqu l normlp lpp proc l normlp lpg plot l normlp lpgx plotx normlp Table 10 5 Format files for the Ip commands 10 11 Display status parameters P 273 file names valid for the lp commands For 2D and 3D data sets the file names are t
57. default XWIN NMR displays help messages in the status line when you move the cursor over the command buttons You may disable the messages by choosing off Background Black white or color You may define whether the background of XWIN NMR s data area the area where the spectrum is drawn is set to black white or to a color If you decide for color you must enable the radiobutton Background in the colors section of the window Then you can adjust the desired color using the sliders or select a color from the table with a double click Colormap Variable or fixed This is not important for Silicon Graphics and other machines which provide several color look up tables Select variable if a second color inten sive application is running parallel to XWIN NMR This ensures that when moving the cursor into an application s window its own color table is loaded and thus colors are displayed 2D mode Contour or Image 2D data sets may be displayed in form of a contour map a colored map image of intensities or an oblique view Contour and image are the most frequently used modes and you may switch between them at any time by clicking on the respective command button The purpose of the 2D mode selection within the User Interface Settings window is to define in which mode a 2D spec trum should come up when you start a new XWIN NMR session and select a 2D data set Status Define how messages in XWIN NMR s bottom status line are prin
58. device on which the out put is to occur must be defined XWIN NMR provides the parameter CURPLOT for this purpose which can be set from the output parameter editor edo type in this command or call edo from the Output gt Setup menu When the edo dialog box is open click on the downarrow rightmost of CURPLOT You will see all plotters configured with cfpp Select the desired one and exit from edo XWIN NMR allows you to define the layout of a plot from the plot parameter editor edg type in this command or call it from the Output gt Setup menu Details about the various layout parameters are described in the chapter The Output Menu When you exit from the edg editor the parameters are stored in the file meta in the cur rent data directory where also the spectrum file is located 1D Data Processing Tutorial P 36 Instead of setting up all layout parameters using edg it is easier to start with a pre defined layout The sample 1D data set exam d contains a meta file representing a layout suitable for an HP Deskjet 550C or another A4 size printer In order to be able to use this layout you should have configured an hpdj550c using cfpp even if your own printer or plotter is of different type remember that cfpp allows you to have several plotters configured Enter the edo command set the parameter CUR PLOT to this printer and exit from edo Open the Windows gt Plot Preview menu and click on the command view you can also type view on
59. documentation directory u prog daisy doc english 9 10 2 1 Program SPECPREP Miscellaneous parameters Title of the data set TEXT No of points used for noise reduction NS No of points in resulting spectrum NOF Usually you should set the number of noise reduction points to 0 Nowadays NMR spectra are good enough for DAISY without further manipulation within SPECPREP The maximum number of points is 16000 Bigger numbers would result in enormous calculation times for the iterators We recommend that you limit the total number of points as follows specify a close overall range see Spectral limits cut out irrelevant sections See Cut outs Baseline correction Enter baseline correction mode Number of Fourier terms displayed only if the mode requires Fourier terms Do you want step control output Y N When you save the data set the editor converts the correction mode into the parameter IFLAT If you select a correction mode you must set the number of Fourier terms cor responding to the variable NFC The Analysis Menu P 220 If you did not select a correction mode this parameter input line will not be dis played Usually you will already have corrected the baseline with XWIN NMR In that case set the correction mode to no correction To get a more detailed protocol output you can activate the step control varia ble IPLOT After each operation the program prints an X Y data section
60. e to display a list of all files of the station available for conversion You select a file by clicking on its name e to convert the next available file If no file is found the program will wait until a file has been transferred The AU program remproc makes use of this feature If more than one file is present all files will be converted but not necessarily in the order in which they were transferred The conversion stores the station name into the parameter INSTRUM You can examine this parameter with commands such as dpa lpa or 2s instrum If data have been acquired through DISNMR automation DISNMR command RUN they will have a name in the form YYYYOF lt nnn gt There will also be a so called extended parameter file YYYYOX lt nnn gt Important note Make sure that the extended parameter file is sent first especially if you use auto matic transfers from the spectrometer to the workstation If both files are sent to the workstation for conversion conv will first convert the extended parameter file The File Menu P 114 The DISNMR extended parameter file contains the parameters NUCLEUS and SOLVENT which will be stored into the corresponding XWIN NMR parameter files If the extended parameter file is not available or if it was not transferred the parameters SOLVENT and NUCLEUS are set to unknown You can set them with the command nuso Both parameters are needed for automatic spectrum calibra tion with the processing
61. empty and XWIN NMR plot commands send their output to the device defined by the parameter CURPLOT set by edo If you enter the name of a plotter configured with cfpp into this field this plotter will gain priority over what is specified in CURPLOT Setting CURPLOT is no longer necessary How ever the flexibility to send plots of different data sets to different plotters if con nected is lost PlotMsg A plot command given in XWIN NMR is passed on to the operating system s spooler where it gets assigned an id number The number is printed in an informa tion window If this message disturbs you select no instead of yes and it will be suppressed ZGsafety If set to off the zg acqusition command overwrites existing acquisition data files fid or ser with the new measurement This is potentially dangerous if you type zg inadvertently because you may loose important data If you select on instead of off zg will ask you whether the data can be deleted if existing The Display Menu P 312 Spectrum Axis Integrals 2nd Spectrum Baseline Background Click on one of these items to define the graphical object whose color you want to adjust Use the sliders to create your own color by mixing the Red Green and Blue components or double click on a pre defined color in the table Click on Apply to make the chosen color effective Integrals denotes the integral traces in manual integration mode 2nd spectrum is spectrum 2 in dual displa
62. ensures that a reference inten sity is plotted in the given size in cm This reference is chosen through the processing parameter PSCAL of the corresponding 1D spectrum y scaling of 1D spectra or for projections of the corresponding dimension PF2CY 1 causes both projections to be scaled equally 11 3 8 Peak list Plotting the peaks of 1D spectra plotted along the F1 and F2 directions of a contour plot is analogous to that of 1D plots and is controlled by the parameters PL1HEI PLICHAR PLIDIG PLIMRK PLICOL PLIUNIT PLIMUL PL2HEI PL2CHAR PL2DIG PL2MRK PL2COL PL2UNIT PL2MUL for the F1 and F2 directions respectively They correspond to the parameters PLHEI PLCHAR PLDIGIT PLMRK PLCOLOR PLUNIT and PLMUL as described in the chapter The 1D Output Menu 11 3 9 Rotation and reflection of a 2D plot These geometric operations are controlled by the parameters WROT and WMIR as described in the chapter for 1D plots 11 3 10 Automatic plotting on several sheets of paper If the parameter CLIP is set to no and CX1 or CX2 have values greater than the paper size the plot is continued on additional sheets in both directions This way even on small plotters a 2D plot may be output in any desired resolution and size 11 3 11 Plotters with endless paper Please refer to the chapter The 1D Output Menu 11 4 Page layout stacked plot edgw The command edgw is used to define the layout of stacked plots Figure 11 4 shows an examp
63. extension e XWIN NMR filename The name as it would appear in the XWIN NMR data directory May be edited manually e Destination User Directory This indicates the data directory into which the converted dataset will be stored i e in the directory lt disk gt data lt Destinationuserdir gt nmr The value of this field is initially set in the Edit options window although it may be edited for each entry This field may also be extracted from the Aspect filename if option 9 has been used in the format e Rename Flag This determines whether a file is to be renamed to the XWIN NMR filename string If this flag is set to off then the original Aspect filename is used in the XWIN NMR data tree and the XWIN NMR filename is completely ignored If renaming has been enabled then the old Aspect filename is stored in the title parameter TI with the processed parameters The flag is ini tially set in the Edit Options window e Conversion Flag If this flag is set to off then the file will be unconverted and will remain in the 5 11 Conversion P 123 BRUKNET directory The value of this flag is initially set by the Select button in the main menu although it may be altered individually for each entry Bruktran automated renaming Renaming Files The Bruktran program offers two possibilities for the user to rename Aspect data files either manual editing or automatic editing Manual editing simply involves entering the new XWIN
64. fid is stored in the file u data guest nmr exam 1 d 1 fid while the processing result ist stored in the files u data guest nmr exam1 d I pdata I Ir and u data guest nmr exam 1 d 1 pdata 1 i pdata is the processed data subdirectory the files Ir and i contain the even and odd data points after the fourier transform the real and imaginary parts of the data 2 Instead of calling the commands from the Process menu you can enter them directly on the keyboard type lb followed by Return enter the line broadening value followed by Return and then type em to execute the function You can also specify the LB value on the command line type lb 0 3 followed by Return 3 The line broadening factor is a processing parameter called LB You can enter all XWIN NMR parameters directly from the keyboard by typing their name in lower case characters You can also view and change all processing parame ters at once by calling the processing parameter editor edp 1D Data Processing Tutorial P 16 4 When you examine the Process menu you will find that XWIN NMR provides a number of additional window functions such as Gaussian but you can also specify your own user defined window functions 5 XWIN NMR allows you to adjust the parameters of window functions interac tively with the mouse and view the effect on the fid and the transformed spec trum simultaneously Open the Process menu and activate the command Manual window adjust Th
65. first mode is enabled data and parameter files are deleted with the consequence that the whole 5 7 Delete Data Files P 105 Figure 5 14 The File gt Delete submenu directory is removed and the corresponding data set no longer exists on disk In the second case only the data files are erased while the parameter files are retained A data set directory therefore still exists after executing the delete command with out any data but containing parameter files which may be used e g for acquiring new data under the same name Deleting data sets del display list of data set names NAME parameter of the current USER stored in the user s data directory DU data USER nmr deldat like del but data sets are ordered according to their acquisition dates delp processed data any dimension e g 1r 1i and 2rr 2ii files dela acquisition data any dimension fid and ser files dirs processed one dimensional data Jr i files del2d processed two dimensional data 2rr 2ii files delf one dimensional fids fid files deli imaginary processed data any dimension e g Ji 2ii Deleting imaginary data can save a substantial amount of disk space After delet ing the imaginary part of spectra phase correction is no longer possible You can get the imaginary part back by re transforming the acquisition data or if those are no longer available by applying a Hilbert Transform to the real data see process ing commands
66. flag having the effect that the parameter files of the last used data set are taken over as soon as the AU program switches to the next data set regardless whether the next data set must first be created or already exists Individual parameters may be adjusted for a particular data set of the series such as P1 in the example The flag set by uselastpars may be cancelled with the command usecurpars From then on the parameters of an existing data set 15 7 Parameters P 327 getcurdata start with data set on screen fetchpar P 1 amp f1 save pulse width P1 in float variable f1 uselastpars set flag to initialize parameters from last data set times 10 begin loop zg start acquisition expno increment EXPNO setcurdata switch to data set with new EXPNO fl 1 increment pulse width by 1 microsecond storepar P 1 f1 store it in parameter file end end of loop quit terminate AU program Figure 15 3 Data set handling with uselastpars will no longer be overwritten by those of the last used data set when switching to it The command getdataset opens a dialog which allows you to enter the desired data set on the keyboard It may replace the getcurdata command at the beginning of an AU program Figure 15 2 gives an overview of which statements must be terminated by a semi colon The rule is XWIN NMR commands contained in the command table aucmd h do not
67. in our example is stored in the first file of Table 3 1 while the u data guest nmr exam2d 1 ser u data guest nmr exam2d I pdata 1 2rr u data guest nmr exam2d I pdata 1 2ri u data guest nmr exam2d I pdata 1 2ir u data guest nmr exam2d I pdata 1 2ii Table 3 1 Acquisition and processed data files of exam2d processing results are stored in the pdata directory which is the processed data 3 5 Applying the 2D Fourier Tranform P 43 subdirectory The file 2rr contains the real data points after the fourier transform and the other files contain the imaginary data points The files 2ri and 2ir are only present in the case of phase sensitive spectra 3 5 Applying the 2D Fourier Tranform Type xfb on the keyboard or open the Process menu and click on 2D transform xfb The tranform starts with the F2 dimension by transforming the individual fids in the ser file of the acquisition data and then continues with the F7 dimen sion The progress is reported on the status line at the bottom of the XWIN NMR window At the end of the transform the software calculates a compressed spec trum corresponding to the display window size from the real part 2rr and stores it in the file dsp This file is loaded to the display whenever this data set is selected as current data set or when the display shows only an expansion of the spectrum and you click on the all button to display the full spectrum When you expand a 2D spectrum on the screen
68. is applied when four Fids separated by DO with phases 0 90 180 270 degrees were acquired this method is also sequential in F1 States States Ruben Haberkorn phase sensitive 4 quadrant transformation is applied when two successive FIDs not separated by DO with phases 0 and 90 degrees were acquired and the next two also with 0 and 90 degrees The FIDs are acquired with the same t simultaneous quadrature detection in F1 States TPPI States Ruben Haberkorn phase sensitive 4 quadrant transforma tion is applied when two successive FIDs not separated by DO with phases 0 and 90 degrees were acquired and the next two with 180 and 270 degrees The FIDs are acquired with the same t simultaneous quadrature detection in F1 Echo Antiecho States Ruben Haberkorn phase sensitive 4 quadrant transfor mation for gradient enhanced spectroscopy Special handling is applied to the raw data Each two consecutive FIDs are replaced by re0 iml im0 im0 rel reO rel rel reO iml iml im0 processing then continues as in the States case The result of the phase sensitive transformations is stored in the four files 2rr 2ri 2ir and 2ii in the current data set directory 2rr purely real data 2ri real in F2 imaginary in F1 2ir imaginary in F2 real in F1 2ii purely imaginary data 7 5 General 2D processing options xfb as well as xf1 xf2 xtrf xtrf2 the latter 2 to be described later may be called
69. is displayed in the status line at the bottom of the XWIN NMR window 1 Multiply magnify data by 2 2 Divide data by 2 3 Reset vertical scaling of the data so that the largest peak fits in the data area 1 Multiply data by 8 2 Divide data by 8 3 Vertically scale data arbitrarily Here you must keep the left mouse button pressed and then move the mouse until the desired scaling is reached 1 Expand zoom data by 2 from the center of the data area without changing the vertical scaling The following describes a method to expand an arbitrary area leaving the y scaling the same Click the left mouse button while the cursor is located in the data area of the XWIN NMR window Now by moving the mouse the cursor will move along the spectrum trace and can be released from there by clicking the left button again Clicking the middle button will mark the current position the mark can be removed using the right button Clicking the middle button a second time at a dif ferent cursor position will expand the area between the marked and the current cur sor position 2 Compress un zoom data by 2 3 Reset zoom region to full spectrum The vertical scaling will remain unchanged 2 2 Manipulating fid or spectrum on the screen P 13 1 Display complete spectrum but do not change the zoom region 2 Display last zoomed expanded region 3 The buttons decribed so far allow you to independently scale the data on screen either h
70. lower case characters For example both ft and FT would execute a fourier transform aucmd h is the command table containing the definitions of the lower case commands a second table aucmd2 h contains the upper case definitions 15 4 Executing XWIN NMR commands Any arbitrary XWIN NMR command may be executed from an AU program using the AU command xcmd or the C function CPR_exec Table 15 1 shows a number Writing AU Programs P 324 xcmd ft CPR_exec ft WAIT_TERM fourier transform xcmd zg CPR_exec zg WAIT_TERM start acquisition xcmd lb 0 3 CPR_exec Ib 0 3 WAIT_TERM set LB 0 3 Hz xcmd swh 5000 CPR_exec swh 5000 WAIT_TERM set SWH 5000 Hz executed com xcmd text CPR_exec text WAIT_TERM mand stored in the string variable text Table 15 1 Executing XWIN NMR commands in AU programs using xcmd or CPR_exec of examples CPR_exec must be terminated with a semicolon according to C syn tax The first argument is a string C type char defining the command to be exe cuted The second argument which is not supported by xcmd is either WAIT_TERM or NO_WAIT If the first value is chosen like in our examples the function will not return until the command is finished e g acquisition has termi nated If the second value is specified the function will return immediately after the command has been sent to XWIN NMR not waiting for its termi
71. multiplication Table 6 3 nary part can be calculated from each other via a Hilbert transformation In XWIN NMR the command ht provides this transformation ht calculates the Hilbert trans formation of the file Zr which is created during the Fourier transformation and contains the real part of the spectrum The result is stored as the new imaginary part i ht is of use whenever the real part of the spectrum was further processed alone for example with baseline correction and afterwards the imaginary part is needed again e g to re phase the spectrum or to calculate a magnitude spectrum etc 6 16 Special transforms P 149 FT_mod effect no no FT will be executed fsr real FT of one channel forward single real fqr real FT of quad data forward quad real fsc complex FT of one channel data forward single complex fqc complex FT of quad data forward quad complex isr real inverse FT of one channel data inverse single real iqr real inverse FT of quad data inverse quad real iqc complex inverse FT of quad data inverse quad complex Table 6 4 PH_mod effect no no phase correction will be executed pk phase correction using the parameters PHCO PHC1 mc magnitude calculation ps power spectrum Table 6 5 ME_mod effect no no Linear Prediction LPbr LPbc Linear Backward Prediction see chapter on 2DFT for details LPfr LPfc Linear Forward Prediction see
72. next subcube starts The order of the data points within one subcube is the same as the order of the subcubes within one data set first F3 the acquisition direction then F2 and finally F1 Figure 16 3 shows the storage order of a processed 3D data file with the N SG GEL Say SSS a VR f j i j Figure 16 3 Subcube format File Formats P 338 16 7 parameters SI F3 16 points SI F2 16 SI F1 16 XDIM F3 4 XDIM F2 8 XDIM F1 4 The upper left part of the figure shows the sequence of the individ ual data points of subcube 1 the lower right part shows the sequence of the sub cubes in the entire spectrum Pulse Shapes 16 7 1 16 7 2 XWIN NMR 2 0 and later Pulse shapes are stored in the directory XWINNMRHOME exp stan nmrlists wave in ASCII format conforming to JCAMP DX Table 16 1 shows a section of a shape file The data points represent the amplitude and phase values XWIN NMR versions earlier than 2 0 Pulse shapes are stored in the directory XWINNMRHOME exp stan nmrlists wave There are two types of data formats a binary one required by XWIN NMR for the execution of shaped pulses generated by the program shape and a text for mat which can be read into shape by the command ar and stored back in binary format by w for use with XWIN NMR Text Format The text format is particularly useful if you want to generate own shapes by a suit able program Figure 16
73. number PROCNO case 3 The data will then be stored under the name of the cur rent 2D data set but with the entered PROCNO If the optional switch parameter is the character n the 2D data set remains the current data set to allow for additional rsr rsc commands Otherwise the extracted row or column will become the current data set and will appear on the display WARNING This description is valid for the case where the 2D data were gener ated by a complete 2D transform If only one dimension was transformed then the following descriptions apply If only xf2 was performed rsc generates a new EXPNO containing the section as an Fid In contrast rsr creates a PROCNO Make sure that all transformation parameters are set up correctly If only xf1 was performed both rsc and rsr gener ate anew PROCNO An fid may be obtained using the command genfid 7 18 Extracting an fid from 2D Acquisition Data rser If the current data set contains multidimensional acquisition data i e a series of fids rser allows one to extract one fid and store it as a 1D data set Syntax e rser e rser_ lt fid number gt e rser_ lt fid number gt lt EXPNO gt lt PROCNO gt lt switch gt In case 1 the program will ask for the number of the fid within the serial acquisi tion data Case 3 allows one to explicitly specify an experiment and a processed data number under which to store the extracted fid The lt switch gt has the same meaning as with
74. of em is automatically preceded by bc i e a base line correction is always executed before the multiplication as long as the parameter BC_mod is not set to no 6 4 Manual window adjustment With this command interactive window adjust mode is entered You will find a detailed description of this mode in the chapter 1D Data Processing Tutorial for Beginners 6 5 Real spectrum size si This command defines the number of points in the real spectrum after Fourier transformation of the fid You can also type in the command or set the parameter SI from the edp processing parameter editor 6 6 Fourier transform ft The command ft transforms the acquisition data of the current data set which may already have been processed using a filter function The result is a spectrum con sisting of SI data points in the real part and SI data points in the imaginary part The value of the processing parameter SI must be set by the operator and must be a power of 2 Alternatively the default value may be used which is set equal to the acquisition parameter TD 2 in the case where TD 2 is also a power of 2 SI values which are not powers of 2 are automatically rounded up to the next highest power of two TD is the number of acquired data points i e the length of the FID If the user sets the value of SI lt TD 2 then the resulting spectrum is correspondingly smaller If the value of SI is greater than TD 2 then the Fid is filled out with
75. on a 2D spectrum the standard deviation and maximum and minimum of the 2D spectrum are calculated and stored as processing status parameters S_DEV YMAX_p and YMIN_p They are used by the command levcalc to determine a suitable threshold for plotting con tours of the spectrum on either display or plotter The automatic contour level calculation levcalc can be influenced by the process The Process Menu for 2D data P 174 ing parameters NLEV LEVO and TOPLEV Levels are calculated between the bottom and top levels The top level must be specified in TOPLEV in per cent of the absolute maximum intensity value in the spectrum the bottom level is a multi ple of the standard deviation S_DEV with the factor LEVO levcalc generates a level file with the specified number of contours and must be called in AU programs after the 2D processing commands if automatic contour plotting follows This method ensures that no spectral peak will affect the result 7 29 Quadrature image correction xqcl xqc2 xqcl and xqc2 are the two dimensional analogues to the quadrature correction command qc for 1D spectra See qc for description The needed correction value ALPHA and GAMMA are determined as in the 1D case with the command gk It is applied to a row or column of the 2D spectrum and the resulting ALPHA and GAMMA are entered as processing parameters for the F1 or F2 dimension of the 2D spectrum before issuing the command xqc2 or xgcl Chapt
76. on all defined integrals delete removes all integrals from the screen if you want to start integration from scratch but not from the intrng file if the regions were already stored on disk The 2 2 etc buttons allow you to expand the integrals simultaneously leaving the spectrum unchanged The lastscal button enables you to scale the integral values relative to the previously integrated spectrum Assume you want to compare the integrals of two spectra Select the first reference spectrum via the File gt Open menu or use the search comand Then proceed as follows enter manual integration mode 2 9 Spectrum integration P 29 2 9 3 define and manipulate the regions as desired store them in the intrng file and exit from integration mode select the second spectrum enter integration mode read in the intrng file via the File gt Read intrng command or define new limits click the lastscal button This command puts the integral values of the current spectrum onto the same scale as the reference spectrum Please note that comparing the integrals of different spectra is only meaningful if the data were acquired under the exactly same exper imental conditions Changing the mouse sensitivity The command buttons 2 2 and DEF in the mouse section of the button panel allow you to adjust the mouse sensitivity for the integral baseline correction slope and bias according to your needs 2 doubles the cha
77. preview commands display the output exactly as it would come out on this type of plotter with the only difference that the absolute size is scaled down to the window size thereby retaining the proportions e The plot layout must be set up using the commands edg edgx or edgw depending on whether spectrum plots 1D or 2D automatically expanded 1D plots or stacked whitewash plots are desired respectively This means you set up a preview exactly the same way as a normal plot Then 13 2 Plot preview P 317 instead of executing a plot command plot plotx plotw you start up the corre sponding preview command view viewx or vieww XWIN NMR will open a win dow containing the desired plot This will be a spectrum plot or a contour plot in the case of view depending on the data set an autoexpanded 1D plot in the case of viewx or a stacked whitewash plot in the case of vieww You may resize the pre view window and XWIN NMR will redraw the plot according to the new window size However the plot will be restricted to an area within this window having the same size ratio as the paper of the selected plotter CURPLOT Usually setting up a plot layout is an iterative process You must modify plot parameters several times before the layout appears satisfactory It is not necessary to close the preview win dow if you want to change a parameter The easiest way is to type in the new value on XWIN NMR s command line e g cy 20 Or yo
78. processing data directory After you have fitted a series of data points the fit parameters are stored in the edt1 editor Type edtl and click on EDPARM to see the fitted parameters The same parameters are of course also documented in the output file created by the fit command nxtp Display the next peak If you have picked the points with the command pd or pdO or if the points are read from the ASCII file t ascii then there might be more than one series of data points each belonging to one peak position In this case only one series of data points will be displayed on the screen at a time If you want to inspect the next series of data points type nxtp If nxtp is used on the last available series of data points then the first series of data points will be displayed wrap around A little window on the screen will contain information about the currently displayed peak Every time you use the nxtp command the parameter CURSOR will be updated The command nxtp will always delete the fit curve if there is one on the screen The command nxtp will always display the next series of data points at maximum vertical expansion A subsequent fit with simfit will rescale the point and fit dis play This is done because simfit scales all data points from all positions to their The Analysis Menu P 198 9 6 4 3 global maximum The commands ctl dat1 ct2 and dat2 only read one series of data points and scale to their maximum
79. projections Sums 3 14 Projections and Cross Sections P 61 Partial projections are projections in the mathematical sense along each projection trace the largest positive or the smallest negative intensity is picked Alternatively XWIN NMR allows you to calculate the sum of the intensities using the sum calc button combination The handling is identical to partial projections the associated commands are flsum and f2sum Disco projections Similar to sums as described in the previous section the sum of a number of col umns or rows is calculated However unlike F7 Sum and F2 Sum F1 Disco adds a column to the sum if the point at which it intersects a reference row is positive otherwise it is subtracted Similarly F2 Disco adds a row to the sum if the point at which it intersects the reference column is positive otherwise it is subtracted Only those data points whose value is greater than the plot parameter MI are used in building the sum The procedure for using the disco buttons is similar to the sum buttons except that once the column or row region has been defined it is necessary to position the cross hair a third time to define the reference row or column respectively and press the middle mouse button once more The calculation of disco projections can also be initiated with the commands fldisco and f2disco type them in or call them from the Process gt Calculate pro jections menu If the user wishes to calcu
80. require one but if you append one it does not hurt All true C stat ments and all C functions statements including parentheses with the arguments must be followed by a semicolon 15 7 Parameters 15 7 1 Storing parameters From an AU program parameters are stored in the parameter files of a data set by means of the CPR_exec function see examples in Table 15 1 or by means of the commands storepar acquisition or processing parameters storeplpar plot param eters storeplxpar expansion plot parameters and storeplwpar stacked plot parameters A storepar example is given in Figure 15 2 The first argument is a string the name of the parameter the second parameter is a variable Please note that the variable type must correspond to the type of the parameter XWIN NMR Writing AU Programs P 328 15 7 2 15 7 3 parameters can be of type int float double char string To find out the type of a particular parameter look it up in the files XWINNMRHOME prog include pstruc_all h XWINNMRHOME prog include pstruc_plot h XWINNMRHOME prog include pstruc_plw h XWINNMRHOME prog include pstruc_ h or for parameters not included in the h files in the format file directories XWINNMRHOME exp stan nmr form For two and three dimensional data sets storeparl and storepar3 access the F1 and F3 dimensions respectively It is also possible to output parameters into the status parameter files with storepars storeparls and st
81. return to return to the main 1D processing menu You can now proceed with the next chapter if you want to define an integral range file for area fitting Or you can immediately return to the T1 T2 menu click on Analysis gt Relaxation Without an integral range file the commands pd and pd0 will complain about the non existence of the intrng file You can ignore this warning if you don t intend to do an area fit at a later stage Create the intrng integral range file for area fitting The Analysis Menu P 194 Switch to the interactive integration menu and define integrals around all peaks which you have selected for the maximum search in the previous step For more details on how you define integrals see Chapter 2 9 2 of the XWIN NMR Manual A slope and bias correction of the displayed integrals is not necessary since each row of the series file has already been Fourier transformed phased and baseline corrected in the F2 dimension After all integral ranges have been defined return to the main 1D processing menu From there switch to the T1 T2 relaxation menu Analysis gt Relaxation pptl Create baslpnts and intrng file automatically An alternative to the steps described in the two previous chapters is the com mand pptl This command performs a peak picking like the pps command peak picking on screen which is described in Chapter 2 10 of the XWIN NMR Manual But in addition to the report box shown on the screen the two fi
82. rsr rsc 7 19 Replacing Rows and Columns wsr wsc wsr and wsc are the complimentary operations to rsr and rsc and replace the speci fied row or column of the current 2D spectrum by the 1D spectrum TEMP 1 1 7 20 Replacing an fid within a ser File wser wserp P 169 cases 1 2 or by the 1D spectrum with the specified processed data number PROCNO case 3 The program will print an error message if the 1D spectrum and the 2D spectrum are of incompatible size The lt switch gt has the same meaning as with rsr rsc Syntax 2 WSC e wsc lt column number gt e wsc lt column number gt lt PROCNO gt lt switch gt e WSr wsr_ lt row number gt wsr_ lt row number gt lt PROCNO gt lt switch gt 7 20 Replacing an fid within a ser File wser wserp wser replaces the n th fid of multi dimensional acquisition data file ser by the original acquisition data file fid of a one dimensional data set This enables one for instance to store a repeated measurement of a single fid of a 2D experiment in a ser file wserp replaces the n th fid of multi dimensional acquisition data file ser by already processed acquisition data files r i of a one dimensional data set This command is usually employed when a fid that was read from a ser file using rser and that was then processed by Is or a similar command is now to be written back into the ser file Syntax also valid for wserp e wser e wse
83. scaling is calcu lated from the plot region taken from the file reg and the width CX of the spectral window In the latter case the plot length is adjusted to fit the plot resolution as set by the user with the parameter SCALEP in ppm cm or SCALEM in Hz cm The parameter window is plotted unrotated left of the spec tral window independent of the setting of the parameters PKULEFT PYULEFT PROT The position of the title window is determined by the parameters TPOS TOFFSET The file reg can be obtained in different ways e With edmisc e By reading it in from a prepared file using rmisc e By generating a intrng file by manually integrating the spectrum in inte gration mode and storing the integration regions or by generating intrng using the command abs If no reg file exists but intrng exists the latter file is copied to reg e If neither reg nor intrng exist intrng is automatically generated through an internal call of the command abs Rotation and reflection The whole plot is rotated by 90 180 or 270 degrees if the parameter WROT is set to one of these values instead of 0 Some plotters allow the reflection of the plot along a vertical line through the middle e g for transparencies cf manufacturer s manual This may then be activated by setting the parameter WMIR to yes instead of no Suppress plot if no peaks found conditional plot The 1D Output Menu P 262 For automated acquisition and processing it is somet
84. set with the fid of the sec ond data set to be defined with edc2 and stores the result as processed data files Ir 1i of the current data set The original fid is retained The fid of the second data set is considered as the user defined window function Its size TD must be equal or greater than the size TD of the fid of the current data set In the latter case the window is truncated before multiplication is applied In order to generate a user defined window proceed as follows 1 Type new and define a new data set whose fid will serve as the window 2 Execute the AU program calfun This AU program calculates an arbitrary func tion and stores it as the file fid in the current data set This will become the user defined window Calfun is set up so that you can modify it by adding your desired window function You must recompile it after changing it Please read the header of calfun how to do that Calfun also contains examples e g how an exponential window is programmed Traficante window multiplication traf trafs Window function according to D D Traficante and G A Nemeth using parameter LB J Magn Res 71 1987 237 Sequential operations These commands provide abbreviations for a sequence of frequently used process ing steps ef corresponds to the execution of em followed by ft efp corresponds to the execution of em followed by pk gf corresponds to the execution of gm followed by ft gfp corresponds to th
85. stan nmr par lt parameter set name gt 5 6 Copy P 103 which were stored there via the command wpar earlier by the user or which have been installed using the command expinstall from the XWIN NMR release the so called Bruker standard parameter sets rpar displays a dialog box containing all currently existing parameter sets After having selected a name rpar allows you to specify which of the parameter files acqu proc meta outd should be copied to the current data directory where existing parameter files are overridden rpar will not destroy any data of the current data set nor will it overwrite the so called status parameter files acqus and procs which describe the acquisition and process ing status of existing data files rpar may also be entered on the command line followd by arguments e g rpar cosy all would copy all parameter files from the directory u exp stan nmr par cosy to the current data directory In addition to the keyword all you could also use any of acqu proc plot outd in order to copy acquisition processing plot or output device parameters only It is also legal to use wildcard characters For example the command rpar C would display all existing parameter sets beginning with the letter C The com mand rpar H Z would display all existing parameter sets beginning with the letters H LJ Z When a parameter set has been copied to the current data directory you can use the comm
86. stop bits RS232C parity Protocol type F F timeout Default Emulation KCGL option RS232C H1 96 H2 08 H3 0l H4 00 H5 03 H9 00 P1 06 GO 04 Table 10 19 KYOCERA F 5500 A4 A3 single sheet feeding Laser Printer XWIN NMR plotter type ps300 For printer settings see printer manual Adobe and PostScript are registered trademarks of Adobe Systems Incorporated in the U S and other countries Table 10 20 Adobe PostScript compatible printer with 300 dpi XWIN NMR plotter type wx4731 Interface PC2601 1 means OPEN or 1 S1 F 1 0 S2 B 1 0 3 D 2 0 2 0 3 0 3 0 4 1 4 0 5 1 5 1 6 0 6 0 7 0 7 0 8 1 8 0 1 2 3 4 5 6 F 8 pi or SWI Interface PC2609 CO OY Ne ae RE D on on on off off on on off SW2 on on off on on off off on Table 10 21 GRAPHTEC WX4731 12 roll pap The 1D Output Menu P 286 Chapter 11 The 2D Output Menu The Output menu Figure 11 1 contains the plot commands and utilities to print Setup 5 Define show plot region Plot commands r Plot editor xedplot Plot print status e Screen dump Print status parameters Display status pars Figure 11 1 The 2D Output menu or display parameters For plotting the following steps are required 1 Make all connected printers or plotters known to XWIN NMR with cfpp 2 For pen plotters specify the pen colors with edpp 3 Define a page layout
87. tf3 tf2 tf1 Unlike in 2D no combined transform commands exist Call the processing parameter editor edp either by typing in this command or by opening the Process menu and selecting General parameter setup edp A dialog box is displayed containing all processing parameters in three colums for the three dimensions to be processed Some parameters exist for all dimensions others only for one dimension It should be mentioned here that the contents and layout of the edp dialog box can be tailored by the user by editing the so called format file u exp stan nmr form proc e The most important parameters you must set in the edp window are SI WDW PH_mod for F3 F2 and F1 AQSEQ for F3 and MC2 for F F2 F3 is the dimension defined by the acquisition of one fid of the 3D experiment F and F2 are the orthogonal dimensions defined by the acquisition status parameters TD for these dimensions of the 3D experiment SI specifies the number of real points the spectrum should have after the transform in the corresponding dimension WDW allows you to select an appropriate window function With PH_mod you can select whether to apply phase correction or not For phase sensitive spectra an extra step is usually required to find the correct phases Phasing is then performed using extra commands after the transform PH_mod also allows you to select magnitude or power spectrum calculation AQSEQ is a parameter describing the order in which the fids
88. that of the current data set without data files but with parameter files In this respect wra and wrpa are different After wrpa the PROCNO subdirectory would additionally contain the processed data files Copy parameter files to wpar XWIN NMR Stores acquisition data fid and ser files in the directory DU data USER nmr NAME EXPNO and processed data r 2rr 3rrr etc files in the directory DU data USER nmr NAME EXPNO pdata PROCNO The acquisition directory contains depending on the dimension of the data the acquisition parameter files acqu and acqu2 The processed data directory contains the processing parameter files proc proc2 proc3 the plot parameter files meta and meta ext and the output device parameter file outd Even if no data fid or spectrum exist yet the data directories already contain The File Menu P 102 parameter files They are generated by the command new when the data directory is created and are taken from the last data set used The purpose of the command wpar is to save these parameter files in a special directory As such a parameter set set of parameter files describes an entire experiment including acquisition processing and plotting it can later be used to retrieve it from the save directory to perform an NMR experiment The storage directory is u exp stan nmr par lt parameter set name gt The name can be chosen by the user wpar displays a dialog box containing all cur re
89. the BRUKNET destination of data directory path The default value is obtained from the contents of the file usr local lib bruknet destination 5 11 Conversion P 121 e Current BRUKNET Station This sub directory refers to the station from which the data was sent e Current User This sub directory contains the transferred data files e Aspect File Format This string defines the way in which the tokens groups of characters are arranged to form the filename A token is defined by a set of digits 111 22 33 etc and each digit refers to a particular token The digits 0 and 9 have special meanings see Bruktran automated renaming The length of the format string must not exceed 8 characters e X32 File Format As above The length of the format string must not exceed 14 characters e Owner Of The Converted Data Set This specifies the user directory into which files will be copied after conversion This parameter is globally defined although the destination directory may be edited for individual files with preview mode selected e Rename Enable Flag This globally defined parameter determines whether the file is to be renamed from the Aspect filename to the X32 filename In preview mode it is possible to change this option for each entry in the table e Preview Enable Flag If preview mode is set to on then a list of files in the cur rent BRUKNET directory with different experiment names is produced along
90. the MEMSYS5 program and should be modified only by a user with detailed knowledge of the MEMSYSS program Please see the User s Manual for Running 1D MaxEnt for more details Start MEMSYSS deconvolution maxent There are two ways of starting a MEMSYSS5 deconvolution e By typing maxent In this case the second and third data set the plot region and the MEMSYSS5 parameters must have been defined already see above 66 99 e By answering y to the question after you have saved the MEMSYS5 parame ters in the editor program maxed At any time during a maxent run you can make use of the dual display function to inspect the progress of the iteration Show MEMSYSS results maxres MEMSYSS writes a report for all iteration steps into the mem log file which can be inspected at any time during or after a maxent run This file contains useful infor mation about the progress of the deconvolution After MEMSYS5 has reached convergence important values like good and evidence are stored in the mem log file The following parameters are especially important Omega Omega is the convergence criterion Convergence is reached when Omega is 1 Checking Omega during a maxent run gives an indication of the progress of the iteration e Evidence Evidence tells you how reliable the result of the deconvolution is compared to an earlier run with different parameters or a different point spread function PSF The smallest
91. the command edmisc You can copy this file from the current data directory to a save directory using the command wmisc and read it back from there to the data directory of another data set with rmisc Both commands can be called from the File gt Copy menu and are described in greater detail in the chapter The File Menu The processing command bcm then allows you to apply exactly the same correction to the other spectrum You can type in bem or call it from the Process gt Special processing gt Baseline correction menu Baseline correction using splines sab The automatic and manual baseline flattening methods described so far try to fit a poynomial or other curve to the overall baseline of the entire spectrum or a selected region The success of this method depends on whether the shape of the baseline can be approximated by such a function In contrast the cubic spline interpolation method provided by the command sab fits the overall baseline piece wise by determining a different set of coefficients between each pair of selected points The necessary condition to achieve a fit requires that the overall curve be smooth and continuous Thus weirdly shaped baselines can be approximated quite 1D Data Processing Tutorial P 24 2 9 accurately The name cubic spline is derived from a thin flexible device used by draftsmen to draw curves Before you can execute the command sab you must define the baseline in the fol lowing way S
92. the extensions p r and s respectively On XWIN NMR release media a number of sample gradient programs are deliv ered After installation of XWIN NMR they are stored in the directory u exp stan umr lists gp exam u exp stan nmr lists gp solids u exp stan nmr lists gp imag The command expinstall see menu Acquire gt Spectrometer setup which must be executed after installation of XWIN NMR will copy the contents of the selected directory to the working directory u exp stan nmr lists gp The command edgp may also be entered on the keyboard followed by the name of 5 3 Open Other Files P 85 the desired gradient program or followed by an argument containing wildcard characters see edpul and how to change the default text editor for details 5 3 6 Automation programs edau Automation AU programs are text files written in the language C with the exten sion that XWIN NMR commands may be included edau allows you to create a new AU program and to edit or view an existing one When exiting from the text edi tor the AU program must be compiled before it can be executed XWIN NMR asks you whether you want to compile the current AU program If yes the computer s C compiler is invoked Details about writing AU programs are described in a special chapter of this manual The purpose of AU programs is to implement user defined commands in XWIN NMR either based on XWIN NMR internal commands or entirely self written T
93. the file grows with time in fact each time you execute a command some lines are appended It is your responsibility to delete it from time to time 12 3 Dual Display The command Dual display equivalent to the keyboard command dual switches XWIN NMR into a special mode where two spectra are displayed above each other for comparison You may scale the spectra individually shift them horizontally against each other and display and store on disk their difference or sum Figure 12 4 shows the window layout of dual display mode The first spectrum displayed in dual mode is the spectrum on screen when invok ing the command Dual display The second spectrum must be defined as the so called second data set by entering the command edc2 A dialog window will be opened where you may enter the name and other characterisitics of the second spectrum If no second data set is defined or the data set specified in edc2 does not exist Dual display will print a message and allow you to reenter edc2 in order to specify a valid data set All scaling and shifting commands located below the label dual in the left hand button panel apply to both spectra on screen The buttons underneath the label spectrum allow you to shift spectrum 1 exactly to the bottom or to the center of the screen or to any other position by moving the mouse The buttons below the label spectrum2 provide the same functions for spectrum 2 In addition you may change its vertical scali
94. the keyboard A win dow will be opened which shows the current plot exactly the way it would be out put by the printer if the command plot would have been given rather than view Depending on the plot type you will have to wait a few seconds until the plot is drawn The previewer is a window which may remain open while you execute other XWIN NMR commands You should now close the previewer by clicking the Quit button set CURPLOT to your own plotter and restart the previewer You may now change any layout parameter using the commands edg or setti set plot title or by entering a plot parameter name such as cy directly on the keyboard Clicking on the Restart button of the viewer window will redraw the spectrum taking into account all parameter changes As soon as the plot looks as you intended you can print it by typing plot In edg you may among many other parameters specify the spectral region to be plotted in Hertz or ppm parameters F1 F2 or F1P F2P In addition you may set these limits interactively according the current display limit from the menu Out put gt Define show plot region XWIN NMR is delivered with a number of parameter sets defining various NMR experiments comprising acquisition processing and plot parameters These sets are available to the user after execution of the expinstall command with the option enabled to install the standard experiments They contain suitable plot layouts which can also serve as a basis f
95. the specified limits absd is an alternate command to abs It uses a slightly different algorithm to detect the baseline and may be of advantage in special cases Please note that abs does not only perform automatic baseline correction but also automatic detection of the spectral regions containing signals as required by auto matic integration Before terminating abs stores the detected regions in a file intrng For this reason abs can also be called from the Analysis menu You will find more details in the section Spectrum integration Manual baseline correction and bem Manual baseline correction is invoked from the menu Process gt Special process ing gt Baseline correction The XWIN NMR button layout will change as shown in 1D Data Processing Tutorial P 22 Figure 2 3 Figure 2 3 Interactive baseline correction buttons This window lets you select a polynomial sine or exponential curve whose coeffi cients A B C D E you can adjust with the mouse by putting the cursor on the corresponding command button and moving the mouse while its left button is pressed Curve equation polynomial A Bx Cx Dx Ex4 sine A Bsin Cx D exponential A Be When you enter the baseline correction mode the default function type is the poly nomial The mathematical equation is displayed in the Info window The sine or expon buttons will bring up the other functions The function trace is displayed simultaneously with the spectrum
96. the statis tical noise To compare two PSF functions SIGMA must be set to an estimated noise value There are three possibilities to determine the noise value You can use the CSIGMA value calculated by MEMSYSS5 at the end of a run see maxres You can use the command noie to determine the noise value Enter 1 as the order of difference You can use the sino command to determine the noise value Select NOISF1 NOISF2 SIGF1 and SIGF2 in such a way that the values roughly correspond to the region you want to deconvolve with MEMSYSS5 FIP F1 F2P F2 The frequency limits reflect the area currently defined as the plot region These values are only displayed for 1D data sets On nD data sets the whole spectrum as you See it on the screen is used for the deconvolution If you want to decon volve only a part of the nD matrix use the strip transform feature to get the region of interest PSFDEF You can run 1D MEMSYSS either with a user defined PSF or with a parametric PSF Use the command psf or wpsf to generate a user defined PSF A parametric PSF is defined by the parameters ASYM PSFWI and PSFSH These parameters correspond to those the user is interactively asked for when running the psf command See the chapter on psf for more details 9 11 MAXENT MEMSYS5 P 231 9 11 4 9 11 5 All other parameters are set to default values which have been found to lead to a reliable deconvolution These parameters are used internally by
97. then view them using the command edp The program then asks you whether to apply the phase cor rection to the entire 2D spectrum To phase all rows the command xf2p is invoked The corresponding command to phase all columns is xflp xfbp phases both rows and columns and is identical to xf2p followed by xflp You need not execute these commands right now You can start them from the Proc ess gt Phase menu outside the manual phase correction screen at a later time using the stored constants 9 In order to phase the spectrum in the F1 dimension proceed in the same way but select columns instead of rows using the col button 3 8 Spectrum calibration XWIN NMR provides manual calibration and automatic calibration with the com mand sref Both can be called from the Analysis menu sref can also be typed on the keyboard Its major application is the inclusion in automation AU programs for auto calibration of data measured with a sample changer or with QUICKNMR sref will only work if the files 2Hlock or 19Flock are installed in the directory u conf instr lt instrument gt for the spectrometer on which your data were measured The edlock menu must be set up properly for frequency locking You can find more details in the chapter The Analysis Menu under sref 2D Data Processing Tutorial P 48 In order to manually calibrate the spectrum click the calibrate button located below the phase button A cross hair will be displayed Move
98. vconv converts Varian Unity and Gemini data sets to XWIN NMR format Only acquired raw data can be converted Up to now data sets of VNMR 4 1 have been successfully converted It could well be that data from older VNMR versions can be converted also but we have not tried it Comments and suggestions for a further improvement of the conversion routine are welcome File formats and setup The VNMR data must reside in a directory with the extension fid Usually the VNMR store functions will generate a directory with this extension It contains the files fid procpar and text All three files are interpreted by vconv yconv will first ask for a file name You can enter the file name in two ways e With its full path name e g usr people guest eva fid In this case vconv only checks for the existence of this file e With its relative path name e g eva fid In this case vconv first checks for the file in the current directory from which XWIN NMR was started If the file cannot be found vconv will check for the environment variable VNMR If VNMR is set e g to usr people guest varian the directory path is added to the file name and vconv checks for its existence If this check also fails vconv will ask for the file name again During this inter active session vconv can be terminated with the Delete key from the keyboard The extension fid can be omitted when you enter the file name vconv will append it if a
99. ways they can all be held fixed at the same value taken from the parameter BAYAOPT BAY VARA no they can be forced to all have the same value which is to be optimized BAY VARA unique or they can be allowed to be optimized independently BAY VARA individual Note that the decay rates in the time domain are equivalent to the line widths in the frequency domain BAYAMAX BAYAMIN These two parameters allow for a range to be specified within which the decay rates should lie Components for which the decay rates move outside this range are removed from the model during the analysis Note however that due to the fact that the analysis is performed in the time domain it is possible that certain compo The Analysis Menu P 238 nents are so strong that they keep appearing in the signal detection or are repeat edly encountered in the maximum search so that an endless loop could occur if the range is set too narrow The main use for these parameters is to allow for a faster than through the model probability test elimination of components that corre spond to noise very small decay rate or to very broad baseline artefacts PEAKLST This parameter specifies a peak list file to be used in parameter estimation This file must have the format of the peak list file described in the chapter on 1D processing and can for example be set up with the peak picking commands BAYNADD BAYELEV After a signal detection pass the highest BAYNADD freq
100. were not found by the maximum search with pd Please check the follo wing in such a case a Is the intensity at this position 0 or almost 0 If so the peak picking routine cannot find the peak and there is nothing you can do b The point or the maximum of the peak lies outside the allowed drift range Increase the number of drift points DRIFT command edt1 and exe cute the command pd again c The point is the maximum of a relatively small peak or is not fully resolved from an adjacent peak Type PC and decrease the peak picking sensitivity The Analysis Menu P 196 constant Execute the command pd again and check whether the point was now found If not decrease PC even further and execute the pd command again d It could be that MI the minimum intensity for peak picking is set too high Type MI and set it to 0 and execute the command pd again e pd0 Pick all points at the exact same position from all rows The pdO command is an alternative to the pd command The values of DRIFT MI and PC are irrelevant when you use the command pd0 No peak picking maximum search is done Instead the intensity values in the rows of the 2D data file at the positions defined in the baslpnts file are simply read If the peaks do not drift at all then the result of the commands pd and pd0 is the same The pdO command can be used if points to be picked lie on the shoulder of bigger peaks The normal maximum search will not be able to pick th
101. where the data sets examld exam2d and exam3d are listed If there are other data sets in the directory u data guest nmr they will also appear in the box Click on exam2d in order to instruct the program to make this data set the current data set XWIN NMR will automatically show the 2D layout because it identifies exam2d as a 2D data set The identification of the layout is not performed via the name of the data set but through the contents of the parameter file meta stored in the directory u data guest nmr exam2d 1 pdata I For space reasons only the P 37 2D Data Processing Tutorial P 38 acquisition data of exam2d are delivered on the release tape You must enter the command xfb to execute a 2D transform After xfb is finished the transformed spectrum will be visible on the screen 3 2 Manipulating the spectrum on the screen You should now have Figure 3 1 on the monitor representing the standard 2D lay devel 1671944 1161072 967560 671916 559928 466608 466608 559928 671916 967560 1161072 1671944 Figure 3 1 The 2D screen layout 3 2 Manipulating the spectrum on the screen P 39 out The data area shows the 2D spectrum in intensity display mode The right side indicates the numerical intensity values of the contour levels The button panel at the left side of the XWIN NMR window allows you to interac tively scale and expand the data to enter various subroutines and to toggle the 2D spectr
102. with edg contour plot edgw stacked plot or rpar predefined layout and a plot title with setti 4 Define with edo to which of the connected plotters the output should be sent P 287 The 2D Output Menu P 288 see also the setres command 5 Preview the plot on screen with view contour plot or vieww stacked plot Adjust the layout if required 6 Output the plot with plot plots flplot plotw The following sections describe these steps in detail We assume however that you are already familiar with 1D spectrum plotting The set up commands are part of the Output gt Setup submenu Figure 11 2 Figure 11 2 The Output gt Setup submenu 11 1 Printer plotter installation cfpp This command is described in the chapter The 1D Output Menu 11 2 Pen setup edpp This command is described in the chapter The 1D Output Menu 11 3 Page layout contour plot edg If the current data set is a 2D spectrum the command edg displays the layout parameters for a contour plot Figure 11 3 11 3 1 Components of a Contour Plot Like a 1D spectrum plot a 2D contour plot also consists of three spectral windows which may be positioned independently They are again the spectral window the title window and the parameter window The latter two will not be discussed in this chapter since they are completely identical to those of a 1D spectrum plot and have already been described in that chapter 11 3 2 The Spectral Window Th
103. with the Multiplier The iteration is now continued with a stronger smoothing function for the generation of the error hyper plane This basically means that the valleys in the error hyper plane are now deeper The Speed factor determines the number of points which are summed up at the beginning of the iteration to speed up the calculation The iteration stops if no better match can be found by the program or if the Maximum number of cycles is reached Halfwidth threshold THRLW Baseline offset threshold THRBI Baseline ascension threshold THRBT If the Convergence matrix factor becomes equal to one of the above values iteration is started on the corresponding parameter Important note If your simulated and experimental spectra match well start with a relatively high Correction matrix factor e g mantissa 10 exponent 2 9 10 DAISY P 225 If they do not match well start with a smaller exponent e g 5 e Region parameters This page is displayed only for DAVSYM2 and DAVCYM2 where the SPECPREP spectrum may contain more than one region of spectral informa tion The number of lines displayed on this page is given by the number of regions If you want to exclude a region set the using range to no If you want to include the region set the using range to yes In that case you can also specify a statistical weight or importance factor with which this region is treated during the iteration Regions with rather li
104. 3200 A3 GRAPHTEC MP4200 A3 GRAPHTEC wx4731 12 el HP 7475A A3 HP 7550A A3 HP 7570A Al HP 7575A Al HP 7576A AO HP 7580B AO HP 7596A 36 el HP DraftPro Plus Al HP LaserJet Id A4 HP LaserJet Ip A4 HP LaserJet 3P A4 HP LaserJet 4 4L 4ML A4 HP LaserJet 5L SP MP A4 Table 10 8 Supported printers plotters 10 13 Supported printers plotters P 277 Type Form t XWIN XWIN NMR PLOT HP LaserJet 4V A3 HP Color LaserJet A3 HP DeskJet 500 A4 HP DeskJet 510 520 A4 HP DeskJet 550C 560C A4 HP DeskJet 660C A4 HP DeskJet 690C A4 2 HP DeskJet 850C A4 HP DeskJet 870C A4 3 HP DeskJet 1200C A4 HP DesignJet 750C AO Al dito Postscript AO HP PaintJet XL300 A3 Kyocera F5000 F5500 A3 LaserImage 1035 A4 LaserPro Gold A4 Lexmark 4079 plus A3 Nofatec RG04 A4 ZETA 8 12 el ZETA 912 12 el ZETA 924 24 el ZETA 936 36 el Table 10 8 Supported printers plotters The 1D Output Menu P 278 XWIN NMR plotter type bj330 SWI 01 on SW2 01 on SW3 01 off 02 on 02 off 02 off 03 on 03 off 03 on 04 off 04 on 04 off OS off 05 off 05 off 06 off 06 off 06 off 07 on 07 off 07 off 08 off 08 off 08 off 09 off 10 off This is the configuration for the ASPECT X32 SW3 is on the serial interface board BJIF 3020 This board is not used for communication
105. 4 shows an example The file starts with the text RFVERSION_F then the pulse shape follows The first column contains the amplitudes the second one the corresponding phases If the phases are omitted the following rule applies the phases are set to O if the amplitudes are positive and to 180 degrees if negative Phases are specified in degrees in the range 0 360 floating point numbers are legal A file must not contain more than 32768 lines Amplitudes and phases are separated by a space tabulator or comma Relative power values may range from 0 100 If a value in the file exceeds 100 it will be rescaled to 100 during execution All other points will be rescaled accord ingly Values less than 100 will not be rescaled Binary Format The binary file format of shape files is as follows 16 7 Pulse Shapes P 339 TITLE u exp stan nmr lists wave CosSinc JCAMP DX 5 00 Bruker JCAMP library DATA TYPE Shape Data ORIGIN Bruker Analytik GmbH OWNER2 lt guest gt DATE 96 09 21 TIME 12 11 57 MINX 0 000000e 00 HMAXX 9 956761e 01 MINY 9 552316e 01 HMAXY 1 794392e 02 SHAPE_EXMODE None SHAPE_TOTROT 0 000000e 00 SHAPE_BWFAC 0 000000e 00 SHAPE_INTEGFAC 2 052226e 03 SHAPE_MODE 4 NPOINTS 256 X YPOINTS XY XY 0 000000e 00 1 869338e 01 7 815741e 01 1 794392e 02 1 522001e 00 1 790653e 02 2 671471e 00 1 783176e 02 2 985925e 00 1 779437e 02 3 074292e 00 1 775699
106. 71 10 11 Display status parameters 0 0 cee eee ee P 273 10 12 Print barcode labels prlabel 0 cece eee eee P 273 10 13 Supported printers plotters oons sn eee eee eee P 275 The 2D Output Menu oeesssssssssssssssssssessssosssssesoss P 287 11 1 Printer plotter installation cfpp 0 0 cee ee eee eee ee eee P 288 112 Pen setup edpp S css cec0 raa ie 88 Galego te ats whee wa A RA P 288 11 3 Page layout contour plot edg 0 0 cee eee eee eee ee P 288 11 4 Page layout stacked plot edgw 0 0 eee P 295 11 5 Use prepared page layout rpar 0 0 eee ee eee ee P 298 11 6 Plotcommands 00 cece teenies P 298 11 7 Other commands 00 cece eee eee P 299 The Display Menu Sa iece Wie aces we aceiwie ios EEEE P 301 12 1 Active Commands gt d neee aea e eE E A ea ee aE an ei P 301 12 2 Status amp HIStory aig supran oaa poe Se E EE pete EE Sede e a aS P 304 12 3 ADU AIDS plays oare 5 paa paie ea n Gea RA cath A A AAA P 305 12 4 OptONS i ne as Thee ree as Sa E E i ee oie eh Sete E P 307 12 5 _ User Interface meae rego 4 EEE Gis BEI A E eee P 308 The Windows Menu cceccceccccecec cece ececvesecves P 313 13 1 Command panel cpan 0 0 ee ee eee eee P 314 13 27 lt PlOR Preview Gens chat See alee aay joe nets te yes als ct one EAN P 316 The Help Memo 0 i6 0 50 504c0 2 955 04 oe 0000s sole ola ocd oie S we
107. 8 948 0 43332 0 15682 38 163 20 1024 453 479 4 71935 4 48056 3 1024 918 948 0 43332 0 15682 13 188 6 9112 1024 453 479 4 71935 4 48056 3 12 Peak picking The following setup is required 1 Select a spectrum region and define it as plot region Alternatively use edg to define the desired region via the parameters FIPLO F1PHI F2PLO F2PHI 2 Set the parameters MI MAXI PSIGN PC for the F2 dimension cf 1D peak picking for a detailed discussion 3 Enter edo and define the output device by setting the parameter CURPRIN to screen to a printer name or to a file name just as for 1D peak picking 4 Enter the command pp2d or xau pp2d to start peak picking In AU programs peak picking can be called with xcmd xau pp2d pp2d first calculates the F1 projection of the specified region and executes a 1D peak picking on the projection For each peak found the corresponding F2 row is extracted from the spectrum and 1D peak picking is applied The AU program pp2dmi is a variant of pp2d which calculates the parameter MI automatically It computes the noise of the 2D spectrum and multiplies it with a number in order to obtain a meaningful intensity threshold This number can be adapted to your needs by setting the constant noise_fac in the AU program to the desired value Additional 2D peak picking algorithms are available in Bruker s AURELIA pro gram 3 13 Plotting Basic plotting was already handled in the
108. 9 See Garret A J M Ockham s Razor in Maximum Entropy and Bayesian Methods Laramie Wyoming 1990 W T Grandy Jr and L H Schick Eds pp 357 364 Kluwer Academic Dordrecht The Netherlands 1991 And Thorburn W M The Myth of Occam s Razor Mind 27 345 1918 The Analysis Menu P 240 Chapter 10 The 1D Output Menu The Output menu Figure 10 1 contains the plot commands and utilities to print or Figure 10 1 The ZD Output menu display parameters Please note that XWIN NMR provides two different plot sys tems The parameter driven plot commands described in this chapter and the inter active plot editor XWIN PLOT described in its own manual The command autoplot displayed in Figure 10 1 plots the current data set based on a layout generated P 241 The 1D Output Menu P 242 with XWIN PLOT The layout can be selected using the LAYOUT parameter to be set with the edo command To use the parameter driven plot system please proceed as follows 1 Make all connected printers or plotters known to XWIN NMR with cfpp 2 For pen plotters specify the pen colors with edpp 3 Define a page layout with edg normal spectrum plot edgx auto expansions or rpar predefined layout and a plot title with setti 4 Define with edo to which of the connected plotters the output should be sent see also the setres command 5 Preview the plot on screen with view normal spectrum plot or viewx auto expa
109. CAMP file tojdx JCAMP file to XWIN NMR data set fromjdx Their syntax and functionality is as follows tojdx output file output type compression mode title origin owner The current data set is converted to JCAMP format The parameters have the following effects e output file name of the output file If it is omitted the name of the current data set is taken and the suffix dx will be appended e output type 0 FID 1 real spectrum 2 complex spectrum e compression mode this can be one of the following formats FIX table format PACKED no spaces between y values 5 11 Conversion P 127 SQUEEZED sign coded into the first digit of the value no spaces DIFF DUP coding the differences of subsequent values in the SQUEEZED format with suppression of repeated values The format must be specified as an integer value with O FIX 1 PACKED 2 SQUEEZED 3 DIFF DUP Because of its maximum compression factor DIFF DUP is the default for both FIDs and spectra e title The text specified here appears as TITLE in the output file The processing parameter TI is taken as default If TI is not specified the current data set parameter NAME is used e origin The text specified here appears as ORIGIN in the output file e owner The text specified here appears as OWNER in the output file If one or more of the parameters which are optional on the command line but required for the ou
110. Conversion P 115 Conversion of MSER files multi slice multi echo data sets conv expects that these files are stored after the transfer under a name in the form NAME MSER You either have to rename the data set before you get it from the Aspect 2000 3000 or after the file was stored in the directory u bruknet Example A multislice multiecho experiment is stored by DISNMR in the file RAT SER After renaming the file to RAT MSER and initiating the file transfer in binary mode as user guest from a spectrometer am400 the file is stored on the workstation as u bruknet am400 guest RAT MSER After the conversion a data set of this type is stored like other 2D data sets on the disk and has an EXPNO experiment number calculated from the formula EXPNOAIS IE IS 1 NE IE IS is the current slice number IE is the current echo number NE is the number of echo pictures Each of these raw data sets can be transformed to an image with the command xfb A series of images can be calculated with a suitable automation program Conversion of RAWD files Another special case are n dimensional raw data sets acquired with the Aspect 3000 TOMIKON program conv expects that these files are stored under a name in the form NAME RAWD and that the additional parameter files NAME PVAR and NAME ACQP have been transferred They contain patient information and acquisition parameters There are special Aspect 3000 PASCAL prog
111. D If TDoff is positive the first TDoff points of the Fid are discarded and zeroes are added and the end This corresponds to a left shift in 1D processing If TDoff is negative zeroes are added at the beginning of the Fid the last TDoff points of the zerofilled Fid are discarded This corre sponds to a right shift in 1D processing As follows from the previous explanation forward LP and backward LP with neg ative TDoff will increase the number of Fid points contributing to window multi plication and further processing steps This number is documented in the processing status parameter TDeff The Process Menu for 2D data P 164 7 7 Phase correction 7 7 1 Manual This command lets you enter manual 2D phase correction mode 7 7 2 Phasing using constants PHC0 PHC1 After a phase sensitive Fourier transformation the data may be submitted to a phase correction in the F1 or F2 dimensions with these commands The phase cor rection is based upon the phase parameters PHCO and PHC1 in the dimension in question If a phase correction has already been carried out then the status param eters PHCO and PHC1 give the sum of all the phase corrections in the F1 and F2 directions respectively Commands xflp and xf2p are analogous to the 1D com mand pk Both dimensions can be phased with a single command xfbp thereby saving computing time 7 8 Magnitude Spectrum xflm xf2m xfbm After the 2D Fourier transformation of a 2D acq
112. D and TDoff TDeff determines the number of points of the Fid which are to be used in the trans formation The default value for TDeff is zero which means that all TD points of the Fid are used in the transformation but at the most 2 SI This number is reduced when TDeff is set to a non zero value The transformation will begin at the data point with number TDoff starting at 0 which corresponds to a left shift by TDoff points If TDoff is negative TDoff zero points are inserted at data start which corresponds to a right shift Processing Parameter SI Size SI determines the number of data points with which the Fourier transformation is calculated After the transformation there are SI real data points and SI imaginary data points The default value for SI is TD divided by 2 rounded to the next higher power of 2 The user can set SI to a larger or smaller value The minimum value allowed for SI is 4 If necessary the data are zero filled or truncated Strip transform The default values of the processing parameters STSR strip start and STSI strip size are zero which means that all data points SI real and SI imaginary points after the Fourier transformation are stored in the data sets for the processed data If STSI is different from zero then only a strip of STSI data points starting from STSR is stored All subsequent data processing such as phase correction whether within xf2 or as a separate command only acts on these STSI da
113. DS YMPLOT the maximum number of nuclei with spin 1 2 is 7 In DCYMPLOT this number reflects the number of magnetically inde pendent groups of nuclei The maximum number of groups is 7 Each group can contain up to 9 magnetically equivalent nuclei Each nucleus can have spin 1 2 or greater Symmetry group DS YMPLOT Number of symmetry groups DCYMPLOT DSYMPLOT works with only one symmetry group which you enter here DCYMPLOT can work with more than one symmetry group and you enter the number of symmetry groups here The next page button displays the menu where you enter the actual symmetry groups Important note The symmetry groups must be entered in decreasing order otherwise the simu lators will not work correctly e Output list generation The menu items listed here determine the contents of the output files To gener ate a spectrum which can be displayed by XWIN NMR the write spectrum to disk in XWIN NMR format button must be set to include When you save the data set the editor converts all included options into the var iable IPRINT e Permutation operators This menu is displayed only if a symmetry group other than C1 was selected see Miscellaneous parameters The first line displays the E identity symmetry operation for the total number of nuclei specified in the Miscellaneous parameters menu One line each is dis played for all other symmetry operations of the character table In each field of these lin
114. Diagonal planes The commands 123d r13d r12d extract the diagonal planes F2 F3 F1 F3 F1 F2 respectively from the real part 3rrr of the current 3D sepctrum The result The 3D Process Menu P 180 tf r23 r13 r12 sequence from to from to from to tf3 3irr 2ir 3irr 2ir tf3 tf2 3rir 2ri 3rir 2ir 3rir rir tf3 tf1 3rri 2ir 3rri 2ri tf3 tf2 3rri 2ri 3rri 2ri 3rri 2ri tf1 tf3 tfl f f2 3rir 2ri 3rir 2ri 3rir 2ri Table 8 4 2D imaginary files generated by read plane commands is stored as a 2D spectrum 2rr It is saved under a new EXPNO requested by the program or specified on the command line e g 123d 5 Chapter 9 The Analysis Menu Figure 9 1 The D Analysis menu 9 1 Manual calibration The manual calibration of a spectrum s frequency axis is described in the chapters ID Processing Tutorial and 2D Processing Tutorial P 181 The Analysis Menu P 182 Manual calibration Auto calibration Esref Manual integration Calc integrals of regions Cint2d Calc integrals rel to a ref Cint2dref Define output device CURPRIN Cedo Output integral values li Relaxation T1 T2 Simulation Figure 9 2 The 2D Analysis menu 9 2 Auto calibration sref The command sref calibrates the TMS peak to 0 ppm It is one of the most impor tant commands used during automatic spectrometer operation where manual cali bration described in the
115. E type instruments PKNL must always be set to true In this case no 5th order correction is applied but a special handling for digital spectrometers is applied Processing Parameter PH_mod phase mode After the transformation of a signal the following processing is done depending on the value of PH_mod no no further processing pk phase correction with the parameters PHCO PHC1 mc calculate the magnitude spectrum ps calculate the power squared magnitude spectrum In the case of mc or ps no Fourier transformation can subsequently be performed in the F1 direction Processing Parameter FCOR The first data point is multiplied by the parameter FCOR immediately before the transform is executed The default value is 0 5 numbers between 0 and 2 are legal Processing Parameter REVERSE If the processing parameter REVERSE is set to true both the real and the imagi nary parts of the spectrum are reflected by a vertical line through the center of the spectrum In other words the spectrum is reversed The same effect can be achieved by the command rev2 7 4 Transform of F1 columns xf1 P 159 7 4 Transform of F1 columns xfi 7 4 1 The xf1 transformation acts on the raw acquisition data the ser file if no data exist that resulted from an F2 transform excuted by xf2 In the first case a data set is cre ated which is only transformed in the F1 dimension and must be further processed with xf2 to complete the trans
116. G IG I0 where R is the real part and I is the imaginary part of the spectrum It can also operate on the Fid like pk see the description of the pk command 6 11 Power spectrum ps The real part of the spectrum is replaced by the square of the absolute value ABSG ABS see mc It can also operate on the fid like pk 6 12 Special window functions P 141 6 12 Special window functions 6 12 1 6 12 2 Exponential em See Exponential multiply em on page 137 Gaussian gm gm multiplies the data by the function exp a t b t 2 where a is negative and b is positive The Fid originally has the exponential envelope of the form exp t T2 Therefore a gaussian line shape exp b t t results when a 1 T2 Since this line shape has less extensive wings than a normal line the resolution of overlapping resonances is improved greatly A suitable choice of parameters can lead to fur ther reduction in the line width a and b have the form a PI LB and b a 2 GB AQ where LB and GB are processing parameters and the acquisition parameter AQ is the acquisition time of an Fid without accumulation The function has a maximum value of exp PI LB AQ 2 when Tmax GB AQ Tmax and therefore GB may be determined once the data has been weighted by a suitable em LB exponential and transformed by taking the reciprocal of the half line width of the line to be sharpened To execute gm LB should be entere
117. GaS SLN L0 GG ke EAE A 4 3027 9 3380 557 Cie lO2Z8 2 29 KE 5 3036 3 3378 163 6 FI 80 S24 HER 6 3057 8 3371 963 Ge TASS LL SAD RRA AAR A 7 3083 2 3364 655 Ga TIELO LIL Ae 8 3110 4 3356 826 6 1153 B68 KEK 9 TETAS 2186 748 A 3TAO RTA RERRAK 10 7223 4 2172 687 43465 8 38 RA 11 7475 8 2100 023 DoZ Cowl eA 12 7498 4 2093 505 4 LEBL S049 ea Example of a list generated by lipp with 4 integral regions defined 1D Data Processing Tutorial P 34 2 11 Current data set NAME examld EXPNO 1 PROCNO 1 USER guest DU u MI 1 82 cm MAXI 31 86 cm PC 4 000 F1 8 221 ppm F2 4 101 ppm Peak Nr Frequency Intensity Integral Hz ppm cm 1 3446 439 6 8946 24 83 2 3431 485 6 8647 8 57 3 3424 995 6 8517 10 58 Int Reg 1 6 9955 6 8020 0 567275 4 3380 557 6 7628 2 29 5 3378 163 6 7580 3 24 6 3371 963 6 7456 11 22 7 3364 655 6 7310 13x21 8 3356 826 6 7153 3 68 Int Reg 2 6 7876 5 3370 0 362723 9 2186 748 4 3746 7 74 10 2172 687 4 3465 8 38 Int Reg 3 4 4487 4 3104 0 110188 11 2100 023 4 2011 DAT 12 2093 505 4 1881 5 49 Int Reg 4 4 2448 4 1094 0 111234 Plotting For historical reasons XWIN NMR provides two different plot systems 2 11 Plotting P 35 2 11 1 2 11 2 Xwinplot Plotting is performed using the interactive What You See Is What You Get plot editor xwinplot Enter this command or invoke it from the Windows menu xwin plot allows you to define the plot lay
118. Position the second cross hair to the lower right corner of the region and click the middle button to fix it Now move the cursor out of the data area and click on the set strip button XWIN NMR will set the parameters STSR STSI to the selected region and ask you to enter the desired transform sizes The Hilbert transform allows you to generate the imaginary part of a spectrum from the real part This enables you to delete the imaginary part of a 2D spectrum using the command deli to save disk space and recreate it if desired e g for an additional phase correction You may even force the 2D transform not to store the imaginary parts at all using the command xfb n instead of xfb 3 7 Phase correction P 45 More details of these transform options are described in the chapter The Process Menu for 2D Data 3 7 Phase correction 2D Manual phase correction can be invoked from the Process menu It is more convenient however to click the command button phase at the left side of the XWIN NMR window A screen according to Figure 3 2 will appear The upper part of the command button panel at the left side is identical to the standard mode It applies to the 2D spectrum window The lower part refers to the selected and moved rows or columns The idea behind manual phase correction of a 2D spectrum is as follows For the correction in the F2 dimension select a row of the 2D spectrum and move it to the first 1D window at the right part of the
119. Should a parameter plot be based on a format file generated by yourself the name of it must be specified in the parameter PFORMAT with edo replacing normpl there The parameters are plotted in the color PCOLOR and with character size PCHAR mm starting at the upper left corner of the parameter window The width of the parameter window is PWIDTH cm If chosen too small the program automatically decreases the character size but only to a minimal still readable size If a parameter line is still too long all characters outside the window are clipped The whole parameter window is rotated about the upper left corner by O or 90 degrees if the parameter PROT is set to one of these values instead of 0 10 3 Page layout edg P 261 10 3 3 1 Miscellaneous topics Taking the plot limits from a region file As described above the parameters Fl and F2 determine the plot limits if the parameter LIMITS is set to fixed If it is set to region the plot limits are taken from the text file reg which must be stored in the current processed data directory The file format of reg equals that of a region file used for integration see The File menu command edmisc The left plot limit is the biggest frequency value listed in reg the right plot limit the smallest one If LIMITS region is used several other parameters specifying the x scaling of the spectrum need to be considered ADJUST can have values scale and CX In the former case the x
120. XWIN NMR version 1 0 JCAMPDX 5 0 DATATYPE Parameter Values ORIGIN X WIN NMR OWNER jos Mon Jul 18 16 30 18 1994 File u data guest nmr IQUIN 128 1 acqu AQ_mod 1 D 0 31 3e 06 2 0 071 0 002 0 015 0 001 0 0005 1 5 100 70000000000 DR 12 LOCNUC lt 2H gt LOCSHFT no NS 8 NUCI1 lt 1H gt PULPROG lt zg gt PW 4 5 RO 20 SW_h 826 719576719577 TD 131072 TE 303 END Figure 16 1 Section of a an acqu parameter file essed is different from that of the acquisition computer Within an fid the data points coming from channels A and B alternate for quadra ture detection data A 1D fid file contains a single fid with TD F2 points which is the time domain size TD stored in the acquisition status parameter file acqus A ser file contains TD F1 1D fids which is the parameter TD in the file acqu2s Each 1D fid in a ser file start at a 1024 byte block boundary even if its size is not a mul tiple of 1024 bytes corresponding to 256 data points 16 3 1D spectra Applying a 1D processing command to a 1D fid or reading a 1D slice from a 2D spectrum generates processed data They are stored in two files r and i corre 16 4 JCAMP DX format P 335 sponding to real and imaginary part Like in 1D fids the data points are stored as a sequence of 32 bit integers Their byte ordering is given by the parameter BYTORDP which may be read from the proces
121. a type Example bconv am300 fid Depending on which data type you specify bconv either converts the acquired data or the processed data of the current data set together with the corresponding parameters Currently the data types according to Table 5 11 are implemented Please note that back conversion of 2D and 3D transformed spectra is not sup ported The conversion writes two files into the current network directory Its base name must be specified in the file zsr local lib bruknet destination e g u bruknet The station name specified with bconv and the user name under which the current data set is stored are appended The File Menu P 118 data type file to be converted fid fid 1D acquisition data ser ser multi dimensional acquisition data procid Zr and Zi 1D processed data 2rr single image data file 2dseq multi image data file Table 5 11 Data types supported by back conversion Example bconv am300 fid on the data set NAME sucrose EXPNO 2 PROCNO 3 DU u USER guest generates the two files SUCROSE 002 and p_SUCROSE 002 in the directory u bruknet am300 guest The first file contains the fid the second file the spec tral parameters The plus sign indicates that the files are stored in 32 bit format The files can now be sent to the destination station e g with BRUKNET Make sure that BRUKNET runs with special parameter file handling enabled and in b
122. absolute fre quency in MHz for the corresponding nucleus preceded by an O and a space char acter The following lines contain offsets in Hz The transmitter frequency is the sum of absolute and offset frequencies The list is evaluated by the variable fre quency statements fql fq8 in pulse programs The command fql uses the cur rent value in the list whose name is defined in the acquisition parameter FQILIST Likewise fg2 gets the list name from the parameter FQ2LIST etc These com mands are valid for AVANCE spectrometers For AMX ARX ASX instruments the frequency setting statements are called 01 02 03 Instead of 8 only 3 list name parameters FILIST F2LIST F3LIST are available A temperature list Table 5 8 left column contains one temperature value in Kel 300 4 320 p 340 20 Table 5 8 Example of a tempearture left and loop counter list right 5 3 Open Other Files P 89 vin per line They are evaluated by the variable temperature statement vt in pulse programs This command uses the list whose name is defined in the acquisition parameter VTLIST A loop counter list Table 5 8 right column contains one positive integer number per line The numbers are evaluated by the variable loop counter statement lo to n times c in pulse programs This command uses the list whose name is defined in the acquisition parameter VCLIST A data set list Table 5 9 contains one data set specification per line in the form
123. ace the cursor shape changes to a watch Projections and Cross Sections XWIN NMR allows you to display rows and columns of a 2D spectrum and projec tions of the entire spectrum or parts of it partial projections onto the F1 or F2 axis Furthermore this data may be stored as 1D spectra and processed or plotted accordingly All these routines are accessible from the utilities screen If you click on the utilities button of the main 2D display the command buttons will change 3 14 Projections and Cross Sections P 57 according to Figure 3 3 E Figure 3 3 The utilities button panel You can enter the utilities screen either with the 2D spectrum shown in colored intensity mode or in contour display mode Please select the desired mode before entering utilities 2D Data Processing Tutorial P 58 Fast row column scanning mode Click on the scan button to enter this mode The program will display a cross hair cursor you can move around with the mouse Clicking the left mouse button will display the horizontal cross section row defined by the position of the horizontal line of the cross hairs Clicking a second time will toggle to the vertical cross sec tion column defined by the position of the vertical line of the cross hairs Click ing a third time will show both the row and the column Clicking a fourth and then a fifth time will once again only display the row etc In any mode you can move the mouse to chan
124. ains the file size the following lines the file offsets and corresponding ppm values within the spectrum from where the spline baseline correction command sab takes its supporting function val ues 6 peaklist Figure 5 10 The first line defines the frequency units H Hertz P ppm of the line position and half width In the right column the gaussian percentage must be specified if the peak list is used for mixed Lorentz Gauss deconvolution command mdcon 5 3 Open Other Files P 93 16384 12438 7 699070 12591 7 677680 12737 7 657277 12892 7 635558 13034 7 615813 13361 7 570071 13653 7 529265 Figure 5 9 Example of an baslpnts file half width gauss 100 H frequency 2761 975 0 86 2760 684 0 86 2755 096 1 01 2753 802 0 86 2752 451 0 86 2746 895 0 86 2745 564 0 86 2739 110 2 47 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 Figure 5 10 Example of an peaklist file 5 3 10 Automation modules edaumod Automation AU modules are like AU programs text files written in the C lan guage or using XWIN NMR commands However AU modules can not be executed by typing their names on the command line or via xau Instead they are called from other XWIN NMR commands For example the AU module qnmr_sx is called by the XWIN NMR command quicknmr and the module stan_sx is called by the command run edaumod allows you to create a new AU module and to edit or view an existing one When exiting from the t
125. ains the real spectrum the others include imaginary components The ser file contains the acquisition data and is stored in the current acquisition data directory tf2 and tf1 only transform real data if MC2 is not equal to gf All transformations only create those imaginary output data needed for the phase correction in the corresponding direction This prevents the creation of 7 more files with imaginary data in addition to the real data 3rrr which would consume disk space and slow down the trans formation 8 2 Fourier Transformation tf3 tf2 tf1 P 177 Command Input files Output files tf3 ser 3rrr 3irr tf2 3rrr 3rrr 3rir tfl 3rrr 3rrr 3rii xfb xf2 xtrf ser 2rr 2ri 2ir 2ii Table 8 2 Files read and written by transform if MC2 gf Command Input files Output files tf3 ser 3rrr 3111 tf2 3rrr 3iii 3rrr 3iii tf1 3rrr 3iii 3rrr 3iii xfb xf2 xtrf ser 2rr 2ii Table 8 3 Files read and written by transform if MC2 qf After invoking a transform command you will be asked whether the imaginary parts should be stored on disk If not disk storage capacity will be saved but an additional phase correction at a later time with the commands tf3p tf2p tflp will not be possible However you may use the Hilbert transform commands tht3 tht2 thtl at any time to calculate the required imaginary parts from the real part 3rrr From the keyboard the transform commands may
126. ak picking pp before trying to decon volve a spectrum Please prepare deconvolution as follows skip item 2 for mdcon 1 Define the desired spectral range from the currently displayed region by choos ing Define region from the Analysis gt Peak picking menu or from the Analysis gt Deconvolution menu 2 Define the MI MAXI and PC peak picking parameters Execute a pps peak picking command and check whether the output contains exactly the lines you want to include in a deconvolution Exclude peaks that are too big or too small by adjusting MI and MAXI Increase or decrease peak picking sensitivity with respect to noise by adjusting PC This will also enable you to include exclude The Analysis Menu P 186 peak shoulders or broad lines 3 Set up the parameter AZFW with a number in ppm units AZFW influences the way deconvolution is performed The spectral region you have selected for deconvolution may contain peaks or peak groups separated from others in that they fall back under noise level before the next group starts You may force the deconvolution commands to fit these peaks or groups separately as if you were to execute an individual deconvolution of each of them For this case set AZFW 0 Otherwise if AZFW is larger than 0 it determines how far the peaks or groups may be apart so as to still consider them as a whole region to be deconvolved together A recommended value is AZFW 0 5ppm While AZFW 0 executes significantl
127. al win dow SHEI the data window i e DHEI will be adjusted shrunk accord ingly The common width of these windows is determined by the parameter CX cm The x axis The x axis is plotted as a horizontal line from the upper left corner of the x axis window the scale marks show towards the bottom The tic marks are located in the lower part of the x axis window The window height XHEI must be set suffi ciently large to hold the axis and its labels Other parameters are XTICLEN mm tic length of scale marks XUNIT physical unit of x axis scaling Hertz or ppm XTICDIS distance between scale tics in the unit given in XUNIT Only values with a mantissa of 1 2 5 or 25 are allowed to ensure reasonable axis labeling Examples 1 0 0 1 0 25 50 0 2 0 Not allowed 3 0 2 2 5 25 etc XCHAR mm character height for axis labels XCOLOR color in which the x axis scale tics and labels will be plotted accord ing to the color pen position assignment command edpp The y axis A y axis can only be plotted with certain limitations the axis will be plotted on the left edge of the spectral window with scale tics showing to the right Labeling of the y axis has not been provided The following parameters determine the plotting of the y axis YTICLEN YTICDIS YCOLOR They have the same meaning as the corresponding parameters for the x axis The numeric integral values The window for the integral values and the plot of their in
128. also be entered in the form tf3 y or tf3 n in order to suppress the question by specifying the answer directly Another option has the form tf3 y a telling the program to store imaginary parts only if enough disk space is available Each of the files 3rrr etc created during the transformation contains the spectrum in a subcube format a generalization of the 2D submatrix format for 3D The sub cube size is determined automatically by the program according to the amount of available memory in order to minimize transformation time After the transforma tion the size can be examined with the commands 3s xdim 2s xdim 1s xdim The maximum subcube size is 64K data points 256K bytes If it is important for you to define the subcube dimensions yourself append the option c to the transform command e g tf3 y ac or tf3 y c The program will ask for the sizes in a dialog 3D data sets often cover a large portion of the disk capacity tf3 usually stores the The 3D Process Menu P 178 transformed data on the same disk partition where the acquisition data are located This would restrict the size of the raw data to about half of the available space In order to circumvent this problem tf3 may be called with another option p The command tf3 p requests the disk partition where the transformed data are to be stored This partition may be located on the same or on a different disk Alternately the partition may be specified directly after the p
129. am as an argument If it exists it is shown in a dialog window in the case of a Bruker pulse program or otherwise loaded into the text editor for modifi cation If it does not exist the text editor is called and a new one can be set up If the argument is not a complete name but contains the wildcard characters or the same dialog window as for edpul without argument appears However this dia log window then only lists those pulse programs which match the wildcard pattern Examples edpul cos list all pulse program beginning with cos edpul m z list all pulse program beginning with m n z Current pulse program edcpul When a data acquisition is started XWIN NMR enforces the execution of the pulse program whose name is stored in the acquisition parameter PULPROG of the cur rent data set The command edcpul does the same as edpul lt PULPROGS i e it uses the name of the pulse program specified in the acquisition parameter PUL PROG as argument The command edcpul lt pulse program name gt does the same as edpul lt pulse pro gram name gt but additionally sets the acquisition parameter PULPROG to the specified pulse program name Composite pulse decoupling programs edcpd Composite pulse decoupling CPD programs are text files containing statements in the Bruker CPD program language described elsewhere in this manual This command allows you to create a new CPD program and to edit or view an existing one
130. ands eda edp edg edo or the commands for setting individual parameters to apply modifications Please note Parameter sets are either of type 1D 2D or 3D XWIN NMR identifies the type by looking at the plot parameter file meta which contains the corresponding informa tion The presence of a 1D meta file in the current data directory will cause the 1D screen layout to be displayed etc Suppose your current data set is a 1D data set containing fid and spectrum data and you invoke the command rpar to copy a 2D parameter set to your current data directory This will turn your current data direc tory to 2D In order to maintain a consistent data set XWIN NMR will ask you whether to delete the 1D data If you confirm the question all data files of the data set are deleted the 2D parameter set is copied and the 2D screen layout appears Now your current data set is a 2D data set without data files fid or spectrum but The File Menu P 104 with 2D parameter files corresponding to the chosen parameter set and can be used as basis for a new 2D experiment 5 6 7 Copy miscellaneous files to wmisc The meaning of miscellaneous files is presented in the description of the command edmisc The purpose of wmisc is to make save copies of miscellaneous files for later retrieval with the command rmisc For example you can integrate a spectrum and copy the intrng file which contains the regions to the directory u exp stan amr in
131. arameters are output The operator may specify which parameters to plot in the order and format he desires In order to do this he must edit the text files format files in The 1D Output Menu P 260 the directory u exp stan nmr form Table 10 2 acqu l normpl for acquisition parameters F2 dimension acqu2 l normpl for acquisition parameters F1 dimension proc l mormpl for processing parameters F2 dimension proc2 l ormpl for processing parameters F1 dimension plot l normpl for plot parameters F1 dimension plot2 l mormpl for plot parameters F2 dimension Table 10 2 Format files for parameter plot The format files that have come with your system may serve as examples If a parameter is to be removed its entry must be deleted up to and including the corre sponding END For adding parameters it is best to use the existing entries as guidelines The parameters appear on the plot in the same order as listed in the for mat file Before modifying any of the standard files it is recommended to make a copy If only those acquisition parameters that were really used in the pulse pro gram are to be plotted all acquisition parameters must be placed after the CON DITIONAL statement at the end of the format file as is the case for the acquisition parameter set up commands as and ased If CONDITIONAL is the last statement of the format file only those parameters that occur before it are plotted
132. arated from it by a space character e g lb 0 5 1 3 Versions This manual corresponds to XWIN NMR version 2 0 XWIN NMR contains the man ual as online documentation accessible from the He p menu In addition this menu provides some additional documentation 1 4 Support Software support is available via e mail from the following address nmr software support bruker de The Bruker ftp servers ftp bruker de and ftp bruker com provide additional infor mation such as known bugs and their workarounds in the directory pub nmr xwinnmr 1 5 Installation of XWIN NMR Installation may depend on the particular program version It is therefore described in it own manual that is distributed together with the release CD Please refer to the NMR Software Release Letters manual part number Z30742 Introduction P 4 1 6 XWIN NMR screen layout The XWIN NMR window Figure 1 1 from top to bottom consists of Figure 1 1 XWIN NMR screen layout 1 The window manager bar with program version and computer host name 1 6 XWIN NMR screen layout P 5 The host name lets you know if you have started the program remotely from another workstation an X terminal or a PC equipped with an X server 2 The main menu bar with pull down menus for XWIN NMR operations While the menu bar remains the same in all program modes the contents of the pulled down menus may change depending on the context For example the Process pull d
133. as described earlier the expansion is stored in the file dsp exp in the current data directory Both files dsp and dsp exp are only needed for data display and if missing are recalculated automatically from the spectrum file 2rr After completion of the xfb transformation the 2D spectrum is corrected for a quad spike i e the center of the 2rr file is replaced by the median of its two neigh boring points in F7 You can apply the transformations in F2 and F1 separately using the commands xf2 and xf1 in this sequence This corresponds to xfb but without quad spike cor rection Some 1D experiments such as T1 measurements are acquired like 2D experi ments The result is a sequence of fids stored in a ser file but need only be trans formed in the F2 dimension using the command xf2 You will find all details about 2D transforms in the chapter The Process Menu for 2D Data Particularly options not yet mentioned such as strip transforms whose result is not the entire spectrum but only a desired frequency range linear predic tion to get rid of artefacts introduced by non decayed fids inverse transforms etc are discussed 2D Data Processing Tutorial P 44 3 6 Strip and other transforms and linear prediction XWIN NMR provides a number of 2D transform options such as linear prediction strip transform inverse transform user defined transform and Hilbert transform Linear prediction is an attractive option to perf
134. ase you set the dipol dipol coupling constants to values not equal to 0 0 The order of magnitude of the dipol dipol coupling constants follows the conventions used in the litera ture 9 10 2 3 Programs DAVSYM1 2 and DAVCYM1 2 In addition to the menu pages for DSYMPLOT and DCYMPLOT the editor dis plays the following menu pages to set up all parameters needed for an iteration of a spectrum e Iteration limits This menu page displays a list of all chemically independent chemical shifts spin spin and dipol dipol coupling constants A parameter will be iterated if the iterate flag is set to yes In that case set the limits between which the parame ters should be varied The default lower and upper limits are calculated from the initial parameter value Iteration parameters Correlation matrix factor mantissa The Analysis Menu P 224 Correlation matrix factor exponent These two values lead to the Correction matrix factor A1 It defines the initial strength of the smoothing function for the error hyper plane Multiplier A2 Convergence criterium SETOUT Speed factor SPEED Negative gradient seek ISD Maximum number of cycles TMAX During the iterative refinement of the parameters several cycles are stepped through to find the best match between the simulated spectrum and the experi mental data If the Convergence criterium is reached the Correction matrix fac tor is multiplied
135. ason XWIN NMR Offers the possibility for a faster generation of an overview plot of spectra whose size in one or the other dimension exceed 512 points they can be plotted with reduced resolution of 512 points by utilizing the file dsp of format 512 512 points in the current data directory that is created for displaying the spectrum rather than the actual 2rr spectrum file The operator selects this fea ture by setting the parameter REDRES reduced resolution to yes the default value is no The contours of a 2D spectrum are plotted in the contour window of height CX1 and width CX2 as has already been mentioned The spectral region is determined by the parameters F1 2 LO and F1 2 HI and F1P 2 LO and F1 2 PHI They may also be set interactively on the display by defining the desired region from the Out put gt Define region submenu FILO Hz F1PLO ppm Left low field limit of spectral region in F1 Changing this parameter causes the The 2D Output Menu P 292 right plot limit F1 HI F1PHI to be adjusted accordingly so that the plot resolution Hz cm and the height of the contour window CX1 remain unchanged the plot region is shifted along F1 F1HI Hz F1PHI ppm Right high field limit of the spectral region to be plotted Changing this parame ter causes the height of the contour window CX1 and the left plot limit FILO FIPLO to be kept constant while the scaling FIHZCM FIPPMCM Hz or ppm per cm is adjusted accordin
136. ata 41 The additional SPECPREP processing number was introduced because one exper iment can be manipulated by SPECPREP in several ways The path to store the results of a simulation with DSYMPLOT is generated as fol lows e name same as the experiment e number expno exp 2000 p number procno exp This results in the following path u data guest nmr 135TFB 2005 pdata 4 The path to store the results of an iteration with DAVCYM2 is generated as fol lows e name same as the experiment e number expno exp 7000 p number procno exp 1000 SPECPREP p number 100 9 10 DAISY P 217 9 10 1 4 9 10 1 5 DAVCYM2 p number 10 output number 1 2 3 The output numbers 1 2 and 3 are generated by DAVSYM1 2 and DAVCYM1 2 automatically They contain the following spectra u data guest namr 135TFB 7005 pdata 4111 experimental u data guest nmr 1 35TFB 7005 pdata 4112_ first simulated u data guest nmr 1 35TFB 7005 pdata 4113 final output The predominant rules for creating a path name are expno all programs expno exp program number 1000 procno SPECPREP procno exp 10 runprocno SPECPREP procno simulators procno exp procno iterators procno exp 1000 runprocno SPECPREP 100 runprocno iter 10 output number If data sets exist for the selected program you can load them by clicking on the Experiment number or the Experiment processing number The exi
137. ayed on screen times 10 set up loop over 10 data sets ef window transform apk auto phasing iexpno next data set increment EXPNO end end of loop quit terminate AU program Figure 15 1 AU program to process 10 data sets will inform you of it s nature and at which line of the program it occurred Pro vided compilation terminates error free you may start the AU program with xau test or just with the command test as if it were a normal XWIN NMR command The latter case requires that no XWIN NMR command of the same name exists XWIN NMR is delivered with a number of AU programs of little and large complex ity If the command expinstall was executed after XWIN NMR installation with compilation of the AU programs enabled you will get a list of them when typing edau Before you start to write your own programs you should take a look at some of them to become familiar with their structure All special commands that may be used in AU programs to execute XWIN NMR commands are contained in the file XWINNMRHOME prog include aucmd h XWINNMRHOME is the location where your current XWIN NMR is installed which is the directory u for a standard installation You may look up this file to find out the exact syntax of an AU command and which commands are currently supported The most important commands are dis cussed in detail in the following sections Commands may be specified in upper case or
138. bined with each other bitwise using the corresponding boolean operation and the result is stored as the current data set The processing parameter DAT MOD determines whether this unification is carried out on the acquisition raw or processed data The following commands are available and logical and of the two data sets or logical or of the two data sets xor logical exclusive or of the two data sets cmpl logical complement of the current data set 6 16 Special transforms P 147 6 15 10 6 16 6 16 1 6 16 2 6 16 3 Negate data nm nm negates the current acquisition or processed data i e they are multiplied by 1 depending on the value of DATMOD Special transforms Inverse ft ift In some cases it is useful to transform a spectrum back to the Fid For example a row of a 2D spectrum can be back transformed to produce a Fid that can again be forward transformed to produce a spectrum of a different size afterwards Back Transformation is accomplished with the command ift It must be noted however that the Fid thus obtained replaces the spectrum i e the real and imaginary parts Ir li of the current processed data set number but never the original Fid of the current experiment number The length of the Fid obtained through ift equals twice the length of the real part of the back transformed spectrum User defined ft trf trf executes a sequence of commands in the order baseline correction bc window Fo
139. bst1 but use a modified algorithm that gives a larger corrected region at the cost of a worse baseline 7 16 Subtraction of 1D Spectra sub sub2 sub1d1 sub1d2 The commands subl and subld1 subtract the real part Jr of the 1D spectrum defined as second data set with the command edc2 from each column of the real part 2rr of the current 2D spectrum sub2 and subld2 subtract from the rows of the 2D spectrum Note When using the commands sub1 and sub2 the subtraction only takes place if the two points to be subtracted from each other have the same sign All points will be set to zero for which the subtraction caused a change in sign 7 17 Extracting Rows and Columns rsr rsc These commands allow a desired row rsr or column rsc to be extracted from the current 2D spectrum and to be stored as a 1D spectrum see also chapter Interac tive Manipulation of 2D Data Syntax 2 rse e rsc lt column number gt e rsc lt column number gt lt PROCNO gt lt switch gt e rsr e rsr lt row number gt e rsr lt row number gt lt PROCNO gt lt switch gt The program will ask for the row or column number if only the command itself The Process Menu for 2D data P 168 was entered case 1 The user can also specify the number directly case 2 The extracted data will then be stored as a temporary data set using the name TEMP with EXPNO PROCNO 1 Furthermore it is possible to specify a processed data
140. button A horizontal line appears which you can move up and down the screen Put it on top of the peak to which you want to assign a certain peak height Then click the left mouse button and enter the desired peak height in cm units the right mouse button allows you to exit without change If you had selected the biggest peak and you examine CY afterwards it will contain the value you typed in If the peak was let s say 1 2 of the largest peak CY will be set to twice the value you entered etc This routine is useful for adjusting CY so that your selected peak gets a well defined height in the peak listing and on the plot Similarly when you click on MI or MAXI a horizontal line appears Shift it to the desired position of the spectrum and click the left mouse button to set the parameter or click the right button to quit All spectra are superimposed with noise not only the signal free regions but also the peaks themselves So even if you have chosen a minimum intensity threshold 1D Data Processing Tutorial P 32 to discard very small signals the peak picking algorithm will depending on the data detect signals in the remaining area which a user would reject as he would consider them as fluctuations due to noise An experienced user however could possibly suppose a peak under such a fluctuation XWIN NMR uses the following approach to influence the peacking sensitivity with respect to noise The process ing parameter PC with de
141. cessing Tutorial cece cee cee cece ee ence P 37 3 1 Getting the data Sets oo sua yer Ces eee ee ed oaks Sa as See des HS P 37 3 2 Manipulating the spectrum on the screen 0 0 0 c ee eee eee P 38 3 3 2D spectrum display modes 0 0 cece cece eens P 41 3 4 Setting up the parameters for a 2D transform 000005 P 41 3 Applying the 2D Fourier Tranform 0 0 0 2 eee eee eee P 43 3 6 Strip and other transforms and linear prediction 04 P 44 3 7 Phase correctione o ee aiana hie pais aes fs EOR OAE RER P 45 3 8 Spectrum calibration s ceser eee e cece e a ia e aa P 47 3 9 Baseline Correction nee ioa sae E e EA A e A han i ee P 49 3 10 Symmetrization Tilting 0 0 00 ia ee E EA E p RSA P 49 3 11 Spectrum intesration e siii onna nE ea SEE E E A A ER aa P 50 312 Pe kpickins iii Tera to mai Rese ees CERO a Lee E Re P 53 3 13 PO Ges ehcp tad ee Ma ee eae ete thd ee eh ae ye bee P 53 3 14 Projections and Cross Sections 00 cece cee cette eee P 56 Chapter 4 3D Data Processing Tutorial ccc cece cece cece ee ences P 63 4 1 Getting the dataset sus ese cosa tela Ses gin a Ganga Raateog dra a8 Magog e dow pet aes P 63 4 2 Manipulating the spectrum on the screen 0 00 00 e cece eee P 64 4 3 Setting up the parameters for a 3D transform 000005 P 70 4 4 Applying the 3D Fourier Tranform 0 0 0 0 cece eee eee P 71 Chapt
142. chiving project Display the projection of the spectrum 4 2 Manipulating the spectrum on the screen P 67 dyl Rotate the spectrum around the horizontal x or vertical y axis or around the axis perpendicular to the screen surface z Click on the desired button to enter rotation mode and move the mouse to rotate the spectrum in real time Press the right mouse button to leave rotation mode 190 yo 20 Rotate the spectrum around the axes described above by 90 degrees reset Reset rotation angles to their default This button also exits from project mode move DEF 1 Enter move mode You may shift the spectrum in real time on the screen Press the right mouse button to quit 2 Reset the position of the spectrum on the screen to its default value movie stop Clicking on this button invokes a demonstration loop where the spectrum is auto matically enlarges rotated and moved on the screen Another click on the same button terminates the movie create 2D 3D Data Processing Tutorial P 68 Click on this button if you intend to execute a 2D transform on 3D acquisition data The result is a 2D spectrum which is a slice of the 3D spectrum The effect of this button is that a new data set is created differing from the current one only in the PROCNO processed data number which you will be asked for The 2D slice will later be stored under this PROCNO In addition to creating the directory for this PROCNO
143. choose data sets according to a desired mask The asterisk serves as a placeholder for a group of unknown char acters the question mark for a single character The re rep command re is usually used for quick operation at the keyboard and may be applied as 5 2 Open Data Files P 79 dir display a list of data set names NAME parameter of the cur rent USER stored in the user s data directory DU data USER nmr dirdat like dir but data sets are ordered according to their acquisi tion dates dirp processed data any dimension e g Ir i and 2rr 2ii files dira acquisition data any dimension fid and ser files dirs dir2d processed one dimensional data 1r i files processed two dimensional data 2rr 2ii files dirf one dimensional fids fid files dirser multi dimensional fids ser files diro users owning data sets in the current data path default u data Table 5 1 The dir commands shown by the examples in Table 5 2 re XWIN NMR asks you to enter the data set specifications re sucrose 2 4 u guest directly specify NAME EXPNO PROCNO DU USER re sucrose 2 4 specify NAME EXPNO PROCNO leave DU USER re sucrose change NAME only re 2 change EXPNO only re 2 4 change EXPNO and PROCNO rep 2 change PROCNO only Table 5 2 Examples of commands re and rep The search co
144. completely once The two methods differ somewhat in the way that the phase angles PHCO and PHC1 for each dimen sion are determined Correction during the transformation Set the parameter PH_mod before issuing the transformation commands for the respective dimension so that the phase angles will be taken into account during the calculation The phase angles are determined as follows F3 dimension 4 6 Phase correction P 73 When applying the 2D transform command xf2 to a 3D data set you will be asked for the slice number to be transformed the rest of the ser file is ignored Please note that xfl xf2 xfb may all be executed on a 3D ser file The desired slice number can be specified as an argument behind the commands In order to display the resulting 2D data set the parameter PARMODE should be changed to 2D The parameter AQORDER is taken into account The phase angles can now be deter mined from the resulting 2D spectrum and may then be used in tf3 These phase angles can also be determined by extracting a single fid from the ser file with the command rser performing a 1D Fourier transformation and then phase correcting the spectrum in 1D mode F2 dimension After the tf3 transformation extract a F3 F2 slice with the command r23 trans form this slice with xf1 and determine the phase angles from the resulting 2D spec trum Then perform tf2 with these phase angles F1 dimension After the tf2 transformation extract a F3 F1 s
145. cquisition parameter AUNM for xaua or from the processing parameter AUNMP for xaup of the current data set The length of the name is limited to 15 characters These commands are mainly employed to start an AU program from within a higher level AU program which can remain unmodi fied but nevertheless call different lower level programs depending on the current data set and the value of the parameters AUNM or AUNMP cpluser cplbruk cpluser compiles all user owned AU progarms cplbruk all AU programs delivered by Bruker cpluser may also be specified with an argument cpluser auprog1 would only compile auprog xmac Invoking xmac from the menu or entering it on the keyboard will display a list of available command macros Select one from the list for execution If you already know the name of the macro you can start it via xmac lt name gt or just with lt name gt leaving off xmac A macro behaves for this reason just like a normal XWIN NMR command You should avoid giving a macro the name of an existing XWIN NMR command If you did and typed in the command name the internal command would be executed not the macro You could still start the macro by calling it via xmac xwish Execute a Tcl Tk script by typing xwish f lt script gt on the keyboard Tcl Tk pro vides a programming system for developing and using graphical user interface applications its name stands for tool command language Please refer to the book Tcl and th
146. curdir lt user gt Exit_unimar Terminate current Tcl Tk script Table 5 14 Tcl Tk interface commands to XWIN NMR tions Then in order to execute the script you just enter its name on the XWIN NMR command line The File Menu P 136 Chapter 6 The Process Menu for 1D Data Basic 1D processing is presented in the chapter 1D Data Processing Tutorial for Beginners This chapter describes the commands located in the Process Menu 6 1 General parameter setup edp The edp command opens a dialog box which allows you to set the parameters required by the various commands in the Process menu The parameters are described along with the commands which make use of them 6 2 Line broadening factor lb The LB parameter is set by calling this command LB is used by the commands em and gm It can also be set in the edp window You can also type lb on the keyboard followed by Return or specify the desired value on the command line e g 1b 0 3 followed by Return 6 3 Exponential multiply em The command em multiplies the data point i by the factor P 137 The Process Menu for 1D Data P 138 exp i 1 LB P 1 2 SW The processing parameter LB in Hertz determines the resultant line broad ening LB is normally greater than zero and improves the sensitivity but with the disadvantage of line broadening The acquisition parameter SW in Hertz is the width of the spectrum Execution
147. d S2 7 data bits S1 7 8 2 stop bits S1 3 4 No parity S1 5 6 automatic formfeed before label printing S3 1 printing speed max 500 Hz S3 2 no XON XOFF protocol S3 3 After entering prlabel the display shows a table which is headed by define new series During the barcode operation XWIN NMR keeps a protocol of which barcode ID numbers have already been measured in the file u conf instr label_inf o Another measurement with the same number is then impossible preventing already acquired data from being overwritten by further measurements It is also impossible to create new labels for these numbers when selecting the first entry none from the table In this case only numbers not used so far are allowed for printing If a certain range of numbers e g 1 10000 is to be released again because the corresponding data sets have already been archived or are no longer needed the respective number range must be selected from the table Now prlabel shows the tables of the user login IDs the solvents and the experi ments After selecting the desired entry the ID number of the label to be printed is asked for and XWIN NMR will offer the next available number Then the number of labels to be printed may be specified If this number n is larger than 1 then n labels will be printed with increasing label ID number but the same user ID the same solvent and the same experiment As soon as the labels have been printed the user tab
148. d The same effect can be achieved by the command rev 6 7 Automatic phase correction apk Please refer to the chapter 1D Data Processing Tutorial for Beginners 6 8 Manual phase correction Please refer to the chapter 1D Data Processing Tutorial for Beginners 6 9 Phase correction with constants PHCO and PHC1 pk The data consisting of real and complex points R i I i is phase corrected using the formulae The Process Menu for 1D Data P 140 ROG RG cos a i IG sin a i 106 IG cos a i RG sin aGi where R and I represent the corrected values and a i PHCO i 1 PHC1 where i gt 0O PHCO and PHC1 are the zero and first order phase parameters respectively and may be set by the user in degrees as processing parameters The values may also be obtained using the interactive phase correction procedure as described else where in this manual pk is mainly used to phase a number of similar spectra with the same phase parameters pk always operates on the processed data if available e g after em or ft other wise the acquisition data Fid are used In order to force pk to use the acquisition data even though processed data exist use trf instead of pk by setting the mode parameters properly as described with the trf command 6 10 Magnitude spectrum mc The command mc replaces the real part of the spectrum by its absolute value according to the formula ABS i SQRT RG R
149. d as a negative value Valid values for GB lie between zero and one If GB 0 33 the Gaussian function has a maximum after 1 3 of the acquisition time gm is automatically preceded by bc baseline correction if the parameter BC_mod is not set to no The Process Menu for 1D Data P 142 6 12 3 Trapezoidal tm tm multiplies the data by a function of the following form w t AQ a 1_ 0_ 0 TM1 TM2 1 The processing parameters TM1 and TM2 determine which region of the data is multiplied by a constant Outside of this region the data is multiplied by a straight line the gradient of which is given by TM1 and TM2 TM1 and TM2 must lie between zero and one and are entered as a fraction of the acquisition time AQ of an Fid 6 12 4 Sine sinm Squared sine qsin The command sinm multiplies the data by a sine function of the form sin PI PHI t AQ PHI 0 lt t lt AQ where PHI PI SSB The processing parameter SSB may have the values 0 1 2 3 A pure sine wave is obtained when SSB 0 or 1 a pure cosine wave when SSB 2 PHI approaches zero for greater values of SSB The command qsin multiplies the data by the square of this function 6 13 Sequential operations P 143 6 12 5 6 12 6 6 12 7 6 13 Sinc sinc Squared sinc qsinc sinc multiplies the data by sin t t 2n SSB GB lt t lt 2x SSB 1 GB User defined uwm The command uwm multiplies the fid of the current data
150. d MAXI are processing parameters that can be entered at the keyboard or from the parameter editor edp They can also be adjusted interactively with the mouse as we shall see in a moment Their units are centimeters cm for the following reason XWIN NMR facilitates the comparison of plotted spectrum and printed peak list by outputting the peak heights in centimeter units The scaling reference peak usually the high est peak in the spectrum when an overview spectrum is plotted will be plotted with the height CY centimeters and will also appear with this height in the peak list You can define CY by typing in the comand in lower case characters or inter actively In order to adjust CY MI and MAXI interactively open the Display gt Options menu and toggle the y axis and cm units on or click the rightmost grid button on the panel Then call the command Adjust min maximum intensity from the Analy sis gt Peak picking menu or alternately click the button utilities at the button panel The button panel layout will change and show the command buttons CY MI and MAXI Before you continue examine the processing parameter PSCAL enter its name in lower case characters and set it to the value global if it does not have this value global means that the largest peak of the entire spectrum will be assigned the height CY centimeters Other values of PSCAL are not considered here because they cannot be used to set CY interactively Now click on the CY
151. d be done The question may be suppressed by giving an argument with the command e g tf3p y to store the imag inary part or tf3p n not to store it In AU programs the phase correction commands must always be given with one single argument which specifies whether the imaginary parts are to be stored e g tf3 66 66 7 4 7 Baseline Correction In the chapter D Data Processing Tutorial we discussed the baseline correction command absf for 1D spectra which assumes that a baseline distortion can be removed by subtracting a polynomial from the spectrum The commands tabs3 tabs2 and tabs1 use the same algorithm to correct a row of a 3D spectrum in the corresponding dimension The commands can be typed in or invoked from the Process gt Baseline correction menu As in 1D the parameter ABSG determines the degree of the polynomial and can be set independently for the three dimen sions from edp The parameters ABSF1 and ABSF2 determine the left and right limits of the region to be corrected In contrast to the 1D command absf the 3D commands do not generate integral range files 4 8 More on 3D Please check the chapter The 3D Process Menu for more details on 3D data processing It should be mentioned here that XWIN NMR only offers a basic set of 3D tools A broad range of 3D visualisation and analysis routines are available in Bruker s AURELIA software package Chapter 5 The File Menu Like the majority of window based programs to
152. d will therefore be The File Menu P 100 5 6 2 5 6 3 created under the same user name and on the same disk partition as the current data set You should invoke the command in this form if not only NAME but also EXPNO and PROCNO are to be changed when copying Example wrpa sucrose 5 2 wrpa NAME EXPNO Please use this command if you want to make a copy that differs only in NAME and EXPNO from the current data set Example wrpa sucrose 5 wrpa NAME Please use this command if you want to make a copy that differs only in the NAME from the current data set Example wrpa sucrose wrpa EXPNO Please use this command if you want to make a copy of the current data set and the copy should bear the same NAME but will have been assigned the new EXPNO The program can differentiate this command from the above one wrpa NAME because EXPNOs consist entirely of digits while NAMEs must begin with a letter Example wrpa 5 Entire data set to other disk wrd This command is for example useful for archiving a data set on magneto optical disk or another device with the directory structure of a magnetic disk While this task could also accomplished via the command wrpa described earlier wrd is sim pler to use When entered at the keyboard the following form is also legal wrd DU In this case the current data set is copied to the specified disk unit and will be stored there under the same NAME EXPNO PROCNO and USER
153. data LPbc for backward LP complex data Real or complex data types depend on the acquisition type See the Table 7 1 in the section describing xfl1 MC2 This distinction is however only important for xtrf type transforms For the commands xf2 xfl and xfb the difference between real and complex LP is handled internally i e LPfr and LPfc will give the same result The same is true for LPbr and LPbc The processing parameter NCOEF represents the number of coefficients used for the LP calculation Ideally this parameter should be set to 2 3 times the number of expected peaks A default value of 100 for a TD of 256 is recommended Forward Linear Prediction Forward linear prediction is performed if the processing parameter ME_mod is set to LPfr or LPfc see above The number of points used for the prediction is TD This number is reduced to TDeff if TDeff gt 0 If this is the case replace TD by TDeff in the following description Forward LP is only performed if 2 SI gt TD and replaces the normal zerofilling The number of predicted points is 2 SI TD One can also use a combination of linear prediction and zerofilling by setting the parameter LPBIN If LPBIN is set between TD and 2 SI it represents the number of output points original predicted of the forward LP The remaining points 2 SI LPBIN are set to zero 7 6 Linear Prediction P 163 7 6 2 Backward Linear Prediction Backward linear prediction is performed if the process
154. day XWIN NMR collects file han dling commands in the File menu Figure 5 1 Figure 5 1 The File menu P 75 The File Menu P 76 5 1 New New creates a new data set This command which is identical to edc is required if the next data acquisition command zg is not to be started from an existing data set but from a new one now to be defined by the user A dialog box according to Figure 5 2 is opened where you must specify the location and name of the new data a es Figure 5 2 The File gt New dialog box set From the parameters NAME EXPNO PROCNO DU and USER a directory is created to contain the new data after acquisition u data guest nmr sucrose l or in general DU data USER nmr NAME EXPNO The parameters in capital letters may be chosen by the user the items data and nmr are inserted by the program automatically DU determines the location of the data set in the file system of the operating system Examples DU u or DU usr peo ple guest Under UNIX it implicitely specifies the physical disk drive used which can be a second drive or a drive mounted from a network USER is the login name of the current user EXPNO the experiment number must be a number and is used to count different experiments with the same NAME The result of an acquisi tion is a file fid for 1D or ser for 2D 3D containing the acquired data which will be stored in this directory When the directory is created it is
155. de the following procedure is adopted 1 Select the 1D spectra and start the nmrquant program either by typing the command or by selecting from the pull down menu Click on the Define button on the left hand side of the display and you will be given a choice of defining the integral baseline regions the proton matrix file or all three By selecting the integral option from the enumeration window instructions for defining integral regions and reentering the program are dis played Define the integral regions as discussed in the chapter 1D Data Processing Tutorial and store with the Save as intrng amp return integral menu item Re enter the program by typing the command nmrquant on XWIN NMR s command line or by calling it from the Analysis menu The main display now shows the number of regions defined on the right hand side Click on the Define button on the left hand side of display and select the base line option from the sub window Again instructions for defining base line regions and reentering the program are displayed Internally the integral regions defined in step 3 are renamed to prevent being overwritten by the intrng file which is set up when defining the base line regions The original integral file is restored after renaming the base line intrng file defined in step 4 to basereg Click on the item Define Components to set up the matrix describing the proton contribution from each compone
156. defined 2D Fourier Transform xtrfp xtrfp2 xtrfp1 The xtrfp transformation differs from the xtrf transformation only in the type of data used as input data Unlike the xtrf transformation the xtrfp transformation uses data that have already been processed with the transformations described above The xtrfp command can be applied to the same data as often as needed with different processing parameters each time e g to apply several filters or to transform the data back and forth xtrfp2 only evaluates the processing parameters in the F2 dimension xtrfp1 only in the F1 dimension 7 22 Inverse Fourier Transformation xif2 xif1 These commands correspond to xtrfp2 and xtrfpl transformations with the processing parameters BC_mod ME_mod WDW and PH_mod set to no The inverse of the processing status parameter FT_mod is used as the transformation mode 7 23 2D Hilbert Transformation xht2 xht1 The commands xht1 and xht2 are the two dimensional analogues of the command ht see description there For phase sensitive spectra the following rules apply From the real part 2rr of the 2D spectrum xhtl creates the imaginary part 2ri Additionally it creates 2ii if the Fourier transformation has created the imaginary part 2ir Likewise xht2 creates the imaginary part 2ir from the spectrum s real part 2rr and in addition the part 2ii if the Fourier transformation has created the imaginary part 2ri Choose the Hilbert trans
157. derived from Marion Ikura Bax J Magn Res 6 15 File algebra P 145 6 15 84 425 430 1989 For X32 CPUs it should be noted that this software is not implemented in the array processor Calculation time grows with the 2nd power of the spectrum size bc is called automatically when the commands em gm or ft are executed The parameter pairs single quad spol qpol and sfil qfil are provided for single detection and quadrature detection data respectively bc is not affected however because Uxnmr knows the data type and uses the correct mode internally The difference is only valid for the command trf where the user can define the type of calculation to be performed File algebra 6 15 1 6 15 2 6 15 3 Define multiplier dc The floating point parameter DC is used by various algebra commands as a multip plier or term of a sum Use dc to set DC or set DC from the edp processing param eter editor Define second and third data set edc2 This command allows you to define the two data sets used by the add command or some other commands that apply to two data sets Add data sets add at These commands multiply the third current data set defined using edc by the processing parameter DC then add to that the second current data set and store the result as the current data set currentdataset second DC third add or at may also be used so that the current second or third data set is substituted overw
158. display processing and plotting utilities For details please refer to the NMRSIM manual DAISY 9 10 1 9 10 1 1 The DAISY program package was developed in cooperation with the Institute of Inorganic Chemistry I University of D sseldorf Germany It allows simulation of 1D NMR spectra taking into account general magnetical and chemical equivalence No line assignments are required because DAISY uses the original experimental line shape Therefore highly symmetrical spin systems can be iterated where packages that require line assignments will fail due to the uncertainty of the assignments Parameter set up and execution take place from within XWIN NMR and the gener ated data are immediately accessible from there For example the experimental and refined spectrum can be viewed in dual display mode DAISY is not a standard component of the XWIN NMR package and must be pur chased as a separate option A complete manual is delivered with the program The command ded available in the Simulation gt DAISY menu is the XWIN NMR interface for the DAISY program package General hints for working with ded The main menu The main menu of the editor has the following contents and options e header line with the name of the program 9 10 DAISY P 215 e status of the editor with selected program type filename of the actually loaded data set title of the data set e menu line with the commands Edit edit l
159. e can be plotted in different colors The corresponding colors are specified by special plot parameters using the command edg The program needs to know which color is to be found in which pen position of the plotter This information is entered by the operator via the parameters BLA_POS BLU__POS etc position of the black blue etc pen Position 0 means that a pen of this color is not available If the operator has accidentally entered a non existent color for an object to be plotted specified position 0 for this color the object will still be plotted in a different color as long as there is an available pen Other pen properties Some plotters allow for different pens to be used at the same time but the types have to be used at different speeds to obtain the best possible plot quality For this reason XWIN NMR Offers the possibility of specifying additional pen properties for different pen types and colors by use of the parameters BLA_PAR BLU_PAR If these parameters do not contain an entry the default parameters of the respective plotter see manufacturer s manual are used The pen parameters are entered in the form 60s 4a 7f 1 2t s speed a accelera tion f force t thickness The numbers in front of the letters are set by the user as desired The units of the parameter t are mm t influences the resolution of the spectra on the paper For laser printers it determines the line thickness The units of the other para
160. e 02 2 907826e 00 1 771960e 02 2 468165e 00 1 768221e 02 1 748423e 00 1 764483e 02 1 689626e 01 8 412024e 00 Table 16 1 JCAMP DX shape file format Header consists of 256 32 bit float words 1 word 1 contains file type information 371242 0 GRADVERSION_F or 18906 0 RFVERSION_F 2 word 2 contains of amplitudes amps stored File Formats P 340 RFVERSION_F 10 0 20 90 30 180 40 270 50 360 Figure 16 4 old ASCII shape file format 3 word 3 contains of phases phas stored 4 word 4 to word 256 are unused e Data consists of amps phas 32 bit float words 1 REVERSION pairs of phases and ampitudes phases in degrees from 0 0 to 360 0 and amplitudes from 0 0 to 100 0 Phases are always stored as first value followed by the corresponding amplitude 2 GRADVERSION only amplitudes are stored values from 0 0 up to 100 0 Phases allowed are 0 0 and 180 0 degrees If the phase is 180 0 degrees the stored amplitude is negated No phases are stored in the file The maximum size of amplitudes for GRADVERSION or pairs of amplitudes and phases RFVERSION is 32K or 32768 points pairs 16 8 Other files Many other files play a role in XWIN NMR such as integral range files peak lists etc They are described in the chapter The File Menu or in conjunction with the command generating them
161. e Tk Toolkit by John K Ousterhout Addison Wesley Publishing Co Table 5 13 shows a simple Tcl Tk script example tcl stored in the user s home directory If you type xwish f example tcl on XWIN NMR s command line a win dow according to Figure 5 19 will be opened consisting of a title a text and an entry field If you enter a number followed by Return the XWIN NMR command processor CPR will be called using the procedure CPR_exec and an exponential multiplication em with the entered number as line broadening factor LB will be executed on the current data set followed by a Fourier transform ft Then the win dow will be closed The File Menu P 134 wm title xwish f example tcl label label text Please enter line broadening factor LB entry entry width 10 relief sunken bd 2 textvariable 1b pack label entry side left padx 1m pady 2m bind entry lt Return gt CPR_exec em lb CPR_exec ft Exit_unimar Table 5 13 Tcl Tk example script l wish Fexampte tO Please enter line broadening factor LB 0 3 Figure 5 19 Window generated by Tcl Tk example script This example shows that you can write your own windows applications with Motif style look and feel without the knowlege of X Windows Motif and the C language In a simple way you can tailor your own user interfaces for XWIN NMR including graphics drawing You may combine Tcl Tk scripts with AU programs For exa
162. e ae P 155 7 3 Transform of F2 rows Xf2 2 0 0 cece nnn P 155 7 4 Transform of Fl columns xfl 0 0000 cc cece cee eee P 159 TS General 2D processing options 0 0 c cee cee cee eee P 160 7 6 Linear Prediction res rroen jeans en dead emyewe ele canes tena P 161 7 7 Phase correction coenae E A E an oad S P 164 Chapter 8 Chapter 9 Chapter 10 7 8 Magnitude Spectrum xflm xf2m xfbm 00000 P 164 7 9 Power Spectrum xflps xf2ps xfops 0 00 0 c eee eee eee P 165 7 10 COSY Type symmetrization sym syma 0 0 002 eee P 165 7 11 J resolved Type symmetrization symj 0 00 00 0 eee ee eee P 165 712 Tilt of a 2D spectrum tilt ptilt 0 eee P 166 7 13 Manual Baseline Correction bcm bem2 0 00000 c eee eee ee P 166 7 14 Automatic Baseline Correction abs1 abs2 20 0 0 cece eee P 166 7 15 Trapezoid Baseline Correction abstl abst2 0 0 02 cee eee eee P 166 7 16 Subtraction of 1D Spectra sub1 sub2 subld1 subld2 P 167 7 17 Extracting Rows and Columns rsr rsc 0 0 cee eee eee eee P 167 7 18 Extracting an fid from 2D Acquisition Data rser 004 P 168 7 19 Replacing Rows and Columns wsr wsc 0 000 c eee eee eee P 168 7 20 Replacing an fid within a ser File wser wserp 00000 P 169 7 21 User defined 2D Fourier Transform xtrf xtrf2
163. e by manipulating the azimuth and zenith angles phi and zeta Put the cursor onto one of the respective buttons depress the left mouse button and move the mouse until you get the desired angle When you release the left mouse button the new view will be calculated and displayed 3 4 Setting up the parameters for a 2D transform The main processing steps to calculate a spectrum from a 2 dimensional fid ser file are window multiplication and fourier transformation In 2D unlike 1D win dow multiplication and fourier transform and optionally linear prediction phase correction or magnitude calculation are part of the transform commands xfb xf2 xf1 The reason for this is the size of 2D data sets Execution speed is considera bly improved if the data need only be read once from disk and stored back after processing However all required parameters must be set up before the transform Call the processing parameter editor edp either by typing in this command or by 2D Data Processing Tutorial P 42 opening the Process menu and selecting General parameter setup edp A dialog box is displayed containing all processing parameters in two colums for the two dimensions to be processed Some parameters exist for either dimension others only for one dimension It should be mentioned here that the contents and layout of the edp dialog box can be tailored by the user by editing the so called format file u exp stan nmr form proc e The m
164. e execution of gm followed by pk The Process Menu for 1D Data P 144 fmc corresponds to the execution of ft followed by mc 6 14 Baseline correction operations 6 14 1 Manual abs absf absd sab Please refer to the chapter 1D Data Processing Tutorial for Beginners 6 14 2 Fid dc offset correction bc be applies a baseline correction to the acquisition data i e the file fid of the current data set depending on the processing parameter BC_mod The result is stored as a processed data set in the files Zr Zi and is ready to be further processed usually by applying a window function and a fourier transform Effect of the parameter BC_mod BC_mod_ Effect no bc performs no operation single quad a constant is subtracted from the fid spol qpol a polynomial of degree 5 is subtracted from the fid sfil qfil filtering of the fid according to Bax Marion Table 6 1 single quad The constant is determined by calculating the average value of the last quarter of the Fid for each channel separately if quadrature detection is active spol qpol The polynomial of degree 5 is the result of a least squares fit again separate for each channel This mode leads to a reduction of strong water signals in the center of the spectrum sfil qfil This mode suppresses signals e g water in the center of the spectrum It is effective over a range defined by the processing parameter BCFW in ppm The algorithm is
165. e identical to those output by the command pp if they all fit into the spectral window of width CX If this is not the case then the available room will first be shared by the highest intensity peaks with the restriction that the horizontal distance between a label and the corresponding peak not be greater than ca 3 cm Therefore the reason for unlabeled lines is usually that there is not enough room available The labeling is controlled by the following parameters PLHEI The 1D Output Menu P 256 10 3 2 Height of the peak list window in cm PLCHAR Height of characters used in mm PLDIGIT Total maximum number of digits to be used for one peak label This allows you to set the number of significant digits for output PLDIGIT includes the deci mal point and the sign PLMRK This parameter can take values yes and no In the former case all intensities found by the peak search will be marked with a little vertical line It appears as a plus sign if it did not fit into the peak list due tp space reasons PLCOLOR Color of peak list characters PLUNIT Units to be used for peak list Hz or ppm PLMUL This parameter with the values yes or no is provided for additional labels specify ing the multiplicity of a line An analysis of multiplicities is prerequisite The Title Window Any text stored in a text file may be output in this region of the plot The name of the text file must be specified in the plot parameter
166. e interactive integration routine on the screen INTSCL 1 Scaling is performed relatively to the last spectrum plotted XWIN NMR maintains the scaling factor in the file u prog lt version gt curdir lt user gt scale The spectrum As has already been mentioned the spectrum will be plotted in the data window of height DHEI within the spectral window The data window is immedi ately above the integral window The zero line of the spectrum with intensities of value zero is placed SZERO cm above the lower edge of the data window and thus SZERO cm above the upper edge of the integral window The horizontal scaling of the spectrum is controlled by the parameters F1 and F2 or FIP and F2P These parameters set the range of the spectrum to be plotted if the parameter LIMITS is set to fixed These parameters are best set with the Define plot region commands of the Output menu after adjusting the desired region on the display or explicitly with the parameter editor The 1D Output Menu P 252 F1 Hz F1P ppm These parameters determine the left low field limit of spectral region to be plot ted If this parameter is changed then the right plot limit F2 F2P is automatically adjusted so that the plot resolution Hz cm and the width of the spectral window CX remain unchanged Therefore a change of F1 F1P means a shift of the plot region F2 Hz F2P ppm These parameters determine the right high field limit of spectra
167. e screen layout will change to that of Figure 2 2 Figure 2 2 Interactive adjustment of window function The upper part shows the fid and the window function the lower part the trans formed spectrum The latter can be the unphased no or phased pk spectrum the 2 4 Applying a window function to the fid P 17 magnitude mc or the power spectrum ps Select your preferred mode from the phase mode button ph mod at the lower left pk mode uses the processing parame ters PHCO and PHC1 for phasing which requires that a phase correction has already been performed In the exam d data set correct phase parameters are already present so you can set pk mode The command button area at the left side is divided into several sections The upper section provides the usual buttons manipulating the spectrum The section fid provides similar functions for the fid and the window function curve The sec tion function allows you to select the desired window function When you activate one of those buttons a small Info window at the upper right will show the chosen function and the parameter s required by this function exponential multiply em requires LB to be adjusted Gaussian multiply gm requires LB and GB sine mul tiplication sin and squared sine multiplication gsin require SSB the phase of the sine The last section parameters allows you to adjust these parameters thereby execut ing the window multiplication and the fouri
168. e spectral window includes the following plot objects 11 3 Page layout contour plot edg P 289 Figure 11 3 Example of a contour plot e contours e axes e coordinate grid e 1D spectra along both coordinates e peak list of the 1D spectra It is divided into 7 non overlapping windows for The 2D Output Menu P 290 the contours NADNBWNKe the F1 axis vertical the F2 axis horizontal a 1D spectrum along F1 peak labels for that spectrum a 1D spectrum along F2 peak labels for that spectrum The sizes of these windows are determined by the following parameters CX1 CX2 size of contour window along F1 and F2 in cm X1HEI X2HEI width height of F1 F2 axis window in cm PFIHEI PF2HEI width height of 1D spectrum window along F1 F2 PLIHEI PL2HEI width height of 1D peak list windows In order to enable or disable a plot object select yes or no for the follwoing param eters displayed on the first page of the edg window CONTPLO CONTADD TITLE XIAXIS X2AXIS PARAM PROJ1 PROJ2 FRAME PLABEL1 PLABEL2 contours contours of a second data set title axes parameter window 1D spectra or projections along F1 F2 frame around contour window and around integration regions peak labeling of 1D spectra or projections along F1 F2 If a plot object is enabled you may open a new page within edg to edit the object s parameters by clicking on the corresponding edit button
169. e the cross section more visible Another click on blank will redisplay the 2D spectrum Another way of improving the visibility of a cross section is to increase the intensity threshold for the 2D spectrum e Use the buttons and located below the 2 and 2 buttons to display the next or previous cross section These buttons allow you to adjust any particular row or column number 3 14 Projections and Cross Sections P 59 e Ifyou want to save the row or column as a 1D spectrum click on the return but ton or open the File menu Select one of the commands Save row col as TEMP or Save row col as PROCNO Projections Click on the button labelled p to display the positive projection onto the corre sponding axis projection of positive intensity values only Click on n to view the negative projection Projections are always calculated over the entire spectrum even if the current display only shows a region of it The calculation takes place during the Fourier transformation and are stored in the current data directory The files names are given in Table 3 3 Axis Projection type File Fl positive p2rl Fl negative n2rl F2 positive p2r2 F2 negative n2r2 Table 3 3 Files containing projections You may vertically scale projections using the 2 and 2 buttons located below the row col buttons Projections may be stored as 1D spectra like rows and columns click on the return button or open the File me
170. e thereby reversed The Process Menu for 1D Data P 152 6 18 8 Build first derivative dt The first derivative of the current data set is calculated by dt 6 18 9 Quadrature image correction qc qk qk quadrature correction using the previously calculated constants ALPHA and GAMMA qc quadrature correction using the current constants ALPHA and GAMMA qk and qc implement Parks and Johannesen s algorithm J Mag Res 22 265 267 1976 In quadrature detection that is AQ_mod qseq or AQ_mod qsim the phase difference between the two channels of the receiver A and B may be exactly 90 degrees and the signal amplitude may differ slightly between them These two errors can cause mirrored signals to arise around the center of the spec trum This correction method replaces the signal A with a corrected signal GAMMA A ALPHA B that is a linear combination of A and B where GAMMA and ALPHA are so cal culated that the corrected signal A is orthogonal to B in vector notation ALPH A A B B 2 GAMMA 2 B 2 A ALPH A B 2 The algorithm can fail when there are signals in the spectrum symmetrical about the center Therefore the processing parameters ALPHA and GAMMA should be determined with gk using a suitable reference sample and then further spectra should be corrected with gc using these parameters In time and using different experimental conditions it will be necessary to redetermine ALPHA and GAMMA
171. ead the selected slice START from the 2D file and you will be put into the main 1D processing menu Create the basipnts baseline points file for intensity fitting You must now define the positions from where peak maxima will be picked along columns from all rows of the 2D data set Switch to the interactive base line correction menu Process gt Special processing gt Baseline correction or type basl Click on define points The cursor will be put onto the spectrum Move the mouse cursor to the top of a peak and click the middle mouse button This selects this peak position for the point picking on the 2D data set Move the cursor to the next peak and click again the middle mouse button You have selected a second position for the point picking After you have selected all positions click the left mouse button The cursor is now free again and you can click on return to return to the main 1D processing menu You can also do this at any stage during the selection of peaks for instance if you want to select a different area for the point selection or if you want to zoom into a region for a more accurate point selection Re enter the baseline menu click again on define points and answer the question with a for append to append more points to the already selected ones Proceed from there as decribed above After you have selected all positions where you want to pick points you click the left mouse button to free the cursor followed by a click on
172. ecessary changes to the file etc inittab and print a few messages on the monitor Next cfpp will print the question Configure like existing plotter y n Type y if the new plotter is to be configured like a previously installed plotter of the same type e g with the same paper feed options and pen positions Otherwise a default configuration is taken from the file u conf plotter init lt chosen plotter type gt delivered with the release software list all existing plotters This is the only option of the table that does not require a superuser password A list of all configured plotters and the channels they are connected to is given remove an existing plotter After execution of this option the plotter will no longer be accessed from XWIN NMR change name of an existing plotter The name of a plotter can be changed if required for some reason Change output device of existing plotter Select this option after connecting the plotter to an output channel different from the channel specified during the first installation change class of existing plotter Change the class assignment of a plotter remove existing plotter from a class Remove it After the installation of a new operating system version from a boot tape the plot ter installation must be repeated Creation of Plot Files The plot commands eventually send their output directly to the plotter or printer XWIN NMR Offers the possibility of storing the plot data i
173. ect initial data points of the acquisi tion data before the transform in order to obtain better baselines Furthermore completing truncated Fids with linear prediction gives better estimates of the data and therefore allows for faster acquisition of multidimensional experiments Lin ear prediction is executed as a part of the 2D transform and is enabled by setting the processing parameter ME_mod to LPfr forward or LPbr backward predic tion The default value of ME_mod is no A strip transform is useful if you are only intereseted in a particular spectral region It allows you to fourier transform only a selected portion of the spectrum defined by the processing parameters STSR strip start measured in points from the beginning of the spectrum and STSI size of region in points The result is a file of significantly smaller size which can be handled faster on the display and consumes less disk space You are also able to set the transform size for the region and therefore its resolution to a larger value than it would be possible when tran forming the whole spectrum You may also combine the strip transform with linear prediction The region limits for the strip transform may be selected interactively For this purpose click on the utilities button Move the cursor into the data area and click the left mouse button Position the cross hair to the upper left corner of the desired region Fix the position by clicking the middle mouse button
174. editing commands eda edp edg edo for acquisition processing plotting and output device parame ters respectively and can be found in the menus Acquire Process Output They are described in more detail in the corresponding manual chapters Copies of parameter files from and to parameter set directories can be made via the com mands rpar and wpar see File gt Copy menu The File Menu P 82 5 3 2 Pulse programs edpul Pulse programs are text files containing statements in the Bruker pulse program language described elsewhere in this manual This command allows you to create a new pulse program and to edit or view an existing one XWIN NMR locates pulse programs in the directory u exp stan nmr ists pp The command edpul displays all pulse programs in this directory in a dialog box On XWIN NMR release media a large number of sample pulse programs are deliv ered After installation of XWIN NMR they are stored in the directories of Table 5 4 u exp stan nmr lists pp exam AMX high resolution u exp stan nmr lists pp rexam ARX high resolution u exp stan nmr lists pp dexam AVANCE u exp stan nmr lists pp solids AMX ASX solids u exp stan nmr lists pp imag micro imaging u exp stan nmr lists pp tomo tomography Table 5 4 Sample pulse program directories The command expinstall see menu Acquire gt Spectrometer setup which must be executed after installation of XWIN NMR will copy the
175. elect the display region on which you want to execute the spline baseline correc tion any desired region or the whole spectrum Enter manual baseline correction mode from the Process gt Special processing gt Baseline correction menu Click on the button def pts Answer the questions allowing you to append new points to an already existing file of baseline points or overwrite this file The cursor will then be bound to the spectrum trace until you click the left mouse button Move the cur sor along the spectrum starting at the left edge although if you want you can select the points in any order Select carefully points on the spectrum you con sider as true baseline points Click the middle button to store the point correspond ing to the current cursor position in the file baslpnts Selected points will be marked by an arrow Proceed to the right until the file baslpnts contains enough points to describe the baseline adequately Up to 200 points are legal When you click the left mouse button point selection is terminated and the baslpnts file is closed You can later append more points by clicking def pts again Now you can execute the command sab type it in or select it from the Process gt Special processing gt Baseline correction menu It calculates the spline from the stored baseline points and subtracts it from the spectrum Only the region between the leftmost and rightmost baseline point stored in the baslpnts file is processed
176. els of your home directory Whenever you invoke cpan the command button panel is displayed according to the definitions in default If you click on a button the corre sponding XWIN NMR command is executed The directory xwinnmr lt hostname gt cmdpanels may contain additional panel files describing different panel layouts The button Load at the bottom of a panel will display a listbox with all these files If you select one with a single mouse click followed by a click on the OK button or by a double click the current layout will be replaced by the new one It is also possible to have more than one panel open at the same time by invoking cpan sev eral times The structure of a panel file is illustrated by the example of Table 13 1 the corresponding panel is shown in Figure 13 2 Empty lines are ignored The line after TITLE will be displayed as a panel title BUTTON starts a button entry NEWROW forces the button to be placed in the next row SAMEROW in the same row as the previous button The next line is the XWIN NMR command followed by the desired button label and a help text to be displayed at the bottom line of the panel when the cursor moves over the button The buttons defined for a row will be centered in this row during display All buttons will get the same size calculated from the longest button label string The keyword END indicates the end of a panel file If you want to start up cpan with a panel other than default pr
177. enabled special parameter file handling disabled The data are changed from 24 bit to 32 bit per word storage The 1 sector and the data are stored in one file The filename on the receiving computer is w bruknet am400 guest SPEC 001 e Binary mode enabled special parameter file handling enabled The data are changed from 24 bit to 32 bit per word storage The 1 sector is stored in a separate file which has the same basic name as the data set but starts with the prefix p_ The filenames on the receiving computer are W bruknet am400 guest SPEC 001 u bruknet am400 guest p_SPEC 001 e Binary mode disabled special parameter file handling disabled The parameters and the data are stored in one file in the 24 bit per word format The filename on the receiving computer is u bruknet am400 guest SPEC OO1 e Binary mode disabled special parameter file handling enabled The 1 sector is stored in a separate file which has the same basic name as the data set but starts with the prefix p_ Both files are stored in the 24 bit per word format The filenames on the receiving computer are u bruknet am400 guest SPEC 001 u bruknet am400 guest p_SPEC 001 All four transfer modes swap the bytes within one word So the byte order after the transfer will be low middle middle high The sign indicates the change from 24 bit to 32 bit per word storage NMRLINK has two transfer modes The File Menu P 112 5 11 1 1 e The data can be tran
178. ents 1D data processing based on the exam d stored in the direc tory XWINNMRHOME data guest nmr Please note that XWINNMRHOME u after a standard installation of XWIN NMR In order to have full access permissions to it you should have a user guest installed on your system and be logged in as guest Start XWIN NMR by typing xwinnmr r The r option ensures that every thing is cleaned up before starting the program even if the last session was termi nated by some problem The program will start without displaying a data set Instead the XWIN NMR logo will be shown in the data area In later sessions you can start XWIN NMR without specifying the r option and you will immediately get the last used data set displayed 2 1 Getting the data set The first step is to get the 1D spectrum examl d on screen Open the File menu select the Open entry and from there the command dir You should get a dialog box where the data sets examld exam2d and exam3d are listed If there are other data sets in the directory u data guest nmr they will also appear in the box Click on examld in oder to instruct the program to make this data set the current data set XWIN NMR will automatically show the D layout because it identifies examld as a 1D data set The identification is not performed via the name of the data set but through the contents of the parameter file meta stored in the directory P 9 1D Data Processing Tutorial P 10 u data guest n
179. enu Example of a region file The first line of the file contains two numbers n and m These are currently set to zero and reserved for future extensions Each spectral region is given by two lines containing the rows and column parameters defining the region Specifically these are the spectrum size in this dimension the row or column numbers and the corre sponding ppm values The codes a indicate whether only positive only negative or all data points should be used by int2d or int2dref to calculate the inte gral of this region 00 a 1024 918 948 0 433316 0 156820 1024 453 479 4 719352 4 480560 1024 918 948 0 433316 0 156820 1024 453 479 4 719352 4 480560 1024 918 948 0 433316 0 156820 1024 453 479 4 719352 4 480560 Example of an int2d results file The format of the results file is similar to the region file except for the additional entries for the integral values The following example shows the format of an int2d file generated by the command int2dref The output format created by the com mand int2d would be same except that the column norm Int normalized inte grals is missing Current data set Name exam2d ExpNo 2 ProcNo 1 User bg Disk u Baseline 0 Noise 0 SI_F1 rowl row2 rowl ppm row2 ppm Integral norm Int Mode SI_F2 coll col2 coll ppm col2 ppm 1 1024 918 948 0 43332 0 15682 24 976 13 089 a 1024 453 479 4 71935 4 48056 3 12 Peak picking P 53 2 1024 91
180. er 5 Chapter 6 Chapter 7 4 5 Strip transform linear prediction other transform options P 71 4 6 Phase COMECHON 5 ces eis Renae kes See Wa ae ae ood He gnc ate P 72 4 7 Baseline Correci n esenee hee Re ew Oa ten bald da sores 2 oan Yen Cae P 74 4 8 Mor On 3D iisair taeda aled we ee aie oe ee ONAN SA wha eae A hare P 74 The File Ment sessir evire erenervi ee ba 0 oie p be eipaseels sce PTS 5 1 NEW ofr AR aes bee et SE a ae E ee le ak Ole P 76 5 2 Open Data Piles sna na Aee io ia ee EAE aE E a G NAS P 78 33 Opens Other FESAI ha ee wee ast Sea eed P 80 5 4 ReGall last wai eile Mette dad A eels WA Ste cy A Alok tladd tele a St toh P 96 5 5 DCAM i int cohcara tale Sart sox ice veacnn a tog page O aera ae Gave hae aa gener e P 96 5 6 COPY 25s 5 sia aslo d tess Gia A E etune cianeds a T ttn EE O P 98 5 7 Delete Data Files 2 0 ce ccc ccc cece eee eter e tenn e ne S P 104 5 8 Delete Other Fil s 2 234 004 24 Sasa SIA es Se a Rnd te Bae kek Bs eet P 106 5 9 RENAME s aed Gee ce eee ee ats lee wht grees tees el ow ee eee P 107 SiO Send RECEIVE ceai erage ae O aaa We waa ee Sioa E ane ea alee as P 108 SAT Conversion sontaa 2 toh tids Rese go eee had Lee a Se Ses bs P 110 D212 Execute tassas te a ada Reed ae ee ohh te Be ay P 131 The Process Menu for 1D Data 0c cece ee cee eec eevee c ee P 137 6 1 General parameter setup edp 0 cece eee cee eee eee P 137 6 2 Line broadening factor Ib
181. er 8 The 3D Process Menu 8 1 General parameter setup edp The command edp invokes the parameter editor for the 3D processing parameters It displays three columns for the dimensions F3 F2 and F1 Set the parameter PPARMOD to the value 3D if this is not yet the case to ensure that parameter files are created for all three dimension The corresponding aquisition parameter is PARMOD which is usually set prior to acquisition with eda Acquisition and processing parameters files are stored in the current acquisition or processed data directory Table 8 1 shows the file names and the associated commands to edit or Acquisition Acquisition Processing Processing Dimension parameters status para parameters status para eda meters dpa edp meters dpp F3 acqu acqus proc procs F2 acqu2 acqu2s proc2 proc2s Fl acqu3 acqu3s proc3 proc3s Table 8 1 3D parameter files P 175 The 3D Process Menu P 176 display the parameters Individual parameters may also be examined by means of keyboard commands such as Is td 2s td 3s td si 2 si 64 etc s denotes status parameters The processing parameters to be set before a 3D transform are straightforward extensions to the 2D case and will therefore not be explained again in this chapter Please refer to the chapter The 2D Process Menu There is one particular status parameter however which is unique to 3D AQSEQ It describes the order 32 or 312 in w
182. er transform in the chosen phase mode Clicking the button will increment the corresponding parameter by the value selected via the button delta and redisplay the new window function curve the fid and the spectrum It is recommended to zoom into the spectrum and to observe a particular peak or peak group to see the effect of line broadening or signal to noise improvement in detail Clicking the button will decrement the corresponding parameter analogously You can also continuously increase or decrease a parame ter by moving the mouse forwards or backwards Set the cursor onto the up down arrow command button rightmost to the button and move the mouse while the left mouse button is depressed You will see window function fid and spectrum changing on line if the time domain and transform sizes are not too big Two special settings for SSB 1 and 2 are provided They result in half a period of a sine wave or a quarter of a period of a cosine wave In order to terminate the window function display mode click the return button at the bottom There are four possible options Cancel leaves you in the window function mode Store amp return will force the program to exit from window func tion mode and store the adjusted parameter in the processing parameter file This means you can the examine it by typing the parameter name on the keyboard or via the parameter editor edp Also note that the next execution of the window fu
183. erates a point spread function fora MEMSYSS5 run with the command maxent A point spread function is basically the lineshape of a single line or peak of a region in an NMR spectrum A PSF can also be the sum of a number of lineshapes defining a more complex peak or peak group Such a PSF must be generated with the command wpsf The point spread function is used for the deconvolution of an NMR spectrum Only 1D MEMSYSS5 will work with a user defined PSF For 2D and 3D the parameters defining the PSF are set in the editor maxed When running psf the user is asked for some parameters which describe the output PSF or lineshape Lineshapes can either be symmetrical or asymmetrical Each half of the lineshape with respect to the highest point can be designed individu ally so that Lorentz Gauss Winged contribution to the lineshape and half width at half height can differ You are asked for the following parameters 1 Number of points defining the lineshape PSF This number should be less than or equal to the number of points in the region of the NMR spectrum you want to deconvolve If the number of points in the PSF is greater than the number of points in the region of the NMR spectrum the number of PSF points is reduced for the deconvolution The selected points are chosen with respect to the center of the PSF 2 Symmetrical or asymmetrical lineshape There are two possible settings symmetrical a symmetrical lineshape will be generated
184. ere the date of acquisition is inserted in the XWIN NMR filename and conversion and transfer to a Unix workstation user specified in the Aspect filename Files used in the Bruktran program For correct operation of the Bruktran program the following files should reside in the home directory of the user e Btran_defs This file contains the program settings such as current BRUKNET station and user Aspect and XWIN NMR filename formats etc This file can be regenerated with default values by selecting the Reset Defaults button e Bt tokens This file contains the tokens elements which constitute the Aspect filename and their replacement values in the XWIN NMR file name Permissions required by the user Since BRUKNET data directories are set up with read write privileges for all users there is no special permission required by the user to convert data However if you wish to convert data sets and copy them to data directories of another user you must have permission to do so i e you must belong to the same user group Bruktran program options During program execution the Bruktran program accesses various parameters stored in the Btran_defs file These parameters include the current BRUKNET directory path the Aspect and XWIN NMR filename formats etc Parameters may be accessed by clicking on the Edit Program Options menu item in the main Bruk tran window and are described below e Current Destination Directory This specifies
185. es you specify the logical number of the nucleus into which the nucleus given in the first line is converted by applying the symmetry operation e Resonance frequencies All Iso values and resonance frequencies are listed in this menu The input val ues for resonance frequencies are interpreted in Hz If a value is followed by 9 10 DAISY P 223 p or P it is accepted as a ppm value and immediately converted to Hz If you change a resonance frequency of a nucleus or a group which is sym metrically equivalent to other nuclei or groups all lines with corresponding values including the Iso values are adjusted automatically Nuclei or groups with the same Iso value are treated by a second order approximation nuclei or groups with different Iso values are treated by first order approximation For DCYMPLOT also the number of nuclei in each composite particle CP group and their single spin is required To allow easier setting of the spin you have to enter 1 for a 1 2 spin 7 for a 7 2 spin nucleus Spin Spin coupling constants All spin spin coupling constants are displayed in this menu Chemically equiv alent values are updated automatically e Dipol Dipol coupling constants The default value for all coupling constants in this menu is 0 0 This is the cor rect setting if you want to simulate a spectrum in isotropical phase However if you want to simulate a spectrum in an anisotropical ph
186. es P 319 Writing AU Programs cece ccc eee cece reece cere eee P 321 15 1 Introduct On 2 35 p32 reg dd Bae ie eee te ee ea ye Ee ed aa P 321 15 2 Bruker standard AU programs 0 0 cece cee eee P 321 15 3 sFhecAU an guage es te une fe ae ee oe eS Cte a Aa P 322 15 4 Executing XWIN NMR commands 0 0 0 2 eee eee eee teens P 323 15 5 Variables aes cc essayist spe aod eh ene hp Sad ep ate ee a aca beg ath P 325 15 6 Selectin Sia data setga a aa n Ge eae aves ites lh oan AA P 325 I5 7 Patameteis y eese Sh cls oder seek ee ee osha E cates BUN Gea a A deh eae P 327 TOSS 5 AAZOOPS Sa deen hres Pct shar T E EEE EE diy Nota att atlas P 329 15 9 Calling other AU programs 00 c cee ee eee P 329 15 10 Terminating an AU program 0 eee eee P 329 15 11 Outputting messages to the screen 21 0 0 eee eee P 330 15 12 Requesting keyboard input 0 0 P 331 15 13 Ordering Screen refresh esvanpsiis aleati eee eis tie eels Sale ee Oe ee P 331 15 14 Executing several AU programs simultaneously 00 P 331 Chapter 16 15 15 Continue execution at a specified time 0 0 0 e eee eee ee P 332 File Formats TETTETETT ETT ES P 333 16 1 Parameter Filesi sa vbertansianien e a E EE E ATA E POEN a P 333 16 2 Acquisition Data meie e a i a oe eae eas a E RAAR AA P 333 16 3 UD spectra sia 4255 50 Bed ee N E E held Sees 2k Mes ee P 334 16 4 JCAMP DX f
187. ese peaks But bear in mind that in such cases the intensity value might not be the real height of the peak And this might obscure your fitting results 9 6 3 2 Pick points from an ASCII file The only thing you have to do is to set up an ASCII file named t ascii This file must reside in the processing data directory The format of the file t ascii is the following 1 line SIMFIT lt number of peaks gt 2 line gt x 1 y1 1 y2 1 y3 1 y number of peaks 1 3 line gt x 2 y1 2 y2 2 y3 2 y number of peaks 2 4 line x 3 yl y2 3 y3 3 y number of peaks 3 n 1 th line x n yl n y2 n y3 n y number of peaks n The maximum number of peaks for fitting with simfit asc is 50 Once the file tlascii is set up you can immediately continue with the fitting procedure described 9 6 The T1 T2 relaxation menu P 197 9 6 4 9 6 4 1 9 6 4 2 in Section 9 6 4 5 The fitting procedure General information The parameter CURPRIN determines where you will get the output of your fitting results Enter the command edo and set CURPRIN screen If you want to see the output on the screen printer If you want to get output on the specified printer filename If you want to get the output in a file named filename The file will be created in the current processing data directory This option is not really needed because an output file called ct t2 out or simfit out with all results is always written to the
188. ess the spectrum again e g by typing fp Run psf and select the output option write 1r or both The PSF will now overwrite the processed data set The size of this new spec trum is adjusted according to the number of points used for the PSF SW and Hz Pt will also be adjusted The PSF will always be centered at 0 ppm Type 2s offset Enter a value which corresponds to the region of interest of your experimental spectrum Switch back to the original data set via the TASKS menu Specify the PSF processed data set as the second data set using edc2 Compare the experimental NMR spectrum and the PSF with the dual display 9 11 MAXENT MEMSYS5 P 229 9 11 2 9 11 3 function Important note Do not use the PSF processed data set number as second or third data set in edc2 for a maxed or maxent run The sizes SW and Hz Pt in the status processing parameters no longer match with the original NMR spectrum Write r file into point spread function wpsf wpsf allows you to generate any lineshape form to be used with MEMSYSS This could be a single line extracted from a 1D data set or the result of adding several PSF functions which were created using the psf command The lineshape to be written as a PSF must exist as a 1D data set an r file The Zr file is copied into a PSF file when running wpsf Edit MEMSYSS5 parameters maxed maxed sets all relevant parameters for a maxent run Before setting up the paramete
189. essary f Is SR if a 1D preparation experiment is available take over the value from there otherwise set to 0 for now 3 9 Baseline Correction P 49 3 9 Baseline Correction 3 9 1 Automatic baseline correction abs1 abs2 In the 1D tutorial chapter we discussed the baseline correction commands abs and absf for 1D spectra which assume that a baseline distortion can be removed by subtracting a polynomial from the spectrum The command abs1 uses the same algorithm to correct each column of a 2D spectrum while abs2 operates on the rows The commands can be typed in or invoked from the Process gt Baseline cor rection menu As in 1D the parameter ABSG determines the degree of the polyno mial and can be set independently for the two dimensions in edp The processing parameters ABSF1 and ABSF2 determine the left and right limits of the region to be corrected and they can be entered from the parameter editor edp For the F2 dimension the limits can also be entered from the keyboard by typing absf1 or absf2 In contrast to the 1D command absf the 2D commands do not generate inte gral range files 3 9 2 Additional methods bcm1 bcm2 sub1 sub2 abst1 abst2 XWIN NMR provides a number of other methods to correct the baseline of rows or columns in a 2D spectrum bcm2 and bem are generalizations of the 1D com mand bcm for all rows or columns You can extract a row or column from a 2D spectrum baseline correct it manually as we
190. et Exiting the editor with ABORT will terminate immediately without calcula tion leaving the parameters unchanged An optional argument of y or yes can be specified with this command See command bayx for an description of its effect vibay The protocol file created during the last calculation is output to the screen If no protocol file exists an error message will come up libay This is the same as vibay except output is sent to the device or file defined in the device parameter CURPRIN to be set up vwith the command edo 9 12 6 Parameters While there are quite a few parameters with which the Bayesian analysis can be controlled the module is set up such that it can operate in a black box fashion without the user having to set any parameters at all Reasonable default values have been assigned to all parameters When the parameter editor for the Bayesian analysis is started via the commands bayed or bayedx for the very first time for the current data set i e Bayesian parameters do not yet exist for the current data set then only a few parameters are brought into the editor The top parameter BAY_ANA controls the extent of the Bayesian analysis to be performed It is initially set to automatic which means that the program will perform repeated Signal Detection passes adding all signals found to the model and optimizing the corresponding parameters until either the model s probability no longer increases or there is no more
191. et to yes instead of no The color is the same as that of the contour window frame FRCOLOR and the label of the integration region is plotted in size FRCHAR mm The characters may be tilted by an angle with the vertical the tangent of which is given by FRS LANT These parameters are accessible through EDFRAME 11 3 7 Plotting 1D spectra or projections along F1 and F2 Along the dimensions Fl and F2 of a contour plot 1D spectra or projections of the 2D spectrum parameters PROJ1 and PROJ2 yes may be plotted Click on EDPROJ1 2 to edit the projection parameters Select the type of projection from PFIEXT and PF2EXT The complete definition of the 1D data set must be given with the parameters PF1IDU PFIUSER PFINAME PFIEXP PF1PROC PF2DU PF2USER PF2NAME PF2EXP PF2PROC i e disk partition user name experiment number and processed data number The distance of the spectrum s zero line from the contour window is PFIZERO PF2ZERO cm and the color is given by PFICOL PF2COL The same spectral region will be plotted in the corresponding direction as was defined for the 2D spectrum In order for the signal positions in contour plot and 1D spectra to agree with the axis labels the 1D spectra must be calibrated to the same reference signal as the 2D spectrum The vertical scaling is controlled by the parameter PFICY PF2CY for horizontal 11 4 Page layout stacked plot edgw P 295 scaling which must be greater than zero and
192. etermine when acquisition is termi nated in such experiments measuring continues until a desired signal to noise ratio is achieved It may be specified by setting the parameter SINO accordingly use the edp parameter editor An example is the AU program au_zgsino which is part of the XWIN NMR distribution Since signal and noise regions are not known in advance for arbitrary samples XWIN NMR provides the following special conven tions If NOISF1 and NOISF2 are both zero the first 1 16th of the spectrum is used as the noise region If both SIGF1 and SIGF2 are zero the maximum value is searched for in the whole spectrum minus its first 1 16th part You can force the program to exclude solvent or other signals from this region depending on the nucleus and the solvent The spectral regions to be excluded for a given NUCLEUS and SOLVENT must be specified in a text file whose name is built from these two parameters lt NUCLEUS gt lt SOLVENT gt e g 13C Aceton The file must be located in the directory u exp stan nmr lists scl For the most convenient nucleus solvent combinations such region files are dis tributed with XWIN NMR in the directory u exp stan nmr lists scl exam 9 5 Deconvolution P 185 Its contents are copied to the scl working directory during execution of the com mand expinstall Whenever the working directory scl contains a suitable region file signal exclusion according to the regions contained in the file
193. evidence for a signal The setting of the parameter BAY_ANA determines which parameters are avail able for editing in order to control the analysis The individual parameters are BAY_ANA BAY_ANA can be set to the values automatic sig_detection mod_selection and par_estimation The first automatic is the default setting when the parameters are first set up and is identical to mod_selection except that default values are assumed for all parameters If the user sets BAY_ANA to mod_selection all relevant param eters will be displayed in the parameter editor With sig_detection the program will only perform the specified number of signal detection passes BAYNPAS opti mizing the parameters for all added lines par_estimation causes the program to simply optimize the parameters for the specified number of lines BAYNLIN The Analysis Menu P 236 which must be listed in the file specified by the parameter PEAKLST BAYPHAS This parameter defines the phase model to be used in the analysis no_phase coherent or individual BAYREST This parameter specifies whether the calculation should start off using the results from a previous analysis BAYREST yes or not The results from a previous analysis are taken from the file bayes mod in the current data set directory During the calculation this file is updated after each completed signal detection pass TDeff TDeff gets the number of points of the FID to be used in the analysi
194. ext editor the AU module must be compiled before it can be called Details about writing AU modules can be found in the chapter on AU programs XWIN NMR locates the C sources of AU modules in the directory u exp stan namr au modsrc and the executables in The File Menu P 94 5 3 11 u prog lt X WIN NMR version gt au modbin The command edaumod displays all AU programs from this directory in a dialog box from where the desired one can be selected edaumod is identical to edau with the difference that initially AU modules are displayed rather than AU programs AU programs may be displayed by clicking on the gt Programs command button at the bottom of the edaumod dialog box On XWIN NMR release media a number of sample AU programs are delivered After installation of XWIN NMR they are stored in the directory u prog lt X WIN NMR version gt au modsrc exam The command expinstall see menu Acquire gt Spectrometer setup which must be executed after installation of XWIN NMR will compile all sample AU modules if user requested and install their C sources in the working directory u exp stan namr au modsrc and their executables in u prog lt X WIN NMR version gt au modbin The command edaumod may also be entered on the keyboard followed by the name of the desired AU program or followed by an argument containing wildcard characters see edpul and how to change the default text editor for details Data set info file
195. f the same size having the same SI parameters the row and column numbers will be used as integration limits otherwise the ppm values are taken Outputting integral values li This is the same command name also used to print the integrals of 1D spectra XWIN NMR knows that you are currently working with a 2D data set and adapts itself accordingly li type it in or call it from the Analysis menu will give you a printout of the integration limits and the integral values as stored by the int2d or int2dref command in the int2d file in the current data directory The output is directed to the current printer or to the screen depending on the setting of the parameter CURPRIN Call the output device editor by typing edo and set CUR PRIN to screen if you want to see the integrals on the monitor Otherwise click on the down arrow button rightmost to CURPRIN and select the printer on which you want to get the listing If no printer name is displayed you or your system admin istrator must install one with the command cfpp see menu Output gt Printer plot ter installation Printer names when inserted in the parameter CURPRIN must always be preceeded by a sign If omitted the name is interpreted as a file name and the list is stored under this name in the current data directory where the spec 2D Data Processing Tutorial P 52 trum is Terminating integration mode Click on the return button or invoke the command Return from the File m
196. fault value 4 0 can be increased to make the peak search less sensitive or decreased to make it more sensitive For example if a peak shoul der is not detected with the default value you should enter a smaller number The best sensitivity is achieved with PC 1 0 but of course many noise peaks could then be contained in the peak list We recommend you work with the default value unless particular data require a change One more parameter must be set before peak picking can be started PSIGN pos will force the peak picking routine to search for positive peaks only PSIGN neg for negative peaks only and PSIGN both for peaks with any sign Type in PSIGN or set it from edp Start peak picking All peak picking commands can be called from from the Analysis gt Peak picking menu or typed in pps displays the peak list on the screen pp pph lipp and lippf on the current printer CURPRIN to be set with edo refer to the command Li ear lier in this chapter where we already described CURPRIN Remember if CUR PRIN screen the output will go to the screen pp outputs the same list on the printer which pps displays in a window pph works like pp but for every peak it prints a number of asterisks at the rightmost column derived from the intensity With a single glance at this histogram you can find the biggest or smallest peaks without having to scan the intensity values This is particularly useful for long lists lipp combines the output of p
197. file without the extension can not be found 5 11 Conversion P 129 5 11 3 2 vconv reads the relevant parameters from the file procpar and converts them into the corresponding XWIN NMR parameters Because of the hardware and software differences not all parameters have equivalents The file procpar will be stored in the XWIN NMR processing directory so that missing or uninterpreted parameters can be inspected During the conversion vconv will check the parameter segfil If it is set e g to s2pul vconv checks for the parameter set u exp stan nmr par s2pul e Ifthe parameter set exists it will be copied into the XWIN NMR data set Those parameters from the s2pul parameter set which are also interpreted and con verted from the original procpar file will be overwritten by vconv e If the parameter set does not exist standard parameters will be copied for instance from u exp stan nmr par standard1D Those parameters from the standardID parameter set which are also interpreted and converted from the original procpar file will be overwritten by vconv Parameter conversion Table 5 12 lists the procpar parameters and their equivalent in XWIN NMR VNMR XWIN NMR VNMR XWIN NMR VNMR XWIN NMR seqfil PULPROG pw90 Pl ss DS ct NS s pslabel AUNM temp TE dl Dl pw PO swl SW_h 2D date DATE pp P3 tn NUCLEUS dfreq BF2 np TD tof Ol dmf P31 nt NS f rp PHCO dn DECNUC sfrq BF1 lp PHC1 fn SI solvent SOLVENT rfl rfp OFFSET fb
198. for the Bayesian analysis are stored in the file baypar in the direc tory of the current data set During the calculation the program will write a proto col file bay__prot unless the parameter VERBOSE is set to no and after each iteration a file bayes mod which contains the model parameters at that point of the analysis The file bay__prot can be viewed or printed with the commands vibay or libay and the file bayes mod can be used to continue a previous calculation with the last model parameters NMR Data Type The Bayesian analysis package was originally developed to handle fids acquired with analog filters in sequential acquisition mode Data of this type are usually generated by Bruker AM AC and AMX ARX type spectrometers depending on The Analysis Menu P 234 9 12 5 the selected acquisition parameters Data aquired using digitals filters on Avance type instruments must be back converted to analog type data with the convdta command before they can be treated with the Bayes algorithm Data acquired in simultaneous acquisition mode which is always true for Avance spectrometers if digital filters were used must be converted to sequential mode data using the fol lowing processing steps 1 Set the desired transform size SI 2 Transform the data using the command ft 3 Set the status parameter FT_mod to sequential mode fqr using the command 2s FT_mod 4 Execute an inverse transform using the command ift 5 From these da
199. form In the second case xf1 completes a partial F2 transform The processing parameters SI STSR STSI TDeff TDoff BC_mod ME_mod WDW PH_mod FCOR and REVERSE for this dimension work just like the ones described above for the F2 dimension However in addition to these the following parameter is important Processing Parameter MC2 The type of transformation is determined from the parameter MC2 according to Table 7 1 MC2 transformation type QF fqc forward quad complex QSEQ fqr forward quad real TPPI fsr forward single real States fqc forward quad complex States TPPI fsc forward single complex echo aatecha fqc forward quad complex Table 7 1 Through appropriate choice of MC2 the transformation is matched to the experi ment which created the raw data QF complex 2 quadrant transformation is applied when only the magnitude or power spectrum is to be obtained The transformed result is stored in the 2 files 2rr real matrix and 2ii imaginary matrix of the current data set QSEQ phase sensitive 4 quadrant transformation is applied when two successive The Process Menu for 2D data P 160 fids separated by the incrementable delay were acquired with the pulse phases 0 and 90 degrees sequential quadrature detection in F1 with t for the second fid being incremented by IN TPPI Time Proportional Phase Increments phase sensitive 4 quadrant transfor mation
200. formation command which creates those imaginary parts that are needed for the subsequent phase correction xflp xf2p The Process Menu for 2D data P 172 7 24 Reflection of a 2D spectrum rev rev2 revl reflects a 2D spectrum about a horizontal line at the center and rev2 about a vertical line at the center Further processing of the data is possible as both the real and imaginary parts are handled 7 25 Create a ser file from processed data genser If an inverse transformed 2D spectrum is to be further processed as an original ser file i e stored under a certain EXPNO then the command genser is to be used It is the two dimensional analogue to the 1D genfid command Similar to the command genfid the command genser generates a ser file from processed 2D data files 2rr and stores it under a new EXPNO genser is required if for futher processing of the data one of the parameters SI STSR STSI TDoff or TDeff must be changed for example in order to combine strip transformation and inverse Fourier transformation Syntax of genser e genser e genser lt EXPNO gt e genser lt EXPNO gt lt option gt e genser lt EXPNO gt lt y option gt lt n option gt genser The new EXPNO is asked for by the program it must be different from the current EXPNO If it already exists the user is asked if the data can be overwritten all raw data and PROCNO 1 of the new EXPNO will be overwritten The new EXPNO w
201. from the data file which may take a few seconds and 2D Data Processing Tutorial P 46 i i Figure 3 2 Interactive 2D phase correction place it into the first 1D window 4 Select one or two other rows Put them into the second or third 1D window by clicking on the mov 2 or mov 3 buttons 5 You may scale and expand the spectra in the 1D windows using the buttons 3 8 Spectrum calibration P 47 below the mov button panel They work analogously to the corresponding 1D spectrum operations described in the last chapter 1D tutorial and influence the active 1D window You can make one of the three 1D windows the active window by clicking on it The window number of the currently active window is highlighted 6 The big and cur button panels allow you to set the zero order phase reference point of the 1D window 1 2 or 3 to the biggest peak or the cursor position 7 The buttons phO and phi allow you to adjust the zero and first order phase of the spectrum contained in the active window Position the cursor on the desired button press the left mouse button and move the mouse You can reset the val ues with the undo button 8 Exit from 2D phasing using the return button A pop up window allows you to return to the main 2D screen without storing the adjusted phases choose return or to store the phase values as parameters PHCO and PHC1 in the processing parameter file of the current data set you can
202. fter having changed one or sev eral user interface items by clicking on the corresponding radiobutton you must click on the Apply button in order to make the modifications effective If you want to close the window click on the File entry of its top bar and choose Exit If you 12 5 User Interface P 309 il a i il ii yii ie lI gt gt SS ead pen PG Pe EI Peed ce ig a eoo e E Figure 12 5 User interface settings want to restore the default settings choose default settings from the File entry and then click on the Apply button All settings are stored on disk in the file xwinnmr resources in the user s home directory The available user interface items are discussed below User interface XWIN NMR standard extended horizontal or UXNMR The standard layout dis plays the quick access buttons at the left side in vertical order 1D and 2D modes are very similar with corrsponding buttons in nearly the same positions The extended mode displays additional quick access buttons These functions are also available in standard mode but you must must open the Display gt Options menu or the Output menu to have access to them The horizontal mode displays all quick access buttons in horizontal order including all buttons of the extended mode The The Display Menu P 310 old style UXNMR interface is also provided Please note that it will stay as it is without further developments Online help On or off By
203. ge the position of the cross hairs and the displayed rows or col umns will follow in real time You may also use the middle or right mouse button to magnify or reduce the size of the current trace Exit from fast scanning mode by clicking the middle and right mouse button at the same time Please note that fast scanning mode operates on the displayed 2D data The rows and columns are not read in from the original 2D spectrum file For this reason the resolution of the displayed rows and columns might not be fine enough to show all details You will have to expand the 2D spectrum before entering fast scanning mode to overcome this limitation Extracting rows or columns Click on the row or col button The program will display a cross hair cursor you can move around with the mouse Clicking the middle mouse button will display the horizontal or vertical cross section row or col defined by the position of the horizontal or vertical line of the cross hairs In this mode you may move the cross hairs to a different place and click the middle button again to get the cross section of this position Click the left mouse button to release the cross hair cursor The following buttons are useful in this situation where the 2D spectrum and a cross section are displayed together e Use the buttons 2 and 2 located below the row and col buttons to scale the cross section e Click on the blank toggle button to switch off the 2D spectrum temporarily to mak
204. given by the acquisition parameters SWH or SW respec tively You can examine them by entering the command dpa on the keyboard which gives a display of the acquisition status parameters Defining the origin of the axis is a procedure called spectrum calibration In XWIN NMR there a two pos sible methods manual calibration and automatic calibration with the command sref Both can be called from the Analysis menu sref can also be typed on the key board Its major application is the inclusion in automation AU programs for auto calibration of data measured with a sample changer sref will only work if the files 2Hlock or 19Flock are installed in the directory i conf instr lt instrument gt for the spectrometer on which your data were measured You can find more details in the chapter The Analysis Menu under sref In order to manually calibrate the spectrum click the calibrate button located below the phase button When you move the cursor into the XWIN NMR data area it will automatically move along the spectrum trace Put it on the desired reference peak and click the middle mouse button A dialog will invite you to enter the fre quency you want to assign to this data point usually 0 for TMS The units of the number to be entered are the same as the current x axis units Hz or ppm You can release the cursor from the spectrum trace by clicking the left instead of the mid 2 8 Baseline Correction P 21 2 8 dle button Baseline
205. gly plot region is expanded along F1 FIHZCM Hz cm FIPPMCM ppm cm These parameters specify the plot resolution along the F1 direction Any change causes the height of the contour window CX1 to be adjusted while keeping the plot region F1LO F1HI constant An analogous set of parameters exists for the F2 direction F2LO F2PLO F2HI F2PHI and F2HZCM F2PPMCM Before plotting the intensity levels on which to search for the contours must be defined This is done either interactively on the display or with the edlev com mand Automatic calculation of the levels can be performed by the command lev calc that generates 6 levels It is mainly used in AU programs The contours are either plotted in different colors when the parameter CPLIN is set to color or with different line styles if CPLIN line types In the latter case the parameter CPLCOL determines the color common to all contours If contours of negative and positive intensity are to be plotted the parameter CPDIFCL should be set to yes instead of no Then the colors line styles of the positive contours are taken from the parameter CPCOLPA CPLTYPP which may hold up to 10 colors line styles The first color line style is assigned to the lowest level The colors or line styles are repeated in a cycle if more levels than colors line styles must be plotted Note that the assignment of colors to plotter pen positions must have been done correctly with edpp for pen plotters
206. have seen in the 1D tutorial and then apply the correction function to all rows or columns See also the description of bcm in the 1D tutorial The commands sub1 sub2 subld1 sub1d2 abst1 abst2 are described in the chap ter The 2D Process Menu 3 10 Symmetrization Tilting XWIN NMR provides commands for these operations If your data set needs to be processed with these routines please refer to the chapter The Process Menu for 2D Data 2D Data Processing Tutorial P 50 3 11 Spectrum integration For 1D spectra XWIN NMR supports manual and automatic integration 2D spectra can only be integrated manually You must interactively define the integration regions which can be stored in a text file of your choice The 2D integration com mands int2d or int2dref will compute the integrals and store the results in the file int2d in the current data directory where the spectrum file 2rr is located It may be output to screen printer or a desired destination file with the li command Defining integration regions Enter integration mode by clicking on the integrate button located at the left hand button panel or call Manual integration from the Analysis menu The program asks you to enter the name of a file which will later contain the frequency limits of the defined integration regions The file will be stored in the directory u exp stan nmr lists roi The screen layout will change to the 2D integration mode In order
207. he desired position and use the backspace or delete keys to erase a character mark a number of characters by positioning the cursor then hold the left mouse but ton depressed while moving the mouse type new text to replace the marked text or use the delete key to remove it Make sure that the mouse pointer is located within the XWIN NMR window before you start entering commands 6 The status line for the display of information during command execution For example when a 2D transform is in progess the currently processed row or column numbers are shown This line is also used to display on line help mes sages for the quick access buttons at the left side of the XWIN NMR window A one line description of a button will appear as soon as the mouse points to the corresponding button Introduction P 6 1 7 Manipulation of the XWIN NMR window Iconify Click on the small dot at right side of the window manager bar in order to iconify XWIN NMR De Iconify Double click on the XWIN NMR icon Resize Move the mouse pointer to one of the window corners where the cursor shape changes Drag the window to the desired size while the left mouse button is depressed Release the button Please note that the window cannot be sized smaller than a certain limit in order to keep the quick access buttons readable Resizing will under the Motif window manager always be carried out such that the height to width ratio remains constant Maximize
208. he trf command and executes the commands e be correction of the fid linear prediction window multiplication fourier transformation and phase correction for each dimension As with trf the individual steps are controlled by the process ing parameters BC_mod ME_mod WDW FT_mod and PH_mod for the respec tive dimension FT_mod can even be set to no if no Fourier transformation is wanted xtrf2 only evaluates the processing parameters in the F2 dimension It behaves like the xf2 transformation with freely selectable transformation type If all XF2 dimension parameters are set to no then xtrf2 only causes the ser file to be re arranged into the submatrix format including zero filling or truncation depending on the parameters TDoff TDeff and SI The ser file itself remains unchanged and the result is stored in the files 2rr even numbered points and 2ri odd numbered points of the current PROCNO non phase sensitive spectra 2rr 2ii This way a two dimensional view of a ser file can be obtained on the screen It appears in the lower left quarter of the display xtrf with all Fl parameters set to no only evaluates the processing parameters in the F2 dimension It behaves like xtrf2 and does no processing or data rearrange ment in the F1 dimension xtrf and xtrf2 always use the acquisition raw data as 7 22 Inverse Fourier Transformation xif2 xif1 P 171 input data and create new data sets for the processed data 7 21 1 User
209. he new command is just the name of the AU program and can be entered on the keyboard or called in other AU programs see menu File gt Execute XWIN NMR locates AU programs in the directories u exp stan nmr au src C sources u prog lt X WIN NMR version gt au bin executables The command edau displays all AU programs in the src directory in a dialog box from where the desired one may be selected The box consists of two halves The left side shows those AU programs which were written by the user himself or which represent modifications of Bruker AU programs Bruker AU programs are write protected and are displayed at the right side of the box When you select one from there you can only scroll through the text but not modify it The superuser of the system however may also modify Bruker AU programs He must activate the command button gt edit at the bottom of the edau dialog box and then select the desired Bruker AU program The superuser password is then requested After a Bruker AU program was modified it will no longer appear on the right side but will be moved to the left side of the edau window You can always restore the orig inal Bruker AU program from the directory src exam to be described below On XWIN NMR release media a number of AU programs designed by Bruker are delivered After installation of XWIN NMR they are stored in the directory u prog lt X WIN NMR version gt au src exam The command expinstal
210. he number of points to be picked from the FID A maximum of 256 points can be fitted LISTTYP a Enter dw if you want to use the dwell time DW for the calculation of the x axis time values b Enter auto if you want to use individual time values on the x axis In this case the parameters X_START and LISTINC must be set START Enter the first point to be picked The first point of the FID has the number 0 But you can start the point picking at any point in the FID INC Enter the increment between the picked points INC 1 means that NUMPNTS are picked starting with START INC 2 means that every second point starting with START is picked until NUMPNTS are reached X_START Enter the start value of the x axis Usually you will set X_START to 0 but you can introduce an offset by setting X_START to a value greater than 0 X_START is used only if LISTTYP auto LISTINC Enter the increment between two adjacent data points LISTINC is independent from INC The correct distance between points picked with INC gt 1 is calculated automatically LISTINC is used only if LISTTYP auto After you have set all relevant parameters leave the editor with SAVE and execute the command pft2 The display should be updated with the picked points see Fig ure 9 3 All points belong to one series or if you compare this case with the one described in Section 9 6 3 1 to one peak You can now immediately proceed with the fitting described in Sectio
211. he queue All plots contained in the queue are plotted on the same sheet of paper by the command fiplot Complicated layouts may thus be created plots can also be included in AU programs from where you can also set plot The 1D Output Menu P 270 parameters with the function storeplpar Layouts with several titles expansions etc can be realized this way A plot queue is stored in the directory u prog lt XWIN NMR version gt curdir lt user gt mgplot The queue consists of the parameter files meta meta 2 corresponding to the number of plots command given and the text files info info 2 containing the data set names and other information 10 7 3 Output queue on separate sheet flplot flplot outputs the contents of a queue filled by one or more plots commands to the current plotter 10 7 4 Remove all plots from queue rmplot All plots issued with the plots command are deleted if they were not sent yet to the plotter with fiplot 10 7 5 Plot expansions plotx The command plotx outputs auto expansions set up with edgx and the corre sponding overview spectrum set up with edg if enabled on the current plotter 10 8 Plot print status The commands plot plotx and fiplot let the operating system s Ip spooler handle the plotter or printer devices p actually sends the data bytes out to the parallel or serial channel Each plot gets a plot request id number assigned which is printed in an inf
212. he same but the files for the second or third dimension are contained in the subdi rectories acqu2 l proc2 1 plot2 1 acqu3 1 proc3 1 The lp commands do not neces sarily use the normlp format files You may setup your own ones and replace normlp in the parameter LFORMAT by the name of your file using the edo com mand 10 11 Display status parameters The commands dp dpc dpa dpp dpg dpgx are analogous to the lp commands described in the previous section Their output goes to screen however rather than to a printer or to a file The format files for these command are listed in Table 10 5 You can specify own format files in the parameter DFORMAT to be set up curd l normdp acqu l normdp proc l normdp BBE e plot l normdp dpgx plotx l normdp Table 10 6 Format files for the dp commands with edo 10 12 Print barcode labels prlabel The command prlabel prints barcode labels on a thermo printer of type HCP 60 This printer is connected to a free RS 232 channel of the computer The interface configuration is demanded by the command cfbacs and stored in the file u conf instr barcode_prn if a barcode reader exists The printer must be configured according to Table 10 7 This corresponds to the following settings The 1D Output Menu P 274 S1 S4 12345678 12345678 on xk k off kek kk ok ok of KK K ok ok ok Table 10 7 Bar code printer configuration 9600 bau
213. he table The corresponding level will be deleted You can delete all levels from a certain number onwards by giving this number the value zero right column Inserting a new level Enter a value in the emtpy field at the end of the table right column The number is automatically sorted in depending on its size Generate table of equidistant levels Click on the INCR command button A number the increment can be entered New values for all levels except for the smallest one are calculated XWIN NMR generates the new level values by successively adding the entered number to the previous level starting with the smallest positive one If the table also contains negative levels subtraction is applied instead The result is a table of equidistant levels Generate a table of levels with constant ratio Click on the FACT command button When this command button is activated a number can be entered that is used to generate new values for all levels except for the smallest one XWIN NMR generates the new levels values by successively mul tiplying the entered number with the previous level starting with the smallest pos itive one The result is a table of levels with constant ratio Accept all changes Click on the SAVE command button All changes in the table are stored in the level file and edlev is terminated 2D Data Processing Tutorial P 56 3 13 2 3 13 3 3 13 4 3 14 Discard all changes Click on the QUIT command butto
214. her that the data set was created during a run of a sample changer equipped with a bar code reader and the bar code label for an experiment contained user nmr2 Then the data set created by this experiment would be stored under USER nmrr2 but get the permissions of nmrl1 2 A data set is retrieved from a tape and stored under USER nmrl e g using the Unix command tar xv The data set on tape however originates from a differ ent laboratory where it belonged to user nmr2 The result is a data set on disk stored under USER nmrl1 but with the permissions of nmr2 depending on the tar options used The XWIN NMR command touser solves this problem Make the respective data set The File Menu P 78 the current data set in XWIN NMR and enter touser on the keyboard The permis sions will be set correctly for user nmr1 and the data set can be further proc essed 5 2 Open Data Files The Open menu Figure 5 3 contains commands which display a list of existing Figure 5 3 The Files gt Open submenu data sets If you select one from the list it will be made the current data set and displayed on the screen The command names in brackets may be used to quickly access the function from the keyboard The commands are described in Table 5 1 The dir commands Please note that all dir type commands can be used with wildcard arguments such as dir dir suc dir abc etc which allow you to
215. herefore recommended to use the proper digital processing algo rithms if available XWIN NMR recognizes the data type automatically and invokes the appropriate routines convdta uses the current acquisition data as input and generates a new EXPNO where it places the converted data The destination EXPNO is asked for by the program It can be specified as an argument also convdta lt EXPNO gt Execute The File gt Execute submenu Figure 5 18 contains the commands which start automation AU programs and command macros Please refer to the description of the commands edau and edmac and how to set up AU and macro files There is also a special chapter in this manual which describes the syntax of AU programs in detail xau The command xau executes an arbitrary AU program if it is available as an execut The File Menu P 132 General automation program xau Acquisition AU program AUNM xaua Processing AU program AUNMP Cxaup Compile user AU program Ccpluser Compile bruker AU program Ccplbruk Tcl Tk script Figure 5 18 The File gt Execute submenu able version For example when terminating the edau command compilation is offered as an option If the compiled version is not available but the source code XWIN NMR will automatically start the compiler and generate the executable code When you call xau from the menu or when entering it on the keyboard the list of compiled AU programs is displayed edau in contras
216. hese specifications which would cause the correspond ing items to be taken over from the current data set For example if only NAME is entered the copy will get a new name but EXPNO PROCNO DU and USER will not change You can also enter the command at the keyboard optionally followed by argu ments The following options are available wrpa NAME EXPNO PROCNO DU USER y The destination data set is completely specified If the y at the end is omitted and a data set of this specification already exists XWIN NMRwill ask whether to over write that data set or not Specifying the y at the end suppresses this question and an existing data set will be overwritten unconditionally By specifying a DU other than the current one the data set may also be copied to another disk A more con venient method to do this is provided by the command wrd see below Example wrpa sucrose 5 2 v guest2 wrpa NAME EXPNO PROCNO USER The destination data set is specified without DU and will therefore be created on the same disk partition as the current data set If a USER other than the current one is specified the new data set will get the ownership of the new user Changing the user is only possible if the current and the new user are in the same user group see your operating system documentation for users and groups Example wrpa sucrose 5 2 guest2 wrpa NAME EXPNO PROCNO The destination data set is specified without USER and DU an
217. hich the 1D fids of a 3D acquisition are stored in the ser file 3 the acquisition dimension 1 and 2 the orthogonal dimensions On Avance type sys tems 3D pulse programs will set AQSEQ automatically if td and td1 are used con sistently within the pulse program However you may explicitly define AQSEQ in the pulse program For this purpose insert one of the following statements in the pulse program header aqseg 321 or agseq 312 On both AMX ARX and Avance type systems you can set or modify AQSEQ using the command 3s AQSEQ before starting the transform 8 2 Fourier Transformation tf3 tf2 tf1 The commands tf3 tf2 tf1 execute the transform in the dimensions F3 F2 F1 and must be invoked in this order to obtain a completely transformed 3D spectrum Depending on the setting of the processing parameters the transform includes the baseline correction of the fid and the application of a window function before the fourier transform and phase correction or magnitude power spectrum calculation after the transform This is just as in the 2D case The 2D commands xfb xf2 and xtrf can be executed on a 3D acquisition data set in order to obtain a selected plain When typing one of these command the trans form direction and the PROCNO where the 2D result is to go are requested Table 8 2 and Table 8 3 show the files involved The files beginning with the char acter 3 are stored in the current processed data directory 3rrr cont
218. ht xht1 xht2 The File Menu P 106 Please note that all del type commands can be used with wildcard arguments such as del del suc del abc etc which allow you to choose data sets according to a desired mask The asterisk serves as a placeholder for a group of unknown char acters the question mark for a single character 5 8 Delete Other Files Figure 5 15 shows the commands to delete files other than data sets Figure 5 15 The File gt Delete gt Other files submenu The purpose and structure of these files have already been described in the section Open Other Files Please note that also these commands allow you to use wildcard characters when entered on the keyboard e g delpul cosy If a command is exe cuted from the menu or typed in without argument a list of existing files is dis played delpar Delete parameter set delpul Delete pulse program delgp Delete gradient program delsh Delete shim value file delau Delete automation AU program Source file and compiled executable file will be deleted delmac Delete command macro file dellist Delete parameter list file delmisc Delete file of miscellaneous type e g saved 5 9 Rename P 107 intrng integral range file delaumod Delete automation module Source file and compiled executable file will be deleted 5 9 Rename The commands of Figure 5 16 allow you to assign new names to data sets and Figure 5 16 The Fi
219. il you click the Seen button of the window containing the message If DEF_ERR_OPT is equal to 0 it will continue immediately after printing the mes sage This mode may have the effect the window not becoming visible at all if another active XWIN NMR command or the AU program itself output Proc_err messages a short amount of time later e g if Proc_err is part of a loop You may use the values 0 or 1 directly as the first argument of Proc_err or you may specify the variable DEF_ERR_OPT which defaults to 1 You may change the value of DEF_ERR_OPT from the keyboard or with CPR_exec from the AU program to or 0 using the XWIN NMR commands setdef_ackn ok or setdef_ackn no respec tively The function Show_status text displays a message in XWIN NMR s status line text must be a char variable The AU program of Figure 15 4 would display the same message in a Proc_err window and in the status line 15 12 Requesting keyboard input P 331 15 12 Requesting keyboard input The commands getstring getint getfloat getdouble request a string an integer number a floating point number or a double precision floating point number from the keyboard and store the entered value in a variable Table 15 4 shows examples getstring Please enter plot title text getint Please enter SI i1 getfloat Please enter LB f1 getdouble Please enter SW d1 Table 15 4 Examples of keyboard input
220. ila ble space optionally with an overview spectrum Figure 10 6 Reasonable auto matic plots may thus be obtained from samples with small signals and integrals in the presence of large ones Auto expansions are set up with the command edgx which is analogous to the command edg Parameterscontained in the edgx dialog window can also be entered from the keyboard by preceding their name with px e g px shei followed by Return or px shei 5 followed by Return The spectral regions to be auto expanded are taken from the text file reg the for mat of which is described in the chapter The File Menu This file is stored in the same directory as the spectrum and may either be set up manually with edmisc read as a previously set up file with the command rmisc or generated in manual 10 4 Page layout for auto expansions edgx P 263 Figure 10 6 Example of auto expanded plot regions integration mode If no reg file exists in the current data set directory but the file intrng does then the reg file is created automatically by copying intrng If intrng also does not exist an error message is issued 10 4 1 The plot limits The plot limits for normal plots are defined using edg for plot expansions they must be set in the file reg as described above There are two special parameters namely EXTF1 and EXTF2 or EXTFIP and EXTF2P respectively which are The 1D Output Menu P 264 10 4 2 10 4 3 10 4 4 specified in Hertz
221. ilar to paropt but allows several parameters to be adjusted e simtoseq Converts acquisition data acquired with AQ _mod qsim to a data set which seems to be acquired with AQ_mod qseq Required to apply Baysian analysis e split2D Splits a 2D spectrum file into a series of 1D spectrum files e splitser Splits an nD acquisition data file into a series of 1D fid files e calfun Calculates an arbitrary function and stored is a an fid The function may be used a user defined window function in conjunction with the command uwm Please note that the list is incomplete Use edau to get an overview of all currently available Bruker AU programs 15 3 The AU language AU programs are C language programs with an interface to XWIN NMR For this reason the usual C header main must be omitted A large number of macros are provided hiding complicated C constructs if XWIN NMR commands are to be accessed Nevertheless all C statements and functions of the C library may be used Figure 15 1 shows a simple AU program Let us call it test You may create it up by typing edau test As soon as you exit from the text editor you will be asked whether test should be compiled Compilation is required after writing a new or modifying an existing program XWIN NMR invokes the system s C compiler and informs you when compilation is finished If the compiler finds a syntax error it 15 4 Executing XWIN NMR commands P 323 getcurdata start with data set displ
222. ill become the current data set and will appear on the display genser EXPNO The new EXPNO is specified directly If it already exists the user is asked if the data can be overwritten genser EXPNO y The new EXPNO is specified directly If it already exists the data are overwritten without warning 7 26 Convert AVANCE data to AMX format convdta P 173 genser n With the optional parameter n the program does not switch to the new data set All arguments of genser can be interchanged The processed data set number PROCNO of this new data set is set to 1 If a 2D dataset was reduced in size with xtrf2 and all processing flags set to no with appropriate values of TDoff and TDeff genser creates a new EXPNO with reduced TD values 7 26 Convert AVANCE data to AMX format convdta Generates an AMX ser file from an Avance ser file Uses the same syntax as genser Use this command before processing Avance data with a Fourier transform written for AMX data 7 27 Add and subtract 2D spectra add2d Processed data of the current data set curdat are replaced by ALPHA curdat GAMMA curdat2 The F2 domain processing parameters ALPHA and GAMMA must obey the fol lowing relation IALPHAI IGAMMAI lt 1 Set both values to 0 5 for addition and use the values 0 5 and 0 5 for subtraction Both real and imaginary part are handled 7 28 Calculate level file levcalc After the Fourier transform or any other operation
223. ill set the PROCNO to 1 The conversion of 2D HSQC and 3D data has also been added to the VNMR data conversion routine as well as the conversion of fids acquired as float If the environment variable VNMR is set all data from that directory are automat 5 12 Execute P 131 5 11 4 5 11 5 5 12 ically displayed if you just type vconv The options were vconv is followed by a name and other additional options remain the same From JNMR The command jconv converts Jeol data sets to XWIN NMR format It allows conver sion of Jeol EX GX and ALPHA 1D 2D and 3D data Only FID type data are converted The conversion of processed data is not supported If the environment variable JNMR points to a directory jconv automatically displays all gxd and nmf files for selection 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 file Digital to analog The command convdta converts digitally filtered Avance acquisition data to analog data format The purpose of this command is to export data to external NMR processing programs not including the processing tools for digital data Please note that by this conversion the quality of the baseline of the data may be slightly affected It is t
224. image files to XWIN NMR format The Aspect 3000 TOMIKON program normally produces single image files The image files of one experiment can be converted either to single image files named 2rr with different processed data set numbers PROCNO or to one multi image file named 2dseq The TOMIKON 3D reconstruction produces one 3D image data file This file is 5 11 Conversion P 117 5 11 1 3 converted to a 2dseq file The Aspect 3000 DISNMR and DISMSL programs produce files with the exten sion IMAG They may contain several images The format is similar to the 3D image data file of TOMIKON The data can be converted either into 2rr files with different processing numbers for every slice or to one 2dseg file If you create e a2rr file the pixels are converted into 32 bit words e a 2dseq file the pixels can be converted into unsigned bytes 16 bit words or 32 bit words The file usr ocalNib bruknet cony par contains the parameters which determine the type of the output file You must create this file as superuser Back conversion bconv Certain XWIN NMR data sets can be converted back to DISNMR format with the command bconv The syntax of bconv is bconv lt station name gt lt data type gt If you type e bconv with both arguments the conversion is immediately started e bconv lt station gt you will be asked for the data type e bconv without any argument you will be asked for the station as well as the dat
225. imes useful if an already issued plot command can suppress the plot when no lines can be found in the plot region To accomplish this the parameter SUPPRESS must be set to yes instead of no The detection of peaks is analogous to that of the processing com mand pp Automatic continuation on additional paper sheets The length of a plot is physically limited by the paper size for single sheet plotters or by a manufacturer s setting for plotters with endless paper If the parameter CLIP is set to yes all plots will be clipped at those limits even if plot parameters like CX or CY specify a larger plot If it is set to no however the plot will always be finished according to the parameters if necessary on several sheets of paper This applies to the x direction as well as to the y direction and is especially impor tant for plots showing sufficient resolution and small paper size The program will draw marks at the edges so that the single sheets may easily be joined together for the whole plot Plotters with cutter accessory Various types of plotters with endless paper can automatically cut off the paper For these plotters the parameter CUTP has been introduced If set to yes the paper is cut off automatically after completion of a plot 10 4 Page layout for auto expansions edgx XWIN NMR allows you to generate plots containing a number of selected plot regions which are automatically expanded in the vertical direction to fill the ava
226. imize the fourier transform time If the entire data set fits in mem ory XDIM F1 will be 1 and a row wise ordering results On disk a complete submatrix is stored before the next submatrix starts The order of the data points within one submatrix is the same as the order of the submatrices File Formats P 336 within one data set first F2 the acquisition direction and then F1 Figure 16 2 shows the file structure of a processed 2D data file with the m E i fe el slz el BARBARO Figure 16 2 Submatrix format parameters SI F2 16 points SI F1 16 XDIM F2 4 XDIM F1 8 The upper left part of the figure shows the sequence of the individual data points of submatrix 1 the lower right part shows the sequence of the submatrices in the entire spec trum 16 6 3D Spectra For 3D processed data the spectrum real part is contained in the file 3rrr the imaginary parts are generated according to the description of the command tfl The files 3rrr 3irr are stored in the so called subcube format a generalization of the 2D submatrix format The subcube dimensions are given by the status parameters XDIM contained in the files procs proc2s and proc3s XDIM is calcu 16 6 3D Spectra P 337 lated by automatically depending on the available computer memory so as to optimize the fourier transform time XDIM is always a power of two On disk a complete subcube is stored before the
227. inary mode The parameters particularly the measurement frequencies correspond exactly to the configuration of the station stored in u conf instr lt station gt disnmr conf If bconv cannot find the disnmr conf file all frequencies correspond to those of the current AMX or Avance configuration Back conversion of 2rr image data files bconv supports conversion of images into the Aspect 3000 TOMIKON format Contrary to fid ser or procld types no special parameter file will be created Therefore data must be transferred with special parameter file handling disabled bconv creates an output file using the following naming convention lt NAME gt lt EXPNO mod 1000 gt lt class gt lt PROCNO mod 1000 gt where class is the image class depending on EXPNO and PROCNO 5 11 Conversion P 119 5 11 1 4 class I default class P if PROCNO 1000 1 class D if PROCNO 1000 2 class Q if PROCNO 1000 3 and in versions later 930101 if EXPNO mod 10000 1000 3 class X if PROCNO 1000 4 class Y if PROCNO 1000 5 class Z if PROCNO 1000 6 Back conversion of 2dseq image data files bconv supports conversion of these images into the Aspect 3000 TOMIKON for mat Contrary to fid ser or procld no special parameter file will be created Therefore data must be transferred with special parameter file handling disabled bconv creates an S image if PROCNO 1000 10 and in version
228. ing over write situation Figure 9 8 The display after the first simfit asc command The Analysis Menu P 206 Figure 9 9 The display after the second simfit command 9 6 5 Interactive manipulations 9 6 5 1 General information The interactive manipulation of the displayed points and the fit curve works exactly like the interactive manipulation of 1D data sets If you have managed to shift all points and the fit curve outside the display region then clicking the following three icons will always bring the data points back into the display region 9 6 The T1 T2 relaxation menu P 207 Click on Zn 9 6 5 2 Interactive elimination of data points If you want to temporarily eliminate points from fitting click the left mouse button in the data display area The mouse cursor will be put onto the nearest point You can now move the cursor along the points Clicking the middle mouse button on a point will eliminate the point temporarily The cursor is freed again afterwards To eliminate another point repeat the above procedure If you want to fit the remain ing data points type the corresponding fit command If you want to get the elimi nated points back type rspc restore eliminated points rspc will only bring back the points eliminated from the currently displayed peak Eliminated points will remain eliminated until you type rspc Switching between different peaks will not bring eliminated points back
229. ing parameter ME_mod is set to LPbr or LPbc In the following description TD must be replaced by TDeff if TDeff gt 0 see forward LP The parameter LPBIN has a meaning different from the case of forward LP The number of points contributing to backward LP input points can be reduced to LPBIN if LPBIN is set between 0 and TD The process ing parameter TDoff represents the number of points to be predicted If TDoff is set to a positive value the first TDoff points are replaced by predicted points If TDoff is set to a negative value TDoff predicted points are added to the beginning of the fid The added TDoff points are discarded from the end of the zerofilled fid Note that fid points are lost if more points are added at the beginning than zero filled at the end TDoff gt 2 SI TD 7 6 3 Combination of Forward and Backward Linear Prediction Forward and backward Linear Prediction can be combined with two succesive processing commands The first command must be xtrf type and performs baseline correction and backward LP Set the flags BC_mod and ME_mod to the desired values the others to no The second command xtrfp xf2 xfl or xfb performs for ward LP window multiplication FT and phase correction Set ME_mod WDW FT_mod and PH_mod to the desired values and BC_mod to no 7 6 4 Zerofilling right shift left shift If ME_mod is set to no or NCOEFF is 0 no linear prediction is done Ordinary zero filling is performed if 2 SI gt T
230. inimum information required by The Analysis Menu P 212 9 7 5 9 7 6 nmrquant However the program may also make use of the basereg file The basereg file can be set up to define two regions of baseline on either side of the sig nals which are then used for slope and bias calculations rather than the regions immediately to the left and the right of each integral region Basereg files are defined in exactly the same way as integral regions i e by tempo rarily exiting the nmrquant program and entering integration mode Note that the program saves any existing intrng file which is then restored on re entering the program Within integration mode instead of selecting regions of signal regions should be defined which contain two regions of flat baseline Note that the integral trails displayed on the screen should be ignored and correcting for slope and bias is not necessary After defining the baseline regions and storing with the Save to intrng amp Return option nmrguant must be restarted in order to handle the basereg and integral files correctly To avoid defining integral regions baseline regions and proton information each time a different spectrum is processed the user can save the files intrng nmrquant basereg for subsequent recall Indeed this must be carried out prior to running the program in automation mode The procedure for saving integral ranges is well established within XWIN NMR wmisc with files being stored i
231. inistrator For example a frequent problem when transfer ring files is that access permissions to the remote computer are not set correctly The command tcps calls the TCP IP rep utility internally Therefore only destina tions providing an rcp server can be accessed tcps opens a dialog window and invites you to enter the host name of the remote computer You can then enter the file or directory name you want to transfer Since the wild card characters and may be used more than one file or directory can be sent at once If you want to send a complete data set you must enter its directory name e g u data guest nmr sucrose The next step is to type in the des tination file or directory name For example if you enter u data guest nmr the data set sucrose would be placed in the same directory on the host as it is stored on your local system The receive command is the inverse of tcps The direction of the data transfer is from the remote to the local system Send data as email smail The command smail calls tojdx and the MIME compliant mail user agent MUA 5 10 Send Receive P 109 zmail internally In order for zmail to work as expected the sendmail program must be running smail opens a dialog window and invites you to enter the JCAMP conversion parameters You have to type the following electronic mail parameters as well e to list email address in the form user address e cc list list of users t
232. initialized with default parameter files which are copied from the current data set visible on the 5 1 New P 77 5 1 1 screen If there is none the parameter files are copied from the standard parameter sets delivered with the XWIN NMR release media XWINNMRHOME exp stan nmr par standard1D where XWINNMRHOME i in an XWIN NMR Standard installation The parameter PROCNO processed data number is used to create a subdirectory u data guest nmr sucrose I pdata 1 or in general DU data USER nmr NAME EX PNO pdata PROCNO which will contain the processed data usually the transformed spectrum of the corresponding acquisition data A 1D real spectrum for example is stored in the file Zr in this directory the corresponding imaginary part in the file Zi The real part of a 2D or 3D spectrum is stored in the files 2rr or 3rrr respectively Data access permissions When a new data set is created it will get the Unix read write permissions of the login user who started XWIN NMR and the group read write permissions of the Unix group she he belongs to Other users will not be able to overwrite or delete these data sets using XWIN NMR commands In certain cases it can happen that the Unix permissions of a data set stored under the parameter USER see previous section are wrong and prevent the user from processing the data Examples for such cases 1 Assume that the login user who started XWIN NMR is nmrl Assume furt
233. inity of the big gest peak The size of this interval must be specified by the processing parameter ASSWID in Hertz CY 0 If CY is zero the spectrum will be plotted with exactly the same vertical scaling as the operator has set up interactively on the display and stored with one of the Define region commands of the Output menu CY N Scale a spectrum on the plot relative to the spectrum last plotted with CY gt 0 and apply the factor N For example if CY 1 the spectrum will be plotted using the scaling of the last plot with CY gt 0 and you can visually compare the plots If CY 10 the spectrum will be 10 fold enlarged with respect to the last plot with CY gt 0 This can be useful for difference spectroscopy The program stores the scaling factor of a plot with CY gt 0 in the parameter file u prog lt version gt curdir lt userloginid gt scale as soon as the plot command is issued The next plot request will cause the scaling factor to be taken from this file if CY lt 0 Color The color in which a spectrum is to be plotted is specified by the parameter SCOLOR The operator is given a choice of several colors In order for the spec trum to actually appear in this color if a pen plotter is used the plotter pens must be in their corresponding holders and the assignment of colors to pen positions must be correct see command edpp 10 3 Page layout edg P 255 10 3 1 5 10 3 1 6 The Integral Like the spectrum
234. ion data directory is displayed If neither r or fid exist the current data set does not contain any data but only parameter files This is the situ ation if either the data set is a new one created by the New command from the File menu or if all data files were deleted using one of the commands dela or delp from the File menu Let s assume both files r and fid are present Then the command Fid will switch the screen to show the fid and the command Imaginary spectrum will change the display to the imaginary part of the transformed spectrum stored in the file i Clicking on Real spectrum will bring you back to the normal spectrum The Display Menu P 308 display The command Separ even odd points changes the display such that the left half of the screen shows the data points with even numbers 0 2 4 and the right half the odd data points 1 3 5 This mode can be useful if an fid is on the screen where the even points have been acquired by the first detector channel the odd points by the second one in quadrature mode The command Undo separation cancels the channel separation By default XWIN NMR connects the data points of a spectrum with a straight line in order to generate a continuous curve on the screen Somtimes it is convenient to observe the data points themselves Clicking on the command Dots solid lines will turn off vector drawing between the data points leaving only the data points Re invoke the same co
235. ion of the title window Two values are selectable top causes the title window to be positioned above the spectral window right causes it to be appended to the right of the spectral window TOFFSET determines the distance in cm between the title window and the left or top edge of the spectral window for TPOS top or right respectively The size of the title window is specified by TWIDTH and THEI in cm as described earlier The title is plotted inside with a white margin of width TMAR GIN cm around it The text is rotated by 90 or 90 degrees if the parameter TROT was set to one of these values instead of 0 The character size is determined by TCHAR in mm The characters may also be tilted with TSLANT specifying the tangent of the angle with the vertical TFONT selects the character set to be used which may be selected from Table 10 1 TFONT Font 0 ISO international ISO BRITISH 2 ANSI ASCII 3 ISO SWEDISH 4 JIS ASCII 5 ISO SPANISH 6 ISO GERMAN 7 ISO FRENCH 8 ISO_NORWEGIAN Table 10 1 Fonts available for plot title If TMODE a auto wrap the plot software will divide a continuous text into indi vidual lines automatically A Return in the text will always cause a new line The 10 3 Page layout edg P 259 10 3 3 user may force a new line anywhere in the text even within a word by inserting the character This character must be defined as the separation character in the parameter TSEP Any special charac
236. ipulation Likewise getcurdata2 and getcurdata3 fill in the second and third data set variables as set up by edg2 If you want to change the current data set by modifying the data set variables of you must execute the AU command setcurdata afterwards to make the changes known to XWIN NMR otherwise you would have only changed local AU program variables From now on all following XWIN NMR commands invoked from the AU program will operate on the new data set Please note that all AU commands contained in the command table aucmd h call setcurdata automatically The com mand setcurdata is analogous to the XWIN NMR command new edc If the data set exists it will become the current data set If it does not exist it will be created Its parameter files will be initialized with the parameter values of the last existing data set used Consider the example in Figure 15 2 Ten acquisitions are performed provided getcurdata start with data set on screen times 10 begin loop zg start acquisition expno go to data set with next EXPNO end end of loop quit terminate AU program Figure 15 2 Data set handling you have already set up the ten data sets with the correct acquisition parameters In contrast the AU program in Figure 15 2 requires only the first data set to be set up the remaining ones will be created automatically if they do not exist In addi tion the command uselastpars will set a
237. is enforced auto matically The structure of a regions file is identical with the structure of intrng files generated by the command abs and is described in the chapter The File menu The command sino uses the magnitude spectrum to calculate the signal to noise ratio Correct phasing of a spectrum is therefore not required for sino to work properly You may however force the program to perform its calculation on the spectrum s real part rather than on the magnitude spectrum by entering the com mand sino real on the keyboard Assume you have applied data manipulations to the spectrum affecting the real part only e g a baseline correction The imaginary part then is no longer valid giving a wrong magnitude spectrum and therefore a wrong SINO value Use sino real in this case or execute a Hilbert transform ht before calling sino in order to re generate a correct imaginary part The commands sino noprint and sino real noprint calculate and set the status parameter SINO without displaying the result you may examine the result by typ ing 2s sino or dpp The noprint option is automatically set when including a sino command in an AU program 9 5 Deconvolution The commands Idcon gdcon and mdcon decompose a specified spectral region into individual signals by approximating the experimental spectrum in this region with a sum of Lorentzian Gaussian or mixed Lorentzian Gaussian lineshapes respectively You should be familiar with pe
238. iscellaneous files directory back to the current data directory where it must be located for a corresponding XWIN NMR command to find it edmisc may of course also be used to set up a file of these types manually The preferred procedure however which ensures correct file formats is to modify a file that was generated by the appropriate XWIN NMR command 5 3 Open Other Files P 91 Examples of Format of miscellaneous files 1 intrng Figure 5 5 generated by manual integration The slope and bias A 1 0 regions in PPM low field high field bias slope 9 3210514094 9 1339532702 6540000 0 region 1 8 6147489426 8 4029001528 7850000 0 region 2 7 9758465528 7 8649580444 4030000 0 region 3 7 8097235415 7 7312765639 6100000 0 region 4 7 7006528774 7 5055841898 00 region 5 Figure 5 5 Example of an intrng file generated by manual integration parameters are taken into account to baseline correct the integrals as soon as they are calculated based on this file either on the display or during the plot or printout 2 intrng Figure 5 6 automatically generated by command abs No slope or bias PO 9 438358 8 147455 7 923863 7 144994 Figure 5 6 Example of an intrng file generated by abs parameters are present to correct the baseline of the integral Automatic base line correction is performed during integral plot or print based on this file if the processing parameter INTBC yes 19 data point
239. ist is stored under this name in the current data directory where the spec 1D Data Processing Tutorial P 30 trum is li reads the intrng file of the current data set calculates the integrals of the regions contained and prints the result XWIN NMR allows you to influence integral calcu lation by changing the processing parameters INTBC and INTSCL and by modi fying the intrng file itself INTBC is only taken into account if the intrng file was generated by abs and not by manual integration If set to yes each integral will be linearly baseline corrected before it is printed If set to no this step is skipped intrng files created by manual intgration contain slope and bias baseline correction values adjusted by the user see command edmisc for the exact file structure of intrng The printed integral values are presented in arbitrary units In manual inte gration you can calibrate a selected integral the other ones are scaled in relation to this reference In automatic integration you can insert scaling factors in the intrng file using a text editor see command edmisc The parameter INTSCL plays a role when you want to compare the integrals of different data sets If set to 1 li scales the calculated integrals relative to the last data set integrated with INTSCL not equal to 1 As usual you can enter INTBC and INTSCL at the keyboard lower case or from the edp editor All integration details described so far for li are also va
240. ition it on top of the desired peak then press the middle mouse button to mark the position The change phase increment buttons 2 2 DEF allow you to modify the sensitiv ity of the mouse The phase change during correction is doubled or cut in half 1D Data Processing Tutorial P 20 thereby reducing or increasing the sensitivity The DEF button resets the increment to its default value The current phase increment value is shown in the info win dow In order to terminate phase mode click the return button at the bottom There are four possible options Cancel leaves you in the phase mode Store amp return will force the program to exit from phase mode store the adjusted parameters PHCO and PHC1 in the processing parameter file and overwrite the unphased spectrum with the phased one Store2D amp return works similarly However the parameters are also stored in the parameter file of the last displayed 2D spectrum assuming that the current spectrum is a row or a column thereof The 2D spectrum is now ready for execution of a 2D phase correction in the corresponding dimension Finally return terminates phase mode without storing the phase parameters and without writing the phased data back to the spectrum file 2 7 Spectrum calibration The x axis of the spectrum is displayed in either Hertz or ppm units If the com plete spectrum is visible on screen the length of the axis corresponds to the sweep width in Hertz or in ppm
241. its sign positive or negative syma must therefore be used for phase sensitive spec tra 7 11 J resolved Type symmetrization symj It is recommended that the spectrum subjected to tilt before symj is applied symj symmetrizes the data points on both sides of a horizontal line which runs through the middle of the matrix The data point with the larger magnitude is replaced by one which has a magnitude equal to that of the smaller data point The status parameter SYMM documents which kind of symmetrization was applied to a given 2D spectrum It may take on the values no sym syma or symj The Process Menu for 2D data P 166 7 12 Tilt of a 2D spectrum tilt ptilt Again due to experimental conditions 2D J resolved spectra may be tilted along a horizontal line through the center of the matrix This distortion may be removed by tilt which shifts the data in points above this line to the right and data below the line to the left n tiltfactor nsrow 2 row where tiltfactor SW_p1 SI1 SW_p2 SI2 nsrow no of rows in the spectrum row the row which is to be corrected The two edges at both sides are filled with those data that are thrown away on the opposite side due to the shifting The status parameter TILT true or false indicates whether tilt was applied to a given 2D spectrum Tilting with arbitrary angles can be achieved with the command ptilt and the processing parameter ALPHA F2 between 1 and 1
242. its center to the desired reference point and click the middle mouse button A dialog will invite you to enter the F2 and F7 dimension frequencies that you want to assign to this data point The units of the numbers to be entered are the same as the current x and y axis units Hz or ppm You can release the cursor from the spectrum by clicking the left instead of the middle button Calibrating the F1 dimension can fail if certain parameters are not set correctly 1 If only the nucleus is wrong use the following commands to set it correctly 2s NUC2 Avance 2s DECNUC AMX etc If only NDO is wrong which is typically the case if SW F1 differs by a factor 0 5 2 or 4 from the correct value use the command 1s ndO to correct it Then reprocess the spectrum with xfb If new processing is not possible correct the sweep width status parameter by doubling it or cutting it in half using the command s SW_p In most cases re calibration of the spectrum is necessary afterwards since these changes affect the parameter OFFSET If the frequencies are completely wrong use the following commands to check the respective parameters and to correct them a ls SFO1 if correct note the value otherwise type Return b Is BF1 set the correct value if required c ls Ol set the correct value If SFO1 was correct BF1 O1 SFO1 must be valid d 1s NDO check and correct if necessary e Is SWH check and correct if nec
243. its processing parameters are initialized such that the slice corre sponds to a F3 F2 section of the 3D spectrum XWIN NMR then switches from the current 3D data set to this new 2D data set where you may execute e g a xfb com mand san Enter scan mode Figure 4 2 In this mode a number of possibilities are offered to view the 2D cross sections of the 3D spectrum parallel to the three main axes 218 Real time display of the F2 F3 F1 F3 or F1 F2 cross section respectively Click on the desired button to enter scan mode Move the mouse to position to the desired plane Press the right mouse button to quit this mode Ee EE aaa Display the next or previous F2 F3 F1 F3 or F1 F2 plane aute stop 2 8 9 Click on the desired button to start auto scanning the F2 F3 F1 F3 or F1 F2 4 2 Manipulating the spectrum on the screen P 69 Figure 4 2 Viewing 2D sections of a 3D spectrum planes Another click on the same button will stop auto scanning 3D Data Processing Tutorial P 70 This command button allows you to select planes by their plane number 4 3 Setting up the parameters for a 3D transform The main processing steps to calculate a spectrum from a 3 dimensional fid are window multiplication and fourier transformation In 3D like in 2D window multiplication and fourier transform and optionally linear prediction phase cor rection or magnitude calculation are part of the transform commands
244. iven at Unix level usually from an Xterm window outside XWIN NMR If the search returns without any infor mation the sample id was not found Otherwise the complete path names of all info files are displayed containing P 2740 In this way the user obtains a list of all experimental data with this sample id 5 4 Recall last XWIN NMR remembers the names of the last data sets you have worked with during your session and collects them in a table The first entry displays this table Clicking on one of the data sets will make it the current data set and show it on screen The other entries allow you to quickly return to the last used data set with a higher or lower dimension This latter feature is frequently used when examining rows of a 2D data set or planes of a 3D spec trum 5 5 Search The command search is an alternate way of finding and selecting a data set for dis play It is an important tool for getting an overview of the data sets stored in differ ent disk partitions for different users and to switch rapidly between data sets 5 5 Search P 97 5 5 1 Data set specifications Directory This field contains the list of directories where XWIN NMR data sets are searched for Assume you want to process data stored in the two directories us1 people guest and u Then you have to add these directories to the list by opening the Edit menu and selecting the command Edit directory list Enter a directory name and click on
245. k contours Similar to the contour representa tion of 2D spectra 3D spectra are displayed by means of contour lines While in the 2D case contours are always calculated in the F1 F2 plane in the 3D case the two additional planes F2 F3 and F1 F3 are present The contour calculation rou tine will ask you whether to compute the contour for a particular plane The best impression of the 3D spectrum on screen is usually achieved by having the pro gram calculate all contours However this takes the longest too 4 2 Manipulating the spectrum on the screen You should now have Figure 4 1 on the monitor representing the standard 3D lay out The data area shows the 3D spectrum in contour display mode The right side indicates the colors assigned to the different intensity values The button panel at the left side of the XWIN NMR window allows you to interac tively scale and expand the data and to enter a subroutine These operations are screen operations only and do not modify the data file You must click on a button to execute a function Some buttons require that you keep the left mouse button pressed while the cursor is located in the command button field and then move the mouse When you move the cursor over the command buttons without clicking their function is displayed in the status line at the bottom of the XWIN NMR win dow aa e ES 1 Enlarge spectrum by a factor of 1 1 4 2 Manipulating the spectrum on the screen P 65
246. k integrals Any command typed in next will now work on the so selected fit type If you want to fit the peak maxima tog gle FITTYPE back to intensity Important notes The commands nxtp ctl datl ct2 and dat2 will always show the points and the fit curve in full scale mode The display is scaled according to the maximum and min imum of the data points of the current peak The simfit commands will always show the data points and the fit curve in an abso 9 6 The T1 T2 relaxation menu P 199 lute scaling mode The display is scaled according to the maximum and minimum of the data points of all peaks Figure 9 5 The display after executing ctl 9 6 4 4 simfit The following parameters must be set in the editor invoked with edtl CURSOR Select the peak you want to fit Normally you will set CURSOR to 1 You can later switch to other peaks with the command nxtp The Analysis Menu P 200 FITTYPE a Select intensity if you want to fit the peak maxima b Select area if you want to fit the peak integrals FCTTYPE Select the appropriate fit function COMPNO Set the number of components which contribute to the intensities of the data points EDGUESS Set an initial estimate for the parameters to be fitted Make certain that the sum of all I O values is not bigger than 1 If COMPNO was set to 1 then the best guess for I O is usually 1 The parameter NUMTERM is set automatically and depends on the
247. l see menu Acquire gt Spectrometer setup which must be executed after installation of XWIN NMR will compile them if user requested The File Menu P 86 5 3 7 5 3 8 and install their C sources in the working directory u exp stan nmr au src and their executables in u prog lt XWIN NMR version gt au bin The command edau may also be entered on the keyboard followed by the name of the desired AU program or followed by an argument containing wildcard charac ters see edpul and how to change the default text editor for details edau is almost identical to the command edaumod The only difference is that when edau is called AU programs are displayed while edaumod shows the so called AU modules You can switch to AU module display by clicking on the gt Modules command button at the bottom of the dialog box Macros edmac Macros are text files containing XWIN NMR commands This command allows you to create a new macro and to edit or view an existing one The purpose of macros is to implement user defined commands in XWIN NMR based on XWIN NMR inter nal commands In contrast to AU programs macros do not allow for control struc tures such as loops and branches nor arithmetic expressions The new command is just the name of the macro and can be entered on the keyboard or called in other macros see menu File gt Execute Macros can also be called in executable AU program XWIN NMR locates macros in the directo
248. l 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 le4 vargrad 1 6 I I 0 exp D SQR 2 PI gamma G LD BD LD 3 1e4 The fitting procedure consists of two basic steps g The data points must be extracted from a data set This step is described in Section 9 6 2 Picking points h The variables of the fit equation are calculated This step is described in Sec tion 9 6 4 The fitting procedure For both steps all relevant parameters are set with the command edtl 9 6 2 Picking points Points for fitting can be extracted from three different data types a from a single FID A typical example is the Carr Purcell experiment pulse program cpmg b from rows of a 2D experiment A typical example is the pulse program tlir where several FIDs are acquired into a 2D series file This ser file is processed with xf2 and phase and baseline corrected The points as either intensities or as integrals are extracted columnwise from each row of the 2D data file c from an ASCII file You can enter the x and y coordinates of the data points in an ASCII file using your preferred text editor The Analysis Menu P 190 9 6 3 pft2 Pick points from a single FID You do not need to process the FID You simply switch to the T1 T2 relaxation menu Analysis gt Relaxation In this menu you select the edtl command The fol lowing parameters must be set NUMPNTS Enter t
249. l integration or intrng automatic integration command abs Used in plotting and integral printout commands li lipp baseline points from manual baseline correction to be Paseanto used by the baseline correction command bem baseline points for spline baseline correction command baslpnts i sab created interactively with the cursor peak information generated by command ppp To be peaklist f used by the deconvolution command mdcon plot regions same format as intrng files used by the plot command if the parameter LIMITS region The plot limits are taken as the largest and smallest frequency values in the file Table 5 10 Miscellaneous files types tor for details When such a file is generated by XWIN NMR it is stored in the current processed data directory DU data USER nmr NAME EX PNO pdata PROCNO For example after manual integration the regions are written into the file intrng in this directory The user might want to have several intrng files available on disk each with different regions In order to save the current file he uses the command wmisc to copy it to the directory u exp stan nmr lists intrng under an arbitrary name intrng is now used as the file type and the directory may contain many range files that differ in their names but have all the same structure File types other than intrng are treated in a similar fashion The command rmisc is used to copy a file from a m
250. l region to be plotted A change in this parameter leaves the width of the spectral window CX and the left plot limit F1 F1P unchanged while the scaling HZCM PPMCM Hz or ppm per cm is adjusted accordingly Therefore a change of F2 F2P yields an expansion or compression of the plot region PPMCM ppm cm HZCM Hz cm These parameters determine the horizontal resolution of a plot If changed the plot region F1 F2 is left constant and the width of the spectral window CX is adjusted according to the expression HZCM F 1 F 2 CX The vertical scaling of the spectrum is controlled by the parameters PSCAL and CY With the processing parameter PSCAL the user defines a position in the spec trum which then serves as a reference for the vertical scaling CY can be positive zero or negative The following paragraphs discuss these values CY gt 0 If CY is greater than zero then the intensity at the reference position will be plotted with height CY cm All other intensities will be scaled relative to that position PSCAL can take the values global preg ireg pireg sreg and noise 1 global The highest intensity of the entire spectrum serves as the reference 2 preg The highest intensity within the plot region i e the spectral window deter mined by F1 F2 serves as the reference 3 ireg The highest intensity in those spectral regions which are specified in the text file reg in the current processed data directory serves as the
251. late a Disco projection from several regions but from the same reference he may once the first calculation is finished activate the appropri ate Disco command once more with the middle button and redefine the new region Since the last reference used is still visible on the screen it is easy to position the cross hair once more in order to have the same reference for the new calculation Available literature about Disco projections Kessler Miiller Oschkinat Mag Res in Chemistry 23 1985 844 2D Data Processing Tutorial P 62 Chapter 4 3D Data Processing Tutorial This chapter presents 3D data processing based on the data set exam3d The data set is stored in the directory u data guest nmr In order to have full access permis sions to it you should have a user guest installed on your system and be logged in as guest Start XWIN NMR by typing xwinnmr r The r option ensures that every thing is cleaned up before starting the program even if the last session was termi nated by some problem The program will start without displaying a data set Instead the XWIN NMR logo will be shown in the data area In later sessions you can start XWIN NMR without specifying the r option and you will immediately get the last used data set displayed 4 1 Getting the data set The first step is to get the 3D spectrum exam3d on screen Open the File menu select the Open entry and from there the command dir You should get a dialog b
252. le consisting of a sequence of 1D spectra They are extracted from the 2rr file real part of a 2D type data set Remember that a such a file is created by one of the transform commands xf2 xf1 xfb xtrf For this reason stacked plots may be obtained from 2D spectra but also from a series of 1D spectra whose fids The 2D Output Menu P 296 Figure 11 4 Example of a stacked whitewash plot were acquired into a ser file by means of a suitable pulse program such as a T1 or T2 experiment They are normally transformed by the xf2 command The 1D spectra in a stacked plot are governed by the following 1D plot parameters SXLLEFT SYLLEFT SHEI CX F1 F1P F2 F2P HZCM PPCM DHEI SHEI XAXIS XHELSZERO CY gt 0 SCOLOR XAXIS XHEI XTICLEN XUNIT XTICDIS XCHAR XCOLOR YAXIS YTICLEN YTICDIS YCOLOR Please refer to the chapter The 1D Output Menu for their description 1D parame 11 4 Page layout stacked plot edgw P 297 ters not mentioned in this list do not play a role for stacked plots The following parameters define the stacked layout STACKED yes no Draw do not draw the spectra of a stacked plot SWID Width cm of whole window DWID S WID ZAXIS ZHEI Shows how much space is left for the stacked data STKZ1 2 Plot region limits in the stacked z dimension The numbers to be specified here depend on the chosen z axis units parameter ZUNIT Assume the z axis units should correspond to the values of a VDLIST
253. le gt Rename submenu other files The rename commands display a list of data sets or other files You can edit each name in the list using the cursor Renaming is complete as soon as you terminate your change with the Return key ren Change a data set NAME reno Change a USER name The command displays a list of USERs i e all subdirectories of DU data You can now change a name in the list For example if guest appears in the list and you change it to newguest your data directory will be renamed from DU data guest to DU data new guest renpar Change the name of a parameter set renpul Change the name of a pulse program rengp Change the name of a gradient program The File Menu P 108 5 10 renau Change the name of an automation AU program renmac Change the name of a command macro renlist Change the name of a parameter list file renaumod Change the name of an automation module Send Receive 5 10 1 5 10 2 The Send submenu contains commands for transferring data sets via rcp remote copy or as email The command names shown in brackets may be used to quickly access the func tion from the keyboard Send or fetch data via rcp tcps The tcps command allows you to transfer files or whole directories to a remote computer which is connected via a network to your system In order for tcps to work as expected the TCP IP network environment must have been installed cor rectly by the system adm
254. le appears again and labels for a different user solvent experi ment combination may be generated prlabel is terminated via the ABORT field of the table 10 13 Supported printers plotters P 275 10 13 Supported printers plotters Table 10 8 presents a list of the plotters supported by XWIN NMR and or XWIN PLOT The tables following Table 10 8 inform you about the switch settings of a number of printers plotters required for them to work correctly The XWIN NMR plotter type specified in the header of these tables is the name to be set in edo parameter CURPLOT to send to output to this plotter For the HPLJSL you can select either hp j5 1 or hplj5ir in cfpp The first mode will generate ouput with 600 dpi the second mode with 300 dpi resolution The stand ard memory equipment of a HPLJSL is 1MB When using 600 dpi mode more memory could be required for certain types of plots especially for contour plots This depends on the number of vectors generated The 1D Output Menu P 276 Type Format XWIN NMR XWIN PLOT The printer plotter was tested The printer plotter will probably work but was not tested and is not sup ported by Bruker Canon BJ200 A4 Canon BJ330 14 el Canon BJC800 A3 Canon BJC4550 A3 1 GRAPHTEC FP6302 A3 GRAPHTEC FP7200 A2 GRAPHTEC GP1002 AO GRAPHTEC GP1002R 36 el GRAPHTEC MP3200 A3 GRAPHTEC MP
255. lel with the first one The 2D processing module is started twice by the XWIN NMR command processor as two Unix processes each copy of the module working on a different data set The purpose of the Show command is to display a table of all commands found in execution or scheduled for execution Figure 12 2 presents the table as it would an Figure 12 2 Table of active commands look after entering the command sequence em ft apk It displays the command names and the data sets on which the commands operate Furthermore the execu 12 1 Active Commands P 303 tion status EXEC indicates which commands are already in progress The status WAIT indicates that a command must wait until a previous command has finished In our example the three commands were typed while the same data set was on screen Therefore they are queued i e ft must wait until em terminates and apk must wait until ft terminates There are two more columns in the table giving the name of the XWIN NMR module containing the program code for the command and the Unix process id number assigned to the module after it was started Figure 12 3 shows an example with two simultaneously executing 2D transforms a Figure 12 3 Simultaneously active commands The Show and allow for killing command displays the same type of tables equiva lent to the kill keyboard command The difference from Show is that you may now click on a command forcing it to terminate im
256. les baslpnts and intrng are written into the processing data directory These files can now be used immediately for the next step the actual maximum search in the 2D data set Return to the T1 T2 relaxation menu by clicking on Analysis gt Relaxation e pd Pick peak maxima along columns from all rows Enter the command pd to pick the maxima along the defined columns from all rows of the 2D data set A peak picking is done in each row of the 2D data file A maximum will be found a if at the given position the peak maximum lies within the allowed drift range and b if the peak maximum is bigger than MI minimum intensity taking into account the peak picking sensitivity constant PC At the same time all data points within the specified integral range will be added up if the file intrng exists The display will be updated with the maxima which were picked at the first peak of each row of the 2D data set The total number of peaks is given by the number of positions defined in the baslpnts file Each series of maxima points for one peak consists of at the most NUMPNTS points A little window on the screen will contain information about the currently displayed peak number and position If you want to see the next peak type nxtp see Section 9 6 4 2 It is possible that maxima at a certain position in one or several rows of the 2D 9 6 The T1 T2 relaxation menu P 195 Figure 9 4 The display after executing pd data set
257. lice with the command r13 trans form this slice with xf1 and determine the phase angles from the resulting 2D spec trum Then perform tfl with these phase angles 4 6 2 Correction after the transformation The phase correction for a certain dimension must follow the transformation in that dimension immediately i e before the next dimension is transformed The reason for this lies in the incomplete storage of imaginary parts after the transfor mations in order to save disk space details are described in the chapter The 3D Process Menu The phase correction commands are tf3p tf2p and tflp for the three dimensions F3 F2 and F1 respectively The spectrum is phase corrected with the correspond ing phase angles PHCO and PHC1 They are to be determined as follows 1 transformation tf3 with PH_mod no 2 extract a F3 F2 or a F3 F1 slice with r23 or r13 3 determine PHCO and PHC1 from this slice in 2D mode 4 execute tf3p The two other dimensions are treated analogously The phase correction com mands read or write the files in Table 4 2 In order to save computation time and 3D Data Processing Tutorial P 74 read write tf3p 3rrr 3irr 3rrr 3irr tf2p 3rrr 3rir 3rrr 3rir tflp 3rrr 3rri 3rrr 3rri Table 4 2 Files read and written by the phase correction commands disk storage the commands also offer the possibility of dropping imaginary parts after execution The user will be asked if this shoul
258. lid for the commands lipp lippf which list peak positions and integrals together see Analysis gt Peak pick ing and the plotting commands when integral plotting is enabled 2 10 Peak picking Invoke the peak picking commands from the Analysis gt Peak picking menu Most of the commands can also be typed in Please use the command names shown in brackets In order to generate a peak list the following steps are required Define spectral region Peak picking can work on the entire spectrum or on a selected region Expand the desired region on screen or reset the horizontal scaling to display the entire spec trum Open the Analysis gt Peak picking menu and activate the command Define region Since this command is also used to define the region for a plot some ques tions will be asked Just answer them with Return The program stores the region limits in the plot parameters F1 F2 in Hertz and F1P F2P in ppm and you can always examine or modify them by typing the parameter names in lower case characters When you change the spectrum expansion or scaling on the screen these parameters will not be affected You can always re display the region via the 2 10 Peak picking P 31 command Show region in the Analysis gt Peak picking menu Define intensity scale thresholds and sensitivity The peak picking routine searches for signals larger than the so called minimum intensity MI and smaller than the maximum intensity MAXI MI an
259. line The same commands may be invoked from the keyboard by typing show cmd kill P 301 The Display Menu P 302 or follow cmd respectively XWIN NMR is a multi tasking program i e several commands may be in progress at the same time For example during automation with a sample changer acquisi tion is performed on a data set 3 While acquisition is in progress the previously measured data set 2 is processed i e transformed phase corrected etc and at the same time the previously processed data set 1 is plotted In addition a user is set ting up the experiments for the next samples In general multi tasking is handled in the following way When you enter com mands either from the keyboard or from a menu they are queued and applied to the current data subsequently For example typing em Return ft Return apk Return will execute these commands in the specified sequence on the current 1D data set However when you apply a command to the current data set then change to a different data set which will become your new current data set and type in a command to process it the command will be executed simultaneously with the first command provided the latter has not terminated in the meantime For example select a 2D data set and type xfb to start a 2D Fourier transform Then while this tranform is executing select another 2D data set and type xfb again This will cause the second transform to be executed in paral
260. line of the XWIN NMR window Every XWIN NMR processing command dis plays a message when it is started or terminated Many commands with longer execution times report special information while they are running For example the 2D transform command monitors the rows or columns being processed On for all data sets is the default setting XWIN NMR tries to output all messages of all cur rently active commands even those executing in background on data sets other than the current data set visible on screen In this case not all messages may be readable because they are sent asynchronously from various modules to the status line and may overlap On for current data set only disables the messages sent from background commands and displays only those generated by commands operating on the currently visible data set On for selected data sets displays a table of active commands if any and the associated data sets You may select one and XWIN NMR will disable the status messages for all other ones Off disables the status line completely and you will never see any messages appear XWIN NMR is capable of monitoring all acquisition processing and plotting com mands together with their start and termination times and possible error messages in a text file 12 3 Dual Display P 305 u prog lt X WIN NMR version gt curdir lt user gt history By default history is disabled When enabling it with Enable history file please be aware that
261. lotter is defined or the parameters for a plotter other than the current one are to be edited edpp will list the plotters configured with cfpp from which one may be selected 10 2 1 Paper feed options Parameters PAPERFD FAMOUNT 1 PAPERFD default Plotters that can change sheets between plots will insert a new sheet after com pletion of the plot For plotters with endless paper the paper will be advanced by an amount derived from the length of the plot The parameter FAMOUNT has no meaning in these cases 2 PAPERFD no After completion of the plot the paper will not be advanced or changed 3 PAPERFD single This option only works for plotters with endless paper It ensures that the plot 10 2 Pen setup edpp P 247 10 2 2 10 2 3 ter will behave exactly like a single sheet plotter with the length of the sheet being determined by the parameter FAMOUNT in cm This has the fol lowing effects If a plot needs more room than given by FAMOUNT the paper will be advanced by FAMOUNT The plot will be finished on the next sheet if the plot parameter CLIP see below is set to no or clipped if CLIP yes 4 PAPERFD multiple This option also is only effective for plotters with endless paper The plot will be drawn correctly even if it is longer than FAMOUNT After completion that paper will be advanced to the next multiple of FAMOUNT Pen positions The various objects of a plot i e spectrum axes integral parameters and titl
262. lowing Aspect fragment CSY an entry in the tokens file is found to be CSY cosy90 The XWIN NMR file format must therefore reserve 6 characters for the string cosy90 If less then 6 characters are reserved then trun cation will occur If more than 6 characters are reserved then the string cosy90 is padded out with the underscore character 5 11 Conversion P 125 5 11 1 5 Bruktran Tokens File The Bruktran program attempts to access the file Bt_tokens which should be stored in the home directory of the currently logged in user If this file is not found then the program accesses the system editor to create this file thus prompting you to input tokens If you do not wish to edit this file then the filename formats are reset to their default values and no automatic renaming is possible Token entries MUST be of the following format TOKEN1 TOKEN2 TOKENI refers to the group of characters in the Aspect file name TOKEN refers to the characters to be inserted into the X32 filename Important note 1 THERE MUST BE NO SPACES BETWEEN THE SIGN AND EITHER OF THE TOKENS 2 THE ENTRY MUST BE LEFT JUSTIFIED 3 THERE MUST BE NO COMMENTARY IN THE TOKENS FILE An example Bt_tokens file would contain the following entries CS cosy TC tocs AA H1 AB C13 AC NI15 10 fred 1 jane 12 jim Parameter Plot of converted Apect 2000 3000 Data When plotting data transferred from Aspect 2000 3000 computers and converted to XWIN NMR f
263. m ple from an AU program a Tcl Tk script can be executed with the AU command CPR_exec xwish f lt script WAIT_TERM From a Tcl Tk script an AU pro gram can be executed with CPR_exec xau lt AU program name gt Table 5 14 shows the commands which may be used within Tcl Tk scripts to access XWIN NMR functions xwish2 The Tcl Tk language has changed significantly since the introduction of the xwish command For this reason the command xwish2 has been introduced If you want to write Tcl Tk scripts based on Tcl 7 5 and Tk 4 1 you must invoke them with xwish2 rather than xwish We recommend to store such scripts in the directory XWINNMRHOME prog tcl xwish2_scripts the environment variable XWINNMRHOME u for XWIN NMR standard installa 5 12 Execute P 135 CPR_exec XWIN NMR command e g CPR_exec zg CPR_exec_wait XWIN NMR command e g CPR_exec_wait swh 5000 Execute XWIN NMR command from a Tcl Tk script Continue executing the script without waiting for the command to be finished Execute XWIN NMR command from a Tcl Tk script Continue executing the script after the command is finished Return the current experiment pre path usually u exp stan nmr Return the acquisition parame Getinstr ter INSTRUM the name of the configured spectrometer Return XWIN NMR s version Getversion number Return the path name u prog Getcurdir lt XWIN NMR version gt
264. m Files with imaginary data points e g 3iii are only present if the transform was executed with the option to store the imaginary data in the case of phase sensitive spectra 4 4 Applying the 3D Fourier Tranform Type tf3 on the keyboard or open the Process gt Fourier transform menu and click on tf3 to transform the acquisition dimension Continue with tf2 and tfl for the other dimensions The progress is reported on the status line at the bottom of the XWIN NMR window At the end of the transform the software calculates a com pressed spectrum corresponding to the display window size from the real part 3rrr and stores it in the file dsp3d if the spectrum is larger than the available memory 3rrr or dsp3d are used to calculate the contours when clicking on the display but ton of the left hand button panel dsp3d is only needed for data display and is recal culated automatically from the spectrum file 3rrr if missing 4 5 Strip transform linear prediction other transform options XWIN NMR provides a number of 3D transform options such as linear prediction strip transform inverse transform user defined transform and Hilbert transform Linear prediction is an attractive option to perfect initial data points of the acquisi 3D Data Processing Tutorial P 72 4 6 tion data before the transform in order to obtain better baselines Furthermore completing truncated Fids with linear prediction gives better estimates of the data a
265. mber of components m number of integral regions comp 1 id lt comp 1 mol wt gt lt comp 1 weight gt comp n id lt comp n mol wt gt lt comp n weight gt np region 1 np region m Proton contributions for comp 1 np region n np region m Proton contributions for comp m Table 9 3 Matrix file format The first line contains the number of components to be analysed which must be greater or equal to the number of integral regions defined on the next line The number of integral regions must match the number of integral regions defined in the intrng file otherwise the matrix becomes undefined The next n lines contain three fields reserved for component identifiers molecular and component weights in grams separated by colons Component identifiers contain the defaults Sample 1 Sample 2 etc The molecular and component weight fields are empty by default and need not be set when calculating mole ratios To peform weight calculations all component molecular weights must be defined as well as the weight of at least one reference component The last part of nmrquant file consists of values for a matrix of dimension number of integral regions times number of components The values represent the number of protons from each component for each integral region defined and each line consists of the number of protons for each integral region separated by colons for a given component The intrng and the nmrquant files contain the m
266. mediately The data set on which the command was operating will be left in an incomplete state You should only kill data processing commands or automation programs this way To stop data acquisition the special commands halt or stop should be used Particularly halt will abort acquisition not before the current scan is complete ensuring correct fid data be stored on disk If acquisition hangs for some reason and does not respond to stop or halt you may try to clear it with kill The Show and update table online displays the same table like Show but updates it according to the progress of the commands until you close the table In our exam ple sequence em ft apk XWIN NMR will delete the entry for em from the table as soon as em is finished and change the status of ft from WAIT to EXEC When all commands have terminated the table will be empty The Display Menu P 304 12 2 Status amp History In the Status amp History submenu the following commands are available On for all data sets default setting On for current data set only On for selected data sets Off Enable history file Disable history file default setting The same commands may be invoked by typing the following commands on the keyboard status all default setting status auto status cmd status off hist on hist off default setting The first four commands control the way messages are displayed in the bottom sta tus
267. mes are legal start XWIN NMR and enter the command setres A list of colors will be shown Double click on a color to see how it looks and feels You may also mix your own color in setres using the sliders The resulting color is displayed with a leading character with 4 digits per Red Green or Blue compo nent Leave the last 2 digits of each component off thus creating a 6 digit color code which you may use in the reource file Introduction P 8 If you change the colors in the XWinNmr file it will change for any user starting XWIN NMR If you rename the file let s say to XWinNmrsave the window color will change to the standard Motif blue If you want to give each user the permis sion to set her his own colors proceed as follows Insert the 4 lines in the file Xresources in the user s home directory create this file if it does not exist and change the color there The entries in the Xresources file will get priority over those in the XWinNmr file The XWinNmr file only influences the main XWIN NMR window not the data objects such as spectra axes integrals etc Their color may be adjusted from the setres window while XWIN NMR is running Furthermore some XWIN NMR com mands such as pulsdisp acbdisp view search etc create own windows whose colors may be adjusted independently All these commands have own resource files in the app defaults directory Chapter 2 1D Data Processing Tutorial This chapter pres
268. meters vary between plotters and have to be taken from the manu facturer s manual It is not necessary to specify all four parameters but if more The 1D Output Menu P 248 than one are specified they must be separated by a blank 10 3 Page layout edg The command edg displays a dialog window with a number of sub pages contain ing parameters to be set up by the user These parameters determine the position color scaling etc of the objects to be plotted XWIN NMR recognizes the following 1D plot objects Spectrum Integral Numeric Integral Values X axis Y axis Peak List Plot Title and Parameter List Figure 10 5 shows a typical basic page layout Figure 10 5 Basic 1D page layout 10 3 Page layout edg P 249 10 3 1 It consists of the following 3 windows which may overlap if desired 1 Window 1 the Spectral Window contains Spectrum Integral Numeric Integral Values X axis Y axis and Peak List The x and y coordinates of its lower left corner are given by the parameters SXLLEFT SYLLEFT cm The window width and height are given by the parameters CX and SHEI cm 2 Window 2 the Title Window contains the Plot Title The x and y coordinates of its lower left corner are given by the parameters TXLLEFT TYLLEFT cm The window width and height are given by the parameters TWIDTH and THEI cm 3 Window 3 the Parameter Window contains the Parameter List The x and y coordinates of its upper left c
269. mination An AU program terminated by one of these commands will return the value of the glo bal variable AUERR A higher level AU program could check AUERR for legality and perform a corresponding action Each macro command used in an AU pro gram e g ft will set AUERR according to the return value of the CPR_exec func tion quit or quitmsg is the last statement of an AU program Thereafter the code of functions written by the user and required by the AU program may follow Writing AU Programs P 330 15 11 If an AU program should be terminated at an arbitrary position of its code due to an error condition abort stop or stopmsg message may be used Abort returns 1 while the stop commands return AUERR just like the quit commands Outputting messages to the screen The function Proc_err DEF_ERR_OPT lt format string gt lt variable list gt gen erates a window containing a message Figure 15 4 shows an example which prints fetchpar NS amp i1 fetchpar D1 amp f1 Proc_err DEF_ERR_ OPT NS d D1 f il f1 sprintf text NS d D1 f 11 f1 Show_status text quit Figure 15 4 AU program using Proc_err and Show_status the parameters NS and D1 as set up by the command eda The format string and the variable list must be used in the same way as in the printf function of the C lan guage If the argument DEF_ERR_OPT is equal to the AU program will not continue unt
270. mmand search also member of the File menu is an alternate way to find and display exist ing data sets It is described later in this chapter The browse command browse yet another way to find and display existing data sets Browse may be The File Menu P 80 specified with a numerical argument e g browse 3 defining the entry level into the data set hierarchy 5 3 Open Other Files Please note In this and other sections of this manual the names of various directories are intro duced containing important files such as lists pulse programs etc These directo ries usually start with the string u This applies for the case of an XWIN NMR standard installation If your XWIN NMR was installed somewhere else u must be replaced by the correct installation directory In order to find it examine the envi ronment variable XWINNMRHOME type env to your operating system com mand shell to display the setting of this variable XWIN NMR must be active while you execute the env command Other than data files XWIN NMR requires special purpose files for a number of operations These files can be accessed via the other files box Figure 5 4 Figure 5 4 The Files gt Open gt Other files submenu 5 3 1 Parameter sets dirpar A parameter set is a collection of parameter files stored in the directory u exp stan nmr par PARSETNAMEY This command displays all currently available parameter sets XWIN NMR is 5 3 O
271. mmand to toggle back to the solid line display The toggle command Y axis on off allows you to enable or disable the display of a y axis If enabled the command Y axis absolute cm units lets you toggle between two types of axis units Absolute units show the intensities on a relative scale They allow you to compare the intensities of different spectra For example if you would under the same experimental conditions acquire two fids the first one with 8 scans and the second one with 16 scans the second signal will be twice the inten sity of the first one The absolute units will reflect this fact In a second example when you multiply the whole spectrum with 0 5 type dc_0 5 then mulc you will see the intensity change by looking at the y axis in absolute mode Setting the y axis to cm units allows you to the view the spectrum in the same way it would occur on a plot The so called plot reference peak often the biggest peak in the spectrum will be plotted with a height of CY cm The plot parameter CY can be set from the plot parameter editor edg or by entering cy on the keyboard If cm scaling of the y axis is selected the axis is labelled such that the intensity of this peak will get the value of CY 12 5 User Interface This command which may also be invoked by typing in setres lets you tailor a number of user interface attributes A window according to Figure 12 5 is opened which allows you to adjust the various settings A
272. mr exam 1 d 1 pdata I The data are now displayed in the data area of the XWIN NMR window If transformed data are already present you will see the spectrum otherwise the free induction decay If no data at all were present for instance after executing a delete command the message No Data Available is shown You will have noticed that the File gt Open menu contains a number of different dir commands which all serve the purpose of locating and loading a data set You can try them out or find detailed information in the chapter The File Menu Another important tool for getting an overview of available data sets is the command search in the File Menu Please note that most XWIN NMR commands can be executed directly from the keyboard The command names are displayed in brackets in the pull down menus e g dir They can also be used to build user defined macros and automa tion AU programs When a data set is visible on the screen the top line of the data display area shows the data set name in our example lt examI d 1 1 u guest gt This information reveals the directory in which data and parameter files are stored on disk namely u data guest nmr exam1 d I pdata 1 The items data nmr and pdata are prescribed by XWIN NMR and cannot be modi fied by the user u is the initial path name of the data set s directory and therefore specifies in which disk partition or on which disk the data set resides The item guest is the l
273. n All changes in the table are discarded i e the level file is not modified and edlev is terminated Defining Projections Often contour maps are plotted together with projections or 1D spectra Enter edg and select EDPROJ1 or EDPROJ2 to open the parameter box for the projection to be drawn along the F1 or F2 axis Click on PFIEXT PF2EXT to get the table of supported projection types Choose external if you want to plot an arbitrary spec trum along this axis In this case use the parameters P1 2 DU P1 2 USER etc to specify the name and location of this spectrum Simulating a large size plotter In XWIN NMR you can generate plots of arbitrary size and resolution even on a small size printer or plotter Use the parameters CX1 and CX2 to define the desired plot size in cm in the F1 and F2 dimensions Set the parameter CLIP to no you can type in cx1 cx2 clip as commands or set the parameters from edg The plot command will generate as many pages as necessary Marks will be drawn at the edges so that the different sheets may easily be joined together Even the previewer command view can handle this mode Click on the Next Page button in the pre viewer window to toggle through the pages Using the previewer For 2D spectra the view command may take some time depending on the size of the plot region before the spectrum is drawn in the previewer window During this time where contour calculation from the data file on disk takes pl
274. n 9 6 4 9 6 The T1 T2 relaxation menu P 191 50000 x 45000 a 25000 20000 x 15000 10000 5000 Figure 9 3 The display after executing pft2 9 6 3 1 pd and pd0 pick points from rows of a 2D experiment e edtl Setting up the parameters rspc read a slice from the 2D The 2D series file must be processed at least in F2 dimension The data should be properly phased and baseline corrected Having done this switch to T1 T2 relaxation menu Analysis gt Relaxation Enter the command edt1 Process gt edt1 and set the following parameters NUMPNTS The Analysis Menu P 192 Enter the number of rows from which you want to pick points When you switch to the T1 T2 menu on this data set for the first time then NUMPNTS is automatically set to the processed number of rows SI F1 You can reduce NUMPNTS if you want to restrict the number of rows from which data points are picked FITTYPE a Select intensity if you want to fit the peak maxima b Select area if you want to fit the peak integrals LISTTYP a Enter vdlist if you want to extract the x coordinates from the vdlist file stored in the acquisition data directory If the file vdlist is not found there the file specified in the status acquisition parameter VDLIST is read from the u exp stan nmr lists vd directory If this file cannot be found either an error message is printed and the point picking command is terminated b Enter vplist if yo
275. n a file At a later time this file can then be sent to a suitable plotter or printer which could even be con nected to a different computer Select the type of output file from the table Specify The 1D Output Menu P 246 the paper correctly since the plot is continued on additional sheets of paper if it was chosen larger than one sheet if the plot parameter CLIP is set to no The gen erated plot files are stored in the user s home directory XWIN NMR creates a subdi rectory plot code there The HPGL or PostScript files are stored in that directory and carry the name of the corresponding plotter type followed by a sequence number For example say you want to write your plot into a file which is suitable for output on a HP7475A A3 plotter Simply set the device parameter CUR PLOT hp_A3 using the command edo and execute the plot command The gen erated file is stored in the subdirectory plot code of your home directory with the file name hp_A3 1 The next plot is accordingly stored in the file hp_A3 2 and so on Supported Plotters and their Switch Settings A plotter must be connected to the X32 using the same type of cable that is used to connect a terminal to a RS232 port if not specified differently in the following tables for a particular plotter 10 2 Pen setup edpp edpp allows these parameters to be set for the current plotter i e the plotter speci fied in the device parameter CURPLOT see edo If no valid current p
276. n the directory u exp stan nmr lists intrng See chapter The File Menu nmrquant requires two additional directories u exp stan numr lists basereg u exp stan nmr lists nmrquant containing globally accessible baseline region and nmrquant workfiles When used in automation the intrng and nmrquant and basereg if required files have the same name Output specification All output from the nmrquant command is redirected to the file quant stored in the processed data directory If the molecular weight and a reference weight is entered an extended output is stored The user interface The options list on the left hand side of the main nmrguant display can be divided 9 8 The Simulation submenu P 213 into 4 distinct groups namely 1 manual setup of parameters 2 reading parameters from disk 3 writing parameters 4 others The first three groups can be considered as separate steps which must be per formed sequentially in order to specify all the information required by the pro gram The last group of options are separate from the other functions as they relate to functions which are not involved with the computation Selecting the Define Components field replaces the main nmrquant display with a prompt for the number of components to be defined If the program verifies the number entered is less than the number of number of integral regions a figure is presented containing the proton contribution of each componen
277. nation It is the responsibility of the user to take care of all the effects that may result from this multi tasking feature As you can see from Figure 15 1 you need not use xcmd or CPR_exec for most acquisition and processing commands since they are defined as macros in the command table aucmd h For example writing zg or ft is sufficient to call XWIN NMR s zg or ft commands A terminating semicolon is not required in this case because it is part of the macro definition xcmd or CPR_exec are however required to execute all command combinations not defined in aucmd h e g if argu ments must be specified along with a command The last command in Table 15 1 is an example of how to execute a command dynamically constructed in the AU pro gram and stored in a string variable text The C statement void sprintf text ns d scans would generate a command to set the number of scans from an integer variable scans which the user could have entered on the keyboard Please note Each explicite call of CPR_exec must be preceded by the AU com mand setcurdata This ensures that the XWIN NMR command executed by CPR_exec will be applied to the correct data set which may have been changed within the AU program prior to the CPR_exec call by appropriate commands or by setting data set variables described later xcmd in contrast invokes setcurdata automatically 15 5 Variables P 325 15 5 Variables Since AU programs are C programs y
278. nc tion command will use this parameter value Store2D amp return works similarly However it does not store the parameter with the data set on screen but in the 1D Data Processing Tutorial P 18 parameter file of the last used 2D data set This operation is only useful if the cur rent fid is a row or a column of a 2D fid Finally return will terminate window function mode without saving the adjusted parameter The original value in the parameter file remains unmodified 2 5 Applying the Fourier Transform The next processing step after window multiplication is the fourier transform The result of the fourier transform is the real spectrum used by peak picking integra tion etc and the imaginary spectrum which is only needed for phase correction and can be deleted afterwards if disk space is to be saved see deli command 1 Open the Process menu and select the command Fourier tranform ft The cal culation is executed and the resulting unphased real spectrum is displayed you can also view the imaginary part or again the fid Open the menu Display gt Options for this purpose What happened to the data files We started off with the fid stored in the file u data guest nmr exam1 d I fid Window multiplication left this file unchanged and stored the result in the files u data guest nmr exam1 d I pdata I Ir and u data guest nmr exam1 d I pdata 1 1i The Fourier tranform operates on these files and replaces their conte
279. nd Gaussian shapes the calculation of T1 and T2 relaxation times and the fitting of multi exponential decays Baysian analysis and an interface to P 1 Introduction P2 the MaxEnt maximum entropy package make advanced methods available which are complementary to the Fouier transform e XWIN NMR is capable of processing data acquired with Bruker spectrometers based on Aspect 2000 3000 and X32 computers and with Jeol and Varian spec trometers using JNMR or VNMR software respectively Furthermore XWIN NMR is able to import and export data in the JCAMP DX ASCII format XWIN NMR data can be further processed and analyzed by other Bruker programs such as AURELIA AMIX DAISY WIN NMR and the results can be re imported Please check the release CD of XWIN NMR for brochures of these programs e Different users may start multiple copies of XWIN NMR on the same computer in a network environment provided a suitable X Windows server is installed on a user s PC or workstation Licensing is discussed further below in this chapter e Bruker provides printed and online manuals for software hardware and appli cations XWIN NMR is delivered with a large set of such documentation Please check the Help menu of XWIN NMR or the subdirectories XWINNMRHOME prog docu english containing the documentation files Use the command acroread at Unix level to open the documentation viewer Throughout this manual XWINNMRHOME will denote an environme
280. nd therefore allows for faster acquisition of multi dimensional experiments Lin ear prediction is executed as a part of the 3D transform and is enabled by setting the processing parameter ME_mod to LPfr forward or LPbr backward predic tion The default value of ME_mod is no The strip transform allows you to execute the fourier transform in such a way that the result is not the entire 3D spectrum but only a selected portion of it defined by the processing parameters STSR strip start measured in points from the begin ning of the spectrum and STSI size of region in points A strip transform is use ful if you are only interested in a particular spectral region The result is a file of significantly smaller size which can be handled faster on the display and con sumes less disk space You are also able to set the transform size for the region and therefore its resolution to a larger value than would be possible when tran forming the whole spectrum You may also combine the strip transform with linear prediction The Hilbert transform allows you to generate the imaginary part of a spectrum from the real part More details of these transform options are described in the chapter The 3D Proc ess Menu Phase correction 4 6 1 The 3D phase correction can either be performed during the 3D Fourier transfor mation or at a later time The former method saves computation time since the entire 3D data set only needs to be processed
281. ng and its horizontal position relative to spectrum 1 Both values are monitored in the Info window opened when entering dual mode The buttons sum and diff cause the sum or difference of the two spectra to be displayed While you are in one of these mode you can save the sum or difference on disk Select the command Save amp return from the File menu or from the pop up win dow which appears when you click the return command button The result will be stored under the data set specifications of the so called third data set which may like the second data set be defined in the edc2 dialog window It is automatically called if the third data set already exists and you decide not to overwrite it with the sum or difference The undo command button terminates sum or difference mode and returns to dual display The Display Menu P 306 a tis el m Figure 12 4 Dual display of an acquired lower trace and a simulated spectrum When you enter dual display mode the two data traces appearing on the screen correspond to the real parts files r of the spectra In order to switch to the corre sponding imaginary parts files 7i open the Display menu and click on the com mands Imaginary spectrum 1 or Imaginary spectrum 2 Likewise you may put the fids on screen by invoking the commands Fid 1 or Fid 2 from the Display menu The Display menu offers additional advanced features which help you to quickly
282. nge applied to slope or bias when moving the mouse 2 decreases the change by the factor 2 and DEF restores the default setting of the increment value Terminating integration mode Click on the return button A window appears from where you can select an imme diate return leaving the intrng file unchanged The integrals on screen are not stored in this case and are discarded You can also take this return if you have stored the integrals earlier from the File menu The other return option stores the defined integral regions automatically in the intrng file The return commands can also be accessed via the File menu List integrals li The command li type it in or call it from the Analysis menu will give you a print out of the integration limits and the integral values The output is directed to the currently defined printer or to the screen depending on the setting of the parameter CURPRIN Call the output device editor by typing edo and set CURPRIN to screen if you want to see the integrals on the monitor Otherwise click on the down arrow button rightmost to CURPRIN and select the printer on which you want to get the listing If no printer name is displayed you or your system admin istrator must install one with the command cfpp see menu Output gt Printer plot ter installation Printer names when inserted in the parameter CURPRIN must always be preceeded by a sign If omitted the name is interpreted as a file name and the l
283. ngelhardt and W Boenigk Simulation und automatisierte Analyse von Kernresonanzspektren Weinheim VCH 1987 ISBN 3 527 26550 3 9 11 MAXENT MEMSYSS5 The purpose of this program is to derive spectral features such as line positions and peak widths from NMR data by using probability theory in this particular case the maximum entropy method Maximum entropy is a procedure for inferring positive distributions from limited data Not only 1D spectra but also multidimensional data and images can be proc essed The method enables the best result meaning the most probable spectrum or image to be accompanied by realistic error bars so that the reliability of any result can be assessed MEMSYSS provides quantification of error limits and gives the scientist increased confidence in the interpretation of the results For 1D NMR spectra for example the result is a deconvolved spectrum which rep resents the best fit of the experimental data Parameter set up and execution takes place from within XWIN NMR and the gener ated data are immediately accessible from there MEMSYSS is a product of Maximum Entropy Solutions Limited Cambridge UK It is not a standard component of the XWIN NMR package and must be pur chased as a separate option The following XWIN NMR commands provide a user interface to the MEMSYS5 maximum entropy package 9 11 MAXENT MEMSYS5 P 227 9 11 1 Generate a Point Spread Function psf The command psf gen
284. noise ratio of a 1D spectrum according to the formula SINO maxval 2 noise maxval is the largest intensity value in the frequency range between SIGF1 and SIGF2 The noise is computed from the data points in the frequency range between NOISF1 and NOISF2 according to the algorithm in Table 9 1 These parameters are processing parameters in ppm units They may be entered by typing sigfl etc on the keyboard or using the edp editor You may also set the parameters interactively from the screen Enter the utilies mode by clicking on the utilities button of the button panel Expand the desired signal region so that it fills XWIN NMR s data area and click on the sigreg button This will set SIGF1 and SIGF2 to the displayed region Reset the horizontal scal ing to redisplay the whole spectrum Expand the desired noise region to full The Analysis Menu P 184 noise sqrt Y2 Y Y 3 KY XY N N 1 N N 1D with N number of points in the noise interval NOISF1 NOISF2 Y sum n lt i lt n y Y2 sum n lt i lt n y i y XY sum 1 lt i lt n i y yCi where y n first intensity value in noise interval y 0 central value y n last value Table 9 1 Algorithm of noise calculation screen and click on the noisereg button This will set NOISF1 and NOISF2 to the displayed region The parameter SINO is sometimes used to control the duration of an acquisition While normally the number of scans NS d
285. nsform is requested in a dimension that already contains frequency domain data or 4 data are power or magnitude data processing status parameter PH_mod is ps or mc in any dimension To make the behavior more transparent the raw option with 2D processing com mands forces use of raw data Also supported is the proc option causing process ing to stop with an error message if it is impossible to continue on processed data Note Do not confuse raw data fid or ser and time domain data Processed data may be in time domain in any dimension if no Fourier transform has been per formed in this dimension Linear Prediction The transform commands described so far execute a number of processing steps in The Process Menu for 2D data P 162 7 6 1 the following sequence baseline correction window multiplication Fourier transform phase correction If linear prediction is to be applied this sequence looks as follows baseline correction linear prediction window multiplication Fourier transform phase correction This means that linear prediction is also part of the transform commands in either dimension and is applied to the acquisition data after the baseline correction Usu ally linear prediction is disabled i e the default value of the processing parameter ME_ mod is set to no In order to enable it Me_mod must be set to LPfr for forward LP real data LPfc for forward LP complex data LPbr for backward LP real
286. nsions Adjust the layout if required 6 Output the plot with plot plots plotx fiplot The following sections will describe these steps in detail The setup commands are part of the Output gt Setup submenu Figure 10 2 Printer Plotter installation cfpp Pen setup Cedpp Page layout Cedg Page layout auto expansions edgx Use prepared page layout Crpar Select plotter CURPLOT Cedol Title setti Figure 10 2 The Output gt Setup submenu 10 1 Printer plotter installation cfpp XWIN NMR can plot spectra on plotters with colored pens pen plotters laser printers and ink jet printers The latter two belong to the class of printer plotters i e they are used to print text as well as graphics The devices are connected to a parallel Centronics type or to a RS232 interface of the computer XWIN NMR can operate several devices on different interfaces simultaneously The purpose of the command cfpp is to tell the program to which interface channel a printer or plotter is connected cfpp must be repeated after installation of a new XWIN NMR version 10 1 Printer plotter installation cfpp P 243 cfpp configuration of plotters and printers opens a dialog window according to Figure 10 3 Select Plotter installation for pen plotter Printer plotter installation a aoe ea e wie ae oee fiat E Aie pe Figure 10 3 Initial cfpp dialog window for laser and ink jet printers and Printer installation fo
287. nt in each integral region If a matrix file already exists in the processed data directory you will be asked whether you wish to define a new matrix or edit the existing file For new matrix files you must first define the number of components which contribute to the signals within the integral regions In order to arrive at a solution the number of com ponents must be greater or equal to the number of integral regions Next fill in The Analysis Menu P 210 the matrix with the number of protons and optionally the component names After defining the number of protons select either the Continue button to return to the main nmrquant window or the Define Weights button to for defining com ponent molecular weights and reference weights for weight calculations If the define weights button is selected then all component molecular weights as well as a reference sample weight must be defined otherwise only mole ratios will be calculated 6 On returning to the main nmrquant window by selecting the Continue button from both proton contribution and component weight dialogue windows the files can be saved for later recall by selecting the Save item on the left hand dis play As in the case of the define option the choice of saving the integral base line matrix or all three files is offered 7 Finally click on the process button to perform the calculation The output is redirected to the device specified in the edo parameter CURPRIN 9
288. nt varia ble representing the directory where XWIN NMR was installed e g u e Data output to plotters and printers can be performed in two ways Using parameter driven plotting software including a plot pre viewer commands cfpp edo edg plot or the interactive What You See Is What You Get plot editor XWIN PLOT commands xwinplot autoplot XWIN PLOT is part of the XWIN NMR distribution media The XWIN NMR manual comes in 2 parts This is part 1 and covers XWIN NMR s general features as well as data processing analysis and plotting using the param eter driven plot commands Part 2 covers data acquisition and pulse programming Please note that there are separate manuals for ICON NMR and XWIN PLOT 1 1 Hardware software requirements Please refer to the NMR Software Release Letters manual part number Z30742 1 2 Notation P 3 1 2 Notation Throughout this manual XWIN NMR commands appear underscored e g ft or zg Executing a XWIN NMR command often requires parameters to be set before Parameters are printed in capital letters e g LB or SWH All parameters may be modified by means of a parameter editor or by typing them on the keyboard using the parameter names as commands For example type lb followed by Return to change LB The current parameter value will be printed and you may change or confirm it with Return You may skip the dialog by entering the desired new value behind the command name sep
289. ntly existing parameter sets You can overwrite one or define a new one by entering a new name After closing the dialog box wpar allows you to select which of the parameter files acqu proc meta outd are to be copied to the parameter set directory In order to set up an and save an experiment proceed as follows define the acqui sition parameters using the command eda define the processing parameters with edp the plot parameter with edg and the output parameters with edo Execute the experiment to verify all parameters Then save everything via wpar The saved parameter files can be restored with the command rpar wpar may also be entered on the command line followed by arguments e g wpar cosy all would copy all parameter files of the current data set to the directory u exp stan nmr par cosy In addition to the keyword all you could also use any of acqu proc plot outd in order to copy acquisition processing plot or output device parameters only It is also legal to use wildcard characters For example the command wpar C would display all existing parameter sets beginning with the letter C The com mand wpar H Z would display all existing parameter sets beginning with the letters H LJ Z 5 6 6 Copy parameter files from rpar The purpose of the command rpar is to overwrite the parameter files acqu proc meta and outd of the current data set by parameter files contained in the directory u exp
290. nts with the transform result r now contains the real spectrum i the imaginary part 2 Like most XWIN NMR commands you can initiate the transform also via key board type ft followed by Return 3 Exponential multiply em and Fourier transform ft can be executed with a single keyboard command ef Be sure that SI and LB have been set before 2 6 Phase correction After the Fourier transform the spectrum is not normally a pure absorption spec trum XWIN NMR provides an automatic and a manual way to correct zero non frequeny dependent and first order proportional to the frequeny phase distor tions Manual phase correction must be applied in cases where the automatic cor rection is not sufficient 2 6 Phase correction P 19 Automatic Open the Process menu and execute the command Auto Phase correction apk or type apk on the keyboard The corrected spectrum is displayed when apk termi nates The computed phase parameters PHCO and PHC1 in degrees can be inspected or modified by typing the commands phcO and phcl or by calling the parameter editor edp When an fid is transformed again or acquired again under similar conditions and then transformed the same phase parameters can be applied In this case the command pk can be used which uses the currently valid PHCO and PHC values but does not recalculate them like apk The command apkO only calculates PHCO and uses the current setting of PHC1 to correct the first
291. nu Select one of the commands Save row col as TEMP or Save row col as PROCNO The calculation of projections can also be initiated with the command proj type it in or call it from the Process gt Calculate projections menu External spectra Click on ext to view an arbitrary but suitable external spectrum to be drawn along this axis You must define this spectrum using the edg plot parameter editor Enter edg and select EDPROJ1 or EDPROJ2 to open the parameter box for the spectrum to be drawn along the F1 or F2 axis Click on PFIEXT PF2EXT to see the table of supported projection types Choose external Use the parameters P1 2 DU P1 2 USER etc to specify the name and location of this spectrum This is also the correct procedure to set up a 2D plot with external spectra as already described in the section about plotting You may vertically scale the displayed spectrum using the 2 and 2 buttons located below the row col buttons 2D Data Processing Tutorial P 60 Partial projections A partial projection is not calculated over the whole spectrum but only over a specified region You must define the region and start the calculation of the partial projection before it can be displayed Click on calc at the right side of the part but ton for the desired dimension The program will display a cross hair cursor you can move around with the mouse Clicking the middle mouse button will display and set the first region limit this is
292. nusoids are there in the data and in fact provides a quantitative statement of the intuitive rule that of several models which fit the data equally well the simplest model should be used The program is therefore capable of performing a fully automatic analysis of the data including the determination of the most probable number of spectral compo nents in the data along with all the corresponding parameters amplitude integral frequency and decay rate line width as well as phase in a black box fashion with out the need of setting any parameters The method proves to be very powerful and reliable and data with very broad overlapping signals together with sharp closely spaced lines and shoulders that almost disappear in the noise are easily handled The Bayesian analysis module in XWIN NMR can perform all of the following tasks parameter estimation signal detection and model selection The user can control every detail of the analysis or more importantly use the program in a black box fashion without having to specify any parameters 9 12 Bayesian Analysis P 233 9 12 2 9 12 3 9 12 4 How the Program Works In parameter estimation the number of exponentially decaying sinusoids to be fit to the data is specified by the user and the optimal parameters are then determined by finding the maximum of the probability surface In signal detection the free induc tion decay is searched for positive evidence of damped sinusoid
293. o receive a carbon copy e subject subject e attachment filename will be added as an attachment to the outgoing message e message text If you click on the button SEND the program will start the JCAMP conversion and mailing according to the parameters you have defined Click on the Last Mail command from Report menu to see whether your electronic mail was sent successfully If you want to start smail without dialog windows you may type the following on Xwin nmr s command line xwish2 f s prog tcl xwish2_scripts smail out usr people hb exam1d dx data 0 mode 3 ti examld or hb ow hb addr hb bruker de sub Test_smail att usr people hb examld dx lt cc tgk bruker de gt Parameter cc is optional The tojdx parameter are e out usr people hb exam1d dx output file name of output file e data 0 output type e mode 3 compression mode e ti examld title e or hb origin e ow hb owner The zmail parameters are e addr hb bruker de to_list e sub Test_smail subject The File Menu P 110 5 11 5 11 1 e att usr people hb exam1d dx name of the attachment file eg DX file e cc tgk bruker de cc list Conversion Conversion commands are used to import data into XWIN NMR and to export XWIN NMR data into other formats Figure 5 17 From A3000 To A3000 A3000 file renaming MSL configuration From JCAMP_DX To JCAMP_DX From JNMR Cjconv ee ey ae r a7 Figure 5 17 The File gt Conversion submenu
294. o your spectrum If you are only interested in the found integral regions but you want to keep the original spectrum you must re process the fid by typing efp equivalent to the command sequence em ft pk after execution of abs This will restore the non baseline cor rected spectrum but keep the intrng file generated by abs A variant of abs is absf which is identical to abs but does not operate on the entire spectrum Instead it only looks at the spectral region defined by the processing parameters ABSF1 low field limit and ABSF2 high field limit There now follows a description of how you can influence the way abs defines the integration limits You can modify the parameters involved by entering their name on the keyboard in lower case characters or by calling the processing parameter editor edp Controlling the separation of integrals Assume your spectrum contains multi plets and you want to have a single integral drawn over the entire multiplet not integrating the individual lines separately The automatic routine would however recognize individual regions when the peaks in the multiplet come down to the baseline In order to force the program to join the individual regions to a single one you can set the processing parameter AZFW to a desired ppm value If two integrals are farther apart from each other than this value they will stay individual integrals Otherwise they will be combined to a single one Extending integral
295. oaded set Save save data set to disk Run quit the editor and run the selected program the programs run in background Quit quit the editor 9 10 1 2 Select the program type Use the Daisy Program Type button to specify the program for which parameters should be loaded You must choose a program before a data set can be loaded and edited 9 10 1 3 Select a data set The editor uses the following from the XWIN NMR foreground data set the experiment name the experiment number the processing number The full path is displayed in the header line Internally the programs have continu ous numbers 1 for SPECPREP 2 for DSYMPLOT 3 for DCYMPLOT 4 for DAVSYM1 5 for DAVSYM2 6 for DAVCYM1 7 for DAVCYM2 The concept of the directory naming convention is the following The files of an NMR experiment of the user guest are stored in u data guest nmr 135TFB 5 pdata 4 The Analysis Menu P 216 which means the name of the experiment is 357FB the experiment number is 5 and the processing numberis 4 To make this experimental data set readable for the iterators SPECPREP creates files in the correct format The name of a SPECPREP data set contains the following parts experiment name same as the experiment experiment number e number of experiment 1000 processing number p number of experiment 10 SPECPREP processing number This results in the following path u data guest nmr 135TFB 1005 pd
296. oceed as follows Write an XWIN NMR macro e g by entering the command edmac cpanl A text editor window will be opened Insert the line 13 1 Command panel cpan P 315 xwish f u exp stan nmr tcl cmdpanel lt panel file name gt TITLE Command Panel Example BUTTON NEWROW edc new Define new data set BUTTON SAMEROW eda eda Acquisition parameter setup BUTTON NEWROW Zg Zg start acquisition BUTTON SAMEROW lb 0 3 LB set line broadening to 0 3Hz END Table 13 1 Panel file structure The Windows Menu P 316 Command Panel Example now i aj Figure 13 2 Panel resulting from example panel file Specify your desired panel file and terminate the text editor You have created a new XWIN NMR command cpan1 which will come up with the desired panel 13 2 Plot preview The plot preview commands send the plot output into a screen window cf the fig ures of 1D and 2D plots in the chapters The 1D 2D Output Menu You may change plot parameters and observe the effect of the modification The plot layout may thus be tailored until it is satisfactory The following preparations are necessary to enable the use of the preview com mands e The plotter configuration command cfpp must have been executed This task is normally accomplished immediately after XWIN NMR installation e The current plotter CURPLOT must be defined command edo This is impor tant because the
297. oefficients file name of the smoothing filter to be used must be entered in the processing parameter DFILT filt may be applied to the acquisition data as well as processed data of the current data set depending on how the processing parameter DATMOD is set raw or proc 6 18 Miscellaneous operations P 151 6 18 Miscellaneous operations 6 18 1 Zero file contents zf zf produces a processed data set files Zr and i which contains only zeroes The current fid remains unchanged 6 18 2 Define NZP parameter nzp The processing parameter NZP is used to define an integer required by the com mand zp Type nzp or set it NZP from edp 6 18 3 Zero first NZP points of data zp The first NZP points of the data are set to zero by zp NZP is a processing parame ter 6 18 4 Define NSP parameter nsp The processing parameter NSP is used to define an integer required by the com mands ls and rs 6 18 5 Left shift data by NSP points ls With ls the complete data field is shifted NSP points to the left NSP is a process ing parameter The end of the data field is zero filled 6 18 6 Right shift data by NSP points rs With rs the complete data file is shifted NSP points to the right The left of the field is zero filled 6 18 7 Reverse data rv By rv the data are reversed about a line vertical to the time or frequency axis and going through the middle of the data set The real and imaginary part of the spec trum ar
298. ogin name for which the data were created and exam d is the data set name You can learn more about data and parameter files in the description of the command New in the File menu 2 2 Manipulating fid or spectrum on the screen You should now have Figure 2 1 on the monitor representing the standard 1D lay out The data area shows the fid Perhaps the data scaling on your display isn t exactly what you re looking for The following pararagraphs describe how you can adjust the data according to your needs If you want to look first at some acquisition parameters which show the status of the fid for example its time domain size TD or the number of scans NS which accumulated the fid you can use the command dpa display acquisition status parameters in the menu Output gt Display status 2 2 Manipulating fid or spectrum on the screen P 11 Figure 2 1 1D layout with fid No transformed data available yet pars The button panel at the left side of the XWIN NMR window allows you to interac tively scale shift and expand the data These operations are screen operations only and do not modify the data file itself You must click on a button to execute 1D Data Processing Tutorial P 12 the function Some buttons require that you keep the left mouse button pressed while the cursor is located in the command button field and then move the mouse When you move the cursor over the command buttons without clicking their function
299. ommand expinstall copies them to the directory scl psreg This is identical to sreg but only those regions in the file which lie within the plot region defined by F1 F2 will be included psreg is an analogue to sreg just as pireg is to ireg noise Instead of the intensity at a certain position of the spectrum the intensity height of noise is plotted with the height CY cm ASSFAC If required the second largest peak can be used for the vertical scaling of a plot rather than the biggest peak This might be desirable if the biggest peak is of no interest for the user and would cause the peaks of interest to be plotted too small The processing parameter ASSFAC accounts for this case If ASSFAC gt 1 the second largest peak will be used as reference for plot scaling if h2 lt hmax ASSFAC The 1D Output Menu P 254 where h2 is the intensity of the second biggest and hmax that of biggest peak If this condition is not fulfilled the biggest peak is taken as reference If ASSFAC lt 1 two plots will be generated on two sheets of paper if h2 lt hmax abs ASSFAC The first plot is performed with the second biggest peak as reference the second plot with the biggest peak However the second plot is omitted in the case of 2D projections or if it was issued with the commands plots or plotx If ASSFAC has any other value the biggest peak serves as reference The search for the second biggest peak is not performed in the vic
300. ommend to set CLIP to no An additonal plot page is generated con taining the title By clicking on the button Next Page you may toggle through all additional pages generated and you can check whether parts of the plot appear on extra pages due to improper setting of layout parameters If the last page is reached you must click on Restart to get the first page back A final preview command remains to be discussed viewmg It displays plots gen The Windows Menu P 318 erated with the command plots Remember that plots does not output a plot directly to the plotter but stores it in a queue This is useful as you might want to add more plots to the same sheet of paper using plots The command fiplot flush queued plot would output all queued plots to the printer or plotter while viewmg draws everything in the preview window Chapter 14 The Help Menu XWIN NMR includes the complete software manual as online documentation If Help Tear of Figure 14 1 The Help menu you select an item from the Help menu the corresponding document file is dis played Document files are stored in the directories XWINNMRHOME prog docu english xwinacqu XWINNMRHOME prog docu english xwinproc P 319 The Help Menu P 320 containing the chapters about data acquisition and processing viewing respec tively The file name extensions of the document files is pdf Their storage format is of type Adobe Acrobat PDF As soon as y
301. on and peak picking P 183 absolute frequency of the reference signal and BF1 is the basic spectrometer fre quency The checklockshift command sets the parameter LOCSHFT to TRUE The parameter LOCSHFT is checked during sref checklockshift is invoked auto matically at the end of an acquisition zg The only task of sref is to correct the remaining error of a few Hertz by searching for the reference signal in a small interval around SF The interval size may be specified in the Width column of edlock Finally sref sets the corrected value of SF and the processing status param eter OFFSET which is the chemical shift of the first data point of the spectrum From this value the program can calculate the shift value of any data point The sref procedure described so far is valid for data acquired with instruments equipped with the BSMS digital lock If LOCSHFT is FALSE the algorithm orig inally supplied for data sets measured with spectrometers equipped with an SCM unit is employed In this case the basic setting of SF is computed from the Dis tance parameter in the lock table For BSMS type data sets this algorithm delivers incorrect SF values 9 3 Integration and peak picking These commands are described in detail in the chapters 1D Processing Tutorial and 2D Processing Tutorial 9 4 Calculate signal to noise ratio sino The command sino calculates sets and prints out the processing status parameter SINO the signal to
302. op counter lists ds data set lists masr MASR rotation values Table 5 6 Types of parameter lists Since pulse CPD gradient programs and macros are stored in the same directory the corresponding list types pp cpd gp and mac will also be displayed when edlist is called It is therefore possible to edit pulse programs etc via the dedicated commands edpul etc but also via edlist by specifying the corresponding list type The command edlist may also be entered on the keyboard followed by the type of the desired list or followed by the list type and the desired list name which may contain wildcard characters see edpul and how to change the default text editor for The File Menu P 88 details Format of parameter lists The length of a parameter list is unlimited A delay or pulse list Table 5 7 left column contains one duration value per line 10s O 500 13 20m 3000 1 5u 3150 Table 5 7 Example of a delay left and frequency list right followed by a time unit s seconds m milliseconds u microseconds The values in a delay list are interpreted by the variable delay statement vd in pulse programs The values in a pulse list are interpreted by the variable pulse statement vp in pulse programs These commands use the list whose name is defined in the acquisition parameter VDLIST or VPLIST respectively The first line of a frequency list Table 5 7 right column contains the
303. or any similar plot In order to make such a layout available for your current data set enter the command rpar or call it from the File gt Copy menu Select the desired experiment from the displayed table then select the plot entry from the next table and click the Copy button to copy the meta file of the chosen experiment on top of the current meta file in your data directory You can now use edg to view the layout parameters and after having defined the desired spectral region to be plotted enter view to preview the plot result Chapter 3 2D Data Processing Tutorial This chapter presents 2D data processing based on the data set exam2d The data set is stored in the directory u data guest nmr In order to have full access permis sions to it you should have a user guest installed on your system and be logged in as guest Start XWIN NMR by typing xwinnmr r The r option ensures that every thing is cleaned up before starting the program even if the last session was termi nated by some problem The program will start without displaying a data set Instead the XWIN NMR logo will be shown in the data area In later sessions you can start XWIN NMR without specifying the r option and you will immediately get the last used data set displayed 3 1 Getting the data set The first step is to get the 2D spectrum exam2d on screen Open the File menu select the Open entry and from there the command dir You should get a dialog box
304. or by typing in the command edp or by opening the Process menu and selecting General parameter setup edp A dialog box is displayed containing all processing parameters You can locate SI enter the desired value and exit from the dialog 2 4 Applying a window function to the fid P 15 window More details can be found in the description of edp It should be men tioned here that the contents and layout of the edp dialog box can be tailored by the user by editing the so called format file u exp stan nmr form proc e 2 4 Applying a window function to the fid The widest used window function is the multiplication of the fid with an exponen tial weighting function which forces the end of the fid toward zero It leads to some line broadening as well as to an improvement in the signal to noise ratio There are several ways in XWIN NMR to apply such a function 1 Open the Process menu and activate the command Enter line broadening factor Lb Type in the desired value in Hertz 2 0 in our exam d data set Open the Process menu again and select the command Exponential multiply em The program will apply the function to the fid and then display the result Please note The program does not overwrite the measured fid with the expo nentially multiplied values Instead it creates new files containing the result This behaviour is actually true for all processing commands of XWIN NMR which will never destroy your acquisition data The
305. or ppm These parameters ascertain that only those regions listed in the reg file which are at least partially contained in the interval EXTF1 EXTF2 are plotted Only plot those regions containing signals The parameter SUPPRESS controls whether only those regions which contain at least one signal searched for with pp are plotted Horizontal scaling The spectral regions listed in the file reg are plotted with the horizontal scaling specified in the parameters SCALEP ppm cm or SCALEH Hz cm The lengths of the region plots are adjusted accordingly Automatic vertical scaling The vertical scaling of the region plots and their integrals is determined auto matically and depends on the room available i e on the difference DHEI SZERO which is the room above the spectrum s zero line DHEI IZERO for integrals In edgx the parameters used for normal plots CY and IHEI are not available The vertical scaling is always an integer multiple of the scaling of the overview spectrum the overview spectrum can be plotted on the same page along with the auto expansions as will be discussed later For the scaling of a region XWIN NMR looks at the intensity of a reference signal in this region Only those signals are considered which are smaller than the plot reference signal of the over view spectrum Except for this restriction the reference signal of a region is the one with maximum intensity therein if the processing parameter ASSFACX i
306. order angle The command apks only calculates PHCO and PHC1 but uses a an algorithm different from apk Manual Manual phase correction can also be invoked from the Process menu It is more convenient however to click the command button phase at the left side of the XWIN NMR window The upper part of the command button panel at the left side is identical to the standard mode Further below there are a few additional buttons required by man ual phase correction Manual phase correction is executed in two steps First phase the biggest peak or a peak of your choice first the so called reference peak for zero order correction This defines the zero order phase PHCO Position the cursor on the command but ton PHO and keep the left mouse button depressed while moving the mouse The current PHCO value is displayed in the small info window at the upper right of the screen When the zero order correction is done use the PH command button in the same way to phase another peak distant from the zero order reference peak The first order phase is also shown in the info window When entering phase mode the zero order reference peak is automatically set to the biggest peak in the spectrum If you click on the button biggest a vertical line indicates the peak position If you prefer to use a different one click on the button cursor When you now move the cursor into the data area of the XWIN NMR win dow it will run along the spectrum curve Pos
307. orepar3s If a parameter is an array such as PO P31 or DO D31 the array index must be sep arated from the parameter name by a space character e g storepar P 1 amp f1 Fetching parameters The commands fetchpar fetchplpar fetchplxpar and fetchplwpar are the inverse commands to storepar etc and read the specified parameter from the correspond ing parameter file into a variable of the same type as the parameter see Figure 15 2 Note that the variable must be preceded by the C address operator amp other wise the AU program is likely to crash For two and three dimensional data sets the additional commands fetchparl and fetchpar3 are provided Status parameters may be accessed with the respective commands fetchpars fetchparls fetchpar3s Copying parameter sets The XWIN NMR commands wpar and rpar which copy parameter files to or from the directory u exp stan nmr par may be called from AU programs in the form wpar cosy all rpar proton proc rpar proton acqu proc The first argument specifies the parameter set name which is a subdirectory of the par directory above The second argument is one or more of the list acqu proc plot outd and selects the parameter files to be copied 15 8 Loops P 329 15 8 Loops Since AU programs are C programs all C loop control structures are legal For the ease of use XWIN NMR provides the loop command times n
308. orizontally or vertically The purpose of this button is to draw a box around the spectrum part you want to zoom Click on the button Position the cursor to the desired screen position Now keep the left mouse button pressed while moving the mouse A rectangle will be drawn until you release the mouse button Then the rectangle will remain on screen with small squares at the edges and in the center The center square allows you to move the rectangle to another screen position the other squares serve to resize the area of the rectangle Again in order to activate such a function move the cursor into a square and move the mouse while its left button is pressed Click the right button to zoom the region define by the rectangle 1 Shift the zero line of the spectrum or fid to the center of the screen 2 Shift the zero line of the spectrum or fid to the bottom of the screen 3 Shift the zero line of the spectrum to an arbitrary screen position Move the mouse while the left button is pressed and the cursor is located within the com mand button 1 Shift data left by 1 2 screen width 2 Shift data right by 1 2 screen width 1D Data Processing Tutorial P 14 1 Display a grid which generates a fixed screen partitioning 2 Display a grid bound to the coordinate axes The grid lines change depending on the selected zoom area Toggle the x axis units between Hertz and ppm If a fid is displayed the axis unit are seconds from 0 to the
309. ormat you usually want to plot the parameters as well However only those acquisition parameters should appear that were actually used in the experiment s pulse program This is possible by using a CONDITIONAL state The File Menu P 126 ment entered into the format files for the parameter plot XWIN NMR needs the corresponding Aspect 2000 3000 pulse program to generate a list of the parameters to be plotted The nameof the pulse program must be con tained in the parameter PULPROG usually set automatically during the conver sion of the Aspect 2000 3000 data set The XWIN NMR release tape contains the required Aspect 3000 pulse programs After the installation of the release they are stored in the directory u exp stan nmr lists pp 3000 However these pulse programs have a special format which can be used only for plotting and they are no longer suitable for experiments The special format can be recognized by the character sequence at the beginning of these files You can add your own pulse programs to this directory As soon as a plot is requested they are converted automatically into the corresponding format and will stay in the directory given above 5 11 2 JCAMP DX Format XWIN NMR supports the JCAMP DX Standard 5 0 Implementation Version 1 0 draft but currently only for the exchange of one dimensional FIDs and spectra The two conversion directions are available through the following commands XWIN NMR data set to J
310. ormatee se e ie a E cece eee ene P 335 1652 2Dspecttas yaos n A Ee a eoa Saeed aE e de NE P 335 16 6 3D Specta s miet D a ar a E EE E E e chee 14 dette P 336 16 7 Pulse S E T S Yeti a Yen a Sa e athe NTS P 338 16 89 Other filesini a Su oo Sy a a r A E ee es P 340 Index TETEE E E E A E E I 1 XWIN NMR Comment Form VII Chapter 1 Introduction XWIN NMR is the standard NMR software package provided by Bruker for spec trometer control and for visualising processing and printing the acquired data The program features the following concepts e Data acquisition using Bruker AVANCE and AMX ARX ASxX spectrometers XWIN NMR supports the power user by allowing for flexible control of all acquisition hardware and software parameters including the design and visual isation of pulse programs real time observation of fid lock signal and trans mitter output and monitoring temperature and magic angle spinning rate The routine user is supported by the simple user interface of ICON NMR which allows for painless execution of complicated measurements using Bruker s standard library of experiments or experiments designed by the laboratory manager e Acquisition of n dimensional data sets and processing of 1D 2D and 3D data sets Bruker s advanced analysis package AURELIA AMIX also treats 4D data and the complicated spectra of mixtures e The data analysis part of XWIN NMR provides line deconvolution based on Lorentzian a
311. ormation window when the plot command is given unless the message is disabled due to the setting of the PlotMsg system variable see command setres When a data file is plotted a copy of it realized via a link is used stored in the directory DU data USER plotfiles lt ProcessID gt created by the plot command This ensures that you can further process the data file even if the plot is not yet complete 10 9 Screen dump P 271 10 8 1 Show status uxlpstat uxlpstat lets you examine the lp status Particularly you can see by the request ids which plots are still waiting for execution For more information on the Ip spooler please refer to the documentation of the operating system e g use the Unix com mand man Ip uxlpstat corresponds to the Unix command Ipstat 10 8 2 Cancel plot print request uxcancel uxcancel allows you to cancel a plot request by specifying its id number If plotting is already in progress you may have to reset your plotter printer afterwards uxcancel corresponds to the Unix command cancel 10 9 Screen dump This command should only be used on AspectStation computers On Silicon Graphics systems we recommend the snapshot program snapshot allows you to make screen dumps of any portion of the monitor and store it in a so called rgb file Programs are available also from public domain or shareware such as convert and xv to convert rgb to any other bitmap format such as bmp ps epsi
312. orner are given by the parameters PXULEFT PYULEFT cm The width is given by PWIDTH cm The height of the parameter window is determined by the number of spectral parameters to be plotted so that only the width need be specified For the same reason its posi tion is given by the upper left instead of the lower left corner In order to plot a certain plot object use edg to set the corresponding object param eters to yes SPECT spectrum TITLE title XAXIS x axis YAXIS y axis INTEG integral PARAM parameter list I LABELS numeric integral values and PLABELS peak list If one of these parameters is set to no the cor respoding object is omitted from the plot In order to set up the layout parameters for a plot object click on the corresponding edit entry EDSPECT EDTITLE EDAXIS EDINTEG EDPARAM EDPLABL Please noted that all plot parameters contained in the edg dialog window pages may also be typed in on the keyboard using lower case characters e g cy followed by Return or cy 20 followed by Return The spectral window This window is subdivided into four non overlapping windows plottet from bot tom to top 1 X axis with height XHEI cm 2 Numeric Integral Values with height ILHEI cm 3 Spectrum and Integral with height DHEI cm 4 Peak List with height PLHEI cm The 1D Output Menu P 250 10 3 1 1 10 3 1 2 10 3 1 3 If the sum of these heights exceeds the specified height of the spectr
313. ost important parameters you must set in the edp window are SI WDW PH_mod for F and F2 and MC2 for F1 F2 is the dimension defined by the acquisition dimension of the 2D experiment and FZ is the orthogonal dimension defined by number of fids acquired in a 2D experiment The parameter SI specifies the number of real points the spectrum should have after the transform in the corre sponding dimension The parameter WDW allows you to select an appropriate window function With PH_mod you can select whether to apply phase correction or not For phase sensitive spectra an extra step is usually required to find the cor rect phases Phasing is then performed using extra commands after the transform PH_mod also allows you to select magnitude or power spectrum calculation XWIN NMR also allows you to modify the parameters by typing the parameter names in lower case letters on the keyboard For example the command si allows you to enter the SI parameter for the F2 dimension and the command 1 si is used for the F7 dimension The command wdw allows you to enter the WDW parameter for the F2 dimension and the command 1 wdw is used for the FZ dimension The command lb allows you to enter the LB parameter for the F2 dimension and the command 1 lb is used for the F1 dimension etc Please note 2D processing commands do not overwrite the measured 2D fid with the processed values Instead they create new files containing the processed data The 2D fid
314. ot parameter TITNAM see command edg must be set to the full path name of the info file or simpler to TITNAM info By default TITNAM is set to title which is the title file set up via the command setti If both the default title and the info file should be plotted you must execute a first plot using the command plots containing e g spectrum parameters and title Afterwards a second plot must fol low again executed via plots in order to put it on the same sheet of paper For the second plot however spectrum and parameter output must be disabled command edg Only the title plot may be enabled with TITNAM info The command The File Menu P 96 flplot will flush both queued plots out to the printer plotter Please refer to the Out put gt Plotting menu for more information on the various plot commands Frequently the user has stored a large number of data sets on his disk The info file may also be used to identify a particular data set by searching for an item con tained in the info file In the example above the sample identification number is P 2740 Lets assume the user s login name is guest and his data are stored in the disk partition u Then the following command would search in all info files of the user s data sets for the sample id grep P 2740 u data guest nmr info The two asterisks indicate that all existing data set NAMEs and EXPNOs should be included in the search The command must be g
315. ot slash then the current data set directory is also the starting point but for each occurrence of Uxnmr moves up one step in the path name Example TITNAMG title4 is resolved to DU data USER nmr NAME EXPNO pdata title4 and TITNAM info is resolved to DU data USER nmr NAME EXPNO info With the latter example it is thus possible to print out the info file which was set up with the command edinfo and which is stored hierarchically together with the acquisition data If TITNAM is not defined at all XWIN NMR automatically substitutes the name title for it so that the parameter TITNAM only needs to be defined if the title text is to be taken from a file other than title The command setti is used to set up this file title in the current data set directory This command calls the system s text edi tor If other files are to be used as title files then these have to be edited by directly calling the system editor As has already been described in the beginning of this chapter the position of the The 1D Output Menu P 258 title window is determined by the parameters TXLLEFT and TYLLEFT all in cm with the following exception If the plot parameters LIMITS and ADJUST see below for their discussion are set to region and CX respectively the total length of the plot is not known in advance In order to avoid overlapping of spec trum and title the following parameters are effective TPOS now determines the posit
316. ottom left corner of the sheet and are plotted one after the other The following rule applies to single sheet plotters and endless paper plotters with PAPERFD single if the next region completely fits onto the same sheet it will be plotted there otherwise a paper feed is performed If the plot of a single region already exceeds the size of the paper the horizontal scaling is increased by an integer factor On endless paper plotters operating with PAPERFD muiltiple all partial plots are done in sequence After the last plot so much paper is advanced that the length of the total plot that is the paper consumption of all region plots together becomes a multiple of FAMOUNT top of one In this case the overview spectrum as well as all the regions specified in the file reg are plotted First the overview spectrum is plotted according to the layout parameters set with edg The regions are plotted above the overview spectrum The sign of the parameter ASSFAC which specifies the reference signal for scaling the overview spectrum is ignored If there is no signal in the region of the overview spectrum and the parameter SUPPRES yes the overview plot is omitted and the region plots are done as for LAYOUT separat The parame ters CLIP MIRROR and ROTATION for the overview spectrum are ignored The three main windows of the overview spectrum i e spectral title and parameter window are positioned on the paper independent of the values of the paramete
317. ou click on a menu item of the Help menu XWIN NMR will display the corresponding document file using the Adobe Acrobat Reader software or the public domain tool xpf of Derek B Noonbourg Please note that for AspectStation systems and IRIX versions lt 5 3 only the latter program is available The viewers are installed from the XWIN NMR release media at installation time of XWIN NMR The Index and Contents entries of the Help menu cause the display of a keyword index and a table of contents Both are organized as hypertext You may click on an index entry such as ft command click on the page number or on a chapter or section number in the table of contents The document file containing the selected item will be displayed with the correct page placed on screen Apart from the XWIN NMR manual the Help gt Other Topics submenu provides a number of other NMR related manuals You may enter the command help on the keyboard In this case the contents of the XWIN NMR manual will be opened from where you can switch to a desired chapter via hypertext click Any document may be opened from within XWIN NMR by entering the following command on the keyboard xhelp lt document path name gt The path name is absolute if it begins with a character Otherwise the specified path is appended to the initial path XWINNMRHOME prog docu english Chapter 15 Writing AU Programs 15 1 Introduction AU automation programs provide in
318. ou may declare your own variables at the beginning e g int variablel float var3 char string 256 etc Table 15 2 shows int il i2 13 float f1 f2 f3 double d1 d2 d3 char text 101 Table 15 2 Predefined variables for free use predefined variables which you may use according to your needs In contrast the predefined variables of Table 15 3 have a well defined meaning in AU programs char name 15 type 15 disk 15 current data set parameters user 15 int expno procno type nmr char name2 3 15 type2 3 15 disk2 3 15 user2 3 15 int expno2 3 procno2 3 parameters for 2nd and 3rd data set correspond to edc2 settings int loopcount1 loopcount2 counters associated with the AU loopcount3 commands times times2 times3 path name of the parameter file con taining the current data parameters char curdat NAME TYPE DISK USER EXPNO PROCNO of the current data set Table 15 3 Predefined variables with predefined meaning 15 6 Selecting a data set The AU command getcurdata makes the data set currently visible on the screen Writing AU Programs P 326 available for manipulation getcurdata is therefore often the first command in an AU program For example a program consisting of the two commands getcurdata and ft would execute a Fourier transform on this data set Furthermore getcurdata sets the current data set parameters of Table 15 3 which are then available for man
319. out interactively on the screen and output it to almost any kind of printer or into a file for inclusion in documents For details please refer to the XWINPLOT manual The command autoplot allows you to plot the current spectrum using an existing plot layout constructed earlier The name of the layout must be defined via the parameter LAYOUT Enter the command edo to set it A number of example layouts is provided Parameter driven plot This is the older XWIN NMR plot system where a plot layout is not defined interac tively like in xwinplot but via a set of parameters to be defined using the com mand edg Before you can output your spectrum integrals peak lists and parameters on a laser printer inkjet thermo printer or pen plotter you or your system administrator must have made known your plotting device to XWIN NMR using the command cfpp type it in or call it from the Output menu This work has usually already been done after XWIN NMR installation cfpp also allows you to check which print ers plotters are currently known to XWIN NMR A detailed description of cfpp can be found in the Chapter The Output Menu This menu in fact contains all details on plotting The following is a recipee how to generate plots quickly XWIN NMR lets you configure several plotters More than one plotter may be con nected to the computer and different plots can be executed at the same time on them This requires that for each data set to be plotted the
320. own menu will contain commands to process 1D data sets if a 1D data set is visible on the screen and 2D commands if the current data set is a 2D spectrum or 2D free induction decay Under certain circumstances it might not be meaningful to execute a command from a menu The menu contents then appears to be grayed i e the intensity of the characters is reduced 3 The data set info a line showing the name of the current data set 4 The data display area with an array of data manipulation buttons which allow quick access to frequently used operations These buttons depend on the context and will for example be different for 1D and 2D data sets They are displayed at the left side of the window An extended mode is provided showing even more buttons for the experienced user In 1D mode you may optionally display the buttons at the top of the window from left to right below the menu bar Enter the command setres to switch between these modes When you exit from XWIN NMR the current setting is saved 5 The command line for keyboard input A large number of commands usually executed from the pull down menus may also be activated by typing them in The command names are displayed within the menus enclosed in brackets For example the Process menu contains an entry fourier transform ft In order to execute this command from the keyboard type ft followed by the Enter key The command line can be edited using the mouse place the cursor at t
321. ox where the data sets examld exam2d and exam3d are listed If there are other data sets in the directory u data guest nmr they will also appear in the box Click on exam3d in oder to instruct the program to make this data set the current data set XWIN NMR will automatically show the 3D layout because it identifies exam3d as a 3D data set The identification is not performed via the name of the data set but through the contents of the parameter file meta stored in the directory u data guest nmr exam3d 1 pdata I For space reasons only the acquisition data P 63 3D Data Processing Tutorial P 64 of exam3d are delivered on the release tape You must enter the transform com mands tf3 tf2 tfl in this sequence to execute a 3D transform type in the com mands followed by Return or invoke them from the Process gt Fourier transform menu The commands will ask you whether to store the imaginary parts You may answer n for no for now to save space on disk An imaginary part is needed if a phase correction is to be applied in the corresponding dimension You may re transform the data later for this purpose and answer y to the question or alternately start a Hilbert transform to obtain imaginary parts from the already existing real part After tf3 tf2 tfl are finished the transformed spectrum will not yet be visible on the screen You must click on the display button on the left hand button panel in order to initiate the calculation of pea
322. p and li integrals in one listing lippf always works on the full spectrum remember that all other commands consider only the defined region As you can see from the following examples signals are listed by peak number address frequency in Hertz ppm and intensity The address is the data point number in the spectrum file at which the peak is located It is not an integer because the true maximum usually lies between two data points and is found by the peak picking algorithm via parabolic interpolation Example of a list generated by pp DU u USER guest NAME examld EXPNO 1 PROCNO 1 2 10 Peak picking P 33 F1 8 221lppm F2 4 10lppm MI 1 82cm MAXI 31 86cm PC 4 000 ADDRESS FREQUENCY INTENSITY Hz PPM 1 2799 1 3446 439 6 8946 24 83 2 2851 1 3431 485 6 8647 8 57 3 2 8 13 s 6 3424 995 6 8517 10 58 4 3027 9 3380 557 6 7628 2 29 5 3036 3 3378 163 6 7580 3 24 6 3057 8 3371 963 6 7456 TI 22 7 3083 2 3364 655 6 7310 L321 8 3110 4 3356 826 6 7153 3 68 9 7174 5 2186 748 4 3746 7 74 10 7223 4 2172 687 4 3465 8 38 11 7475 8 2100 023 4 2011 5 47 12 7498 4 2093 505 4 1881 5 49 Example of a list generated by pph DU u USER guest NAME examld EXPNO 1 PROCNO 1 F1 8 221lppm F2 4 10lppm MI 1 82cm MAXI 31 86cm PC 4 000 ADDRESS FREQUENCY INTENSITY HISTOGRAM Hz PPM 1 2799 1 3446 439 6 8946 LO 83 KERR RA EK 2 2851 1 3431 485 C8647 Sp AAA 3 2873 6 3424 995
323. pen Other Files P 81 always delivered with a large number of parameter sets which include predefined acquisition processing and plot parameters and cover the most important NMR experiments After installing XWIN NMR from the release media these parameter sets are contained in the directory u exp stan nmr par 300 and are prepared for a spectrometer frequency of 300 MHz For example one of the standard parameters sets is called C13DEPT135 and is prepared for such an experiment The command expinstall see menu Acquire gt Spectrometer setup which must be executed after installation of XWIN NMR will convert the parameter sets to your spectrometer frequency and place them in the working directory u exp stan nmr parl A parameter set directory e g u exp stan nmr par C13DEPT135 usually con tains the files of Table 5 3 acqu acquisition parameter file acquisition parameter file for 2nd 3rd acqu 3 dimension if 2D parameter set proc processing parameter file processing parameter file for 2nd 3rd proc2 3 dimension if 2D parameter set meta plot parameter file plot parameter file for automatic plot meta ext expansions parameter file with output device names oui for plotting and printing Table 5 3 Parameter file names Parameter files are stored in ASCII format conforming to the JCAMP DX stand ard for NMR files They are set up by the user via the parameter
324. put listing of the commands ctl dat1 ct2 or datl simfit out Output listing of any simfit command tpar Contains all parameters shown by the command edt1 t1_disp Contains the points currently displayed on the screen tlelim Contains the information which points were eliminated tints Contains all integrals of all peaks after the point picking or maxi mum search was done t peaks Contains all points of all peaks after the point picking or maximum search was done The auxiliary files t _disp tlelim tlints and tI peaks are created by the point pick ing commands They cannot be edited because they are binary files 9 7 Quantitative NMR nmrquant 9 7 1 Program requirements The nmrquant command is required to perform reliable quantitative analysis of 1D spectra comprising complex overlapping spectra The program must be able to e Perform mole ratio calculations given integral heights and number of protons per signal e Perform absolute weight calculations given the information detailed in 1 plus molecular weights of all components and the weight of a reference component 9 7 Quantitative NMR nmrquant P 209 Permit analysis of spectra characterised by poor baseline Run in automation 9 7 2 Typical interactive session The procedures for quantitative determination are described in example sessions for interactive and automated execution For quantitative analysis of a data set in interactive mo
325. r lt fid number gt e wser lt fid number gt lt EXPNO gt lt PROCNO gt lt switch gt e wser lt fid number gt lt EXPNO gt lt PROCNO gt lt NAME gt lt USER gt lt DISK gt lt fid number gt is the number of the fid to be replaced in the ser file while the remaining arguments define the data set of the ser file if the current data set is the single fid to be stored If the current data set however is the data set of the ser file the arguments must define the fid to be stored The Process Menu for 2D data P 170 If EXPNO and PROCNO are not specified the data set TEMP 1 1 replaces the fid in the ser file This is useful if for instance 7EMP 1 1 was obtained by rser With wser a conflict can arise if one tries to write a data set into the ser file that is larger than the fid to be replaced XWIN NMR solves this problem by truncating the data set to the suitable size before executing wser lt switch gt has the same meaning as with rsr rsc Please check the AU command table in this manual if you want to use wser or wserp in AU programs 7 21 User defined 2D Fourier Transform xtrf xtrf2 Unlike with the xfb transformation the type of transformation to be performed can and must be set with the processing parameter FT_mod Table 6 4 The baseline correction mode for the fids BC_mod must specify single or quad data ME_mod must specify real or complex operation xtrf is the two dimensional analogue of t
326. r Name Expno Procno to the first data set of the logged in user Quit Terminate search command and close window 5 5 4 Other functions 5 6 You may resize the entire search window to give more space for data sets You may also increase the size of the data set columns at the expense of the portfolio or vice versa Click on the button located at the right side of the line that separates the portfolio from the first part of the window Keep the left mouse button depressed and move the mouse until you get the desired effect Copy 5 6 1 The Copy entry of the File menu Figure 5 13 provides a number of commands to make copies of entire data sets or parts of it i e of processed data or of acquisition data only In addition parameter and other files used in XWIN NMR can be copied to other directories for saving and retrieving Entire Data Set wrpa A copy of the current data set is created The user is prompted for the new name of the copy The entire data set including acquisition and processed data are copied The destination must be specified in the form NAME EXPNO PROCNO DU USER 5 6 Copy P 99 Entire data set to same disk L wrpal Entire data set to other disk wrd Processed data only Curp Acquisition data only Cwral Parameter file to Cupar Parameter file from Crpar Miscellaneous files to Miscellaneous files from Figure 5 13 The File gt Copy submenu It is legal to omit parts of t
327. r is no only the spectrum region is stored but the contour levels remain as defined earlier i e the level file will not be changed In the same menu you can alternatively specify the exact frequency limits of the region you want to plot by calling the command Enter region limits numerically The region limits are stored in the meta file At any time you can inspect the region limits by looking at the parameters F1 and F2 using the plot parameter editor edg gt EDCONTP You can force the program at any time to display the plot region by invoking the command Show plot region from the menu Output gt Define show region levels The contour levels to be plotted are stored in the file level in the current data direc tory It is stored in a binary format with the internal structure of Table 3 2 Instead of defining the plot levels interactively as described above you can define their numeric intensity values using the command edlev type it in or call it from the menu Output gt Define show region evels A dialog window according will be opened allowing the following operations 3 13 Plotting P 55 Total number of contours to be plotted Number of negative levels Intensity of level 1 Intensity of level 2 Table 3 2 Structure of level file Changing a level Move the cursor on to a value of a level and click the left mouse button Enter a new number Deleting a level Click on a level number left column of t
328. r printers which are only able to output text but no graphics Select Plot code file generator installation if you want to define a special plotter type which outputs to a file rather than to a printing device HPGL and PostScript file generators are available Plotter installation Printer plotter installation Printer installation A dialog window such as the one shown in Figure 10 4 appears Except for listing Figure 10 4 Plotter installation dialog window The 1D Output Menu P 244 all existing plotters the superuser password is requested when you click on one of the items In XWIN NMR a plotter is uniquely defined by the following four specifications e The plotter type e g Apdj550c all supported plotters are listed at the end of this chapter e The individual name of the plotter assigned to it by the operator distinguishing plotters of the same type from each other e The plotter class This is only of interest if there are several plotters connected which the user may want to divide into classes If a plot command is issued a class instead of an individual name can be specified The spooler of the operat ing system will then send the plot to the first free device of that class e The parallel or serial interface to which the plotter is connected install new plotter Click on install new plotter XWIN NMR will first list all supported plotter types in a dialog window This information is stored in the directory u
329. ral parameter setup edp All parameters required for 2D processing can be displayed and modified using this command Most parameters exist for both dimensions The effect of a parame ter is described along with the command that it influences 7 2 2D Transform xfb The command xfb executes the two commands xf2 and xfl in sequence but requires less computation time than the separate execution of the two commands After completion of an xfl transformation the middle point of the 2rr file is cor rected for a quad spike i e it is replaced by the median of its two neighboring points in F1 7 3 Transform of F2 rows xf2 The xf2 transformation acts on the raw acquisition data the ser file if no data exist that resulted from an F1 transform executed with xf1 In this case a data set is P 155 The Process Menu for 2D data P 156 7 3 1 7 3 2 7 3 3 created which is only transformed in the F2 dimension and can be further proc essed with xf1 to complete the transform The file 2rr contains the real data The imaginary data are stored depending on the xf1 processing parameter MC2 i e in the case of qf in the file 2ii and in all other cases in the file 2ir The transformation mode is independent of the processing parameter FT_mod but depends on the acquisition status parameter AQ_mod If it is equal to qsim a complex forward transformation is performed otherwise a real one Processing Parameters TDeff effective T
330. rams avail able to create these parameter files in TOMIKON Conversion of Image files Another special case are TOMIKON image files structured as follows lt NAME gt lt anumber gt lt class gt lt inumber gt The File Menu P 116 e lt NAME gt normally the name of a patient which will become the name of the XWIN NMR dataset e lt anumber gt An optional number appended to the name which will become the EXPNO otherwise EXPNO is set to 1 e lt class gt is a single character image class e lt inumber gt is a 3 digit image number For the different image classes the EXPNO and PROCNO is determined in the following way class I EXPNO lt anumber gt PROCNO lt inumber gt An exception are images of multi oblique examinations For every subpackage a different EXPNO is taken EXPNO lt anumber gt 10000 number of subpackage class P PROCNO lt inumber gt 1000 class D PROCNO lt inumber gt 2000 class Q EXPNO lt anumber gt 10000 lt inumber gt 3000 PROCNO is the image number stored in the original file class X PROCNO lt inumber gt 4000 class Y PROCNO lt inumber gt 5000 class Z PROCNO lt inumber gt 6000 class S EXPNO lt anumber gt 10000 lt inumber gt PROCNO 1 The file 2dseq will be created Editing image conversion parameters The command edit_conv allows you to edit the parameters which control the con version of Aspect 3000
331. ration Dialogue MONITOR MODE DATA FLOW BYPASS HANDSHAKE DUPLEX PARITY BAUD RATE SERIAL OFF REMOTE STAND ALONE OFF XON XOFF DIRECT HALF 8 BITS OFF 9600 Table 10 12 HEWLETT PACKARD 7550A A3 single sheet feede 10 13 Supported printers plotters P 281 XWIN NMR plotter type hpdj500 A 1 up down up down down up down down Interfacing minimum of 0 085 mm 1 300 down up down down down down down CY DAMN RF WN down serial or parallel The pen thickness is realized in steps of 0 17 mm 1 150 with the All other pen parameters have no meaning and are ignored Table 10 13 HEWLETT PACKARD DeskJet 500 A4 single sheet feeding printer The 1D Output Menu P 282 A 1 black blue violet red orange yellow green brown magenta up down up down down up down down Interfacing turquoise XWIN NMR plotter type hpdj550c 660c B down down down down down down down o n Hn FW NY down serial or parallel The logical XWIN NMR colors are realized in the following way black ink MY blue MY magenta MY yellow C C C C CMY red C CMY green C C MY black The pen thickness is realized in steps of 0 17 mm 1 150 with the minimum of 0 085 mm 1 300 All other pen parameters have no meaning and are ignored
332. re in the parameter section will terminate the program probably with an error message If you want to edit a params file by hand in principle this is possible you have to be very careful If all parameters are set you must return to the main menu to save them After sav ing you can easily set up new parameters or modify parameters by incrementing the Experiment processing number The parameters of the previously edited data set are used to initialize the new parameter file Save With save the editor creates two files for each data set params contains the parameters for the selected program callfile contains all filenames needed for the run If the data set does not exist these files are stored to disk If the data set exists already you can either overwrite it or cancel the save operation In either case the program returns to the main menu page Run The following files resulting from DAISY runs are written into the same directory as the params and callfile Lst files the output results of a DAISY program run 9 10 DAISY P 219 Ir the simulated data set proc procs processing parameter files outd output device file for XWIN NMR meta meta ext the plot parameters for XWIN NMR 9 10 2 Input pages for the programs Parameters written in capital letters and enclosed in brackets refer to the original parameter names used in the DAISY programs Detailed information can be found also in the files of the
333. red in the file DISVMR CONF If you use the DISMSL software the configuration information is stored in the file DISMSL SYST The commands conv and btran need to know the spectrometer configuration for a cor rect conversion of the parameters SW and OFFSET For DISNMR files get the DISNMR CONF file from your spectrometer Become superuser and do the following 1 Transfer the file from the spectrometer e g an am400 to your workstation The file will be put into u bruknet am400 root DISNMR CONF 2 Run the command u prog lt XWIN NMR version gt mod config 3 Answer the question for the station name e g with am400 This converts u bruknet am400 root DISNMR CONF to u conffinstr am400 disnmr conf 5 11 Conversion P 113 4 Leave the superuser mode You can now get and convert data files from the spectrometer For DISMSL files run the command convsys in XWIN NMR This will generate the file u conf instr lt station gt dismsl conf You do not need to transfer the file DISMSL SYST from the spectrometer The convsys command will ask you for the spectrometer name and its basic spectrometer frequency No configuration file is required if you want to convert files from a spectrometer running TOMIKON conv conv will ask you for the station name 1 Enter the name of the station e g am400 conv will then ask for a file name 2 Enter one of the following e a file name without the to convert the file
334. reference This text file can either be created manually by use of the command edmisc or by entering XWIN NMR s integration mode Define the integration regions and store them with the command Save as reg of the File menu If no such file 10 3 Page layout edg P 253 4 6 exists global is assumed pireg As with ireg the highest intensity within the spectral regions stored in the file intrng serves as the reference Only those regions of the file which lie within the plot range i e within the spectral area F1 F2 will be considered If no such file exists preg is assumed sreg As in the case of ireg the highest intensity of a set of spectral regions stored in a text file will serve as the reference However these regions will not be taken from the file reg Instead these regions need to be entered into a file whose name is stored in the processing parameter SREGLST This file is located in the directory u exp stan nmr lists scl and must contain the desired spectral regions in the same format as reg sreg makes it possible to define spectral regions dependent on solvents SREGLST is automatically set to the file name NUCLEUS SOLVENT by the automation command rjx rjxn for example SREGLST 3C Acetic if NUCLEUS 3C and SOLVENT Acetic For a large number of nucleus solvent combinations the XWIN NMR release tape contains the corresponding region files in the directory u exp stan nmrllists scl exam The c
335. regions on either side An integral region begins where a sig nal emerges from the noise level and ends where the signal disappears in noise These limits are stored in the intrng file as one region If you want to let the region start a little earlier at its left side and to let it end a little later at its right you must specify the desired amount via the processing parameter AZFE in ppm default 1D Data Processing Tutorial P 26 value 0 lppm There is of course the danger that due to the extension the region will now overlap with the previous or next one In such a situation the center point between the overlapping regions will become the region limit for both Changing the signal detection threshold An integral region begins where a sig nal emerges from the noise level and ends where the signal disappears in noise The noise level is calculated as the product ABSL standard deviation ABSL is a processing parameter which you can increase to make integration less sensitive The standard deviation is calculated by the program from the data The default value of ABSL is 3 Discarding small integrals Automatic integration does not store those integral regions in the file intrng with integral values too small to be of interest An integral is rejected if it is ISEN times smaller than the largest integral in the whole spec trum ISEN is a processing parameter Its default value is 128 2 9 2 Manual integration This command allo
336. release the cursor from 2 9 Spectrum integration P 27 m TEE Figure 2 4 Manual integration the spectrum when you are finished Storing integration regions on disk When you have defined the desired integrals as described above you can save the regions in the disk file intrng which is stored with the current data set in our example in the directory u data guest nmr examld l pdata 1 Open the File menu and execute the command Save as intrng or Save as intrng amp return The latter one will terminate integration mode The screen manipulations with integrals to be presented in the following paragraphs will not change the intrng file You can easily restore the integrals on screen by executing the command Read intrng 1D Data Processing Tutorial P 28 from the File menu You can also save different sets of integration regions with the copy command wmisc described in the chapter The File Menu and retrieve them with rmisc A special storing option in the File menu is the command Save as reg The defined regions are now stored in a file called reg rather than intrng It is only used by the command plotx which plots the spectral regions contained in reg thereby applying an automatic y scaling for each region to fit into the available space on the paper Defining and manipulating the current integral In order to mark one of the defined integrals as current integral move the cursor into the da
337. resulting in a tilt between 45 and 45 degrees ptilt can be applied more than once to the same spectrum 7 13 Manual Baseline Correction bem bem2 If a row or column is extracted from a 2D spectrum a manual baseline correction can be applied within the basl menu The same correction can be applied to all rows or columns of the 2D spectrum with the commands bem2 and bem1 7 14 Automatic Baseline Correction abs1 abs2 The command abs performs a baseline correction of all columns for the current 2D spectrum while abs2 corrects all rows This is done in a manner analogous to the 1D command absf Only that part defined by the 2D and 1D processing parameter pairs ABSF1 and ABSF2 respectively is used No region files are created 7 15 Trapezoid Baseline Correction abst1 abst2 The effect of these commands is similar to abs1 abs2 The corrected region how ever is not the same for all 1D sections but is shifted from section to section by a 7 16 Subtraction of 1D Spectra sub1 sub2 subld1 sub1d2 P 167 constant amount For the first section it is given by ABSF2 ABSF1 for the last one by the parameters SIGF2 SIGF1 The region limits for the sections in between result from an interpolation Only the case ABSF2 less than ABSF1 is treated In the orthogonal dimension the corrected region is limited by the orthogonal param eters ABSF2 ABSF1 The 2D basline correction commands absot2 absotl are similar to abst2 a
338. ritten by the result The processing parameter DATMOD determines whether add or at uses acqui sition data DATMOD raw or processed data DATMOD proc therefore DATMOD must be set correspondingly for the second and third data set The Process Menu for 1D Data P 146 6 15 4 Add raw data sets addfid Like command add above but works on fids only independent of parameter DAT MOD and generates a new fid in the current data set 6 15 5 Add constant DC to current data addc addc adds the value of the processing parameter DC to the acquisition data or the processed data depending on the status of DATMOD 6 15 6 Multiply current data by DC mulc mulc multiplies the current acquisition or processed data by the processing param eter DC depending on the value of DATMOD 6 15 7 Multiply two data sets mul mul multiplies the second and third current data set to be defined with edc2 together The result is stored as the current processed data set The acquisition or processed data are used depending on the status of DATMOD 6 15 8 Divide two data sets div With div the second current data set is divided by the third data set to be defined with edc2 and the result is stored as the current data set The acquisition or proc essed data are used depending on the value of DATMOD 6 15 9 Logical Or And XOR complement or and xor cmp The data in the second and third current data set to defined with edc2 are com
339. rm ing you that the calculation is still in progress As opposed to the commands Idcon and gdcon which pick the peaks to be decon volved automatically based on the peak picking parameters mdcon extracts the signals from a file The file must contain one line per peak specifying peak start peak center and peak end In addition since mdcon supports mixed Gaussian 9 6 The T1 T2 relaxation menu P 187 Lorentzian line shapes you must specify the desired Gaussian fraction 0 1 The name of the file is peaklist see Table 9 2 It must be located in the current data frequency 20969 627 20962 563 20960 182 20957 709 20950 609 Table 9 2 Example of a peaklist file half width gauss 100 5 18 3 74 2 02 4 03 5 18 0 8 0 0 0 1 0 5 1 0 directory where the spectrum file is The simplest way to create the file is with the command ppp available in the Analysis gt Peak picking menu after having defined the spectral region as descibed above Then you can modify the file con tents using your preferred text editor 9 6 The T1 T2 relaxation menu 9 6 1 Introduction The T1 T2 relaxation menu has its name for historical reasons However in addi tion to T1 T2 this XWIN NMR version allows fitting of data points from a variety of experiments The Analysis Menu P 188 FCTTYPE Experiment uxnmrtlt2 1 or T2 invrec inversion recovery satrec satura
340. rs i e the command uselastpars causes the Bayesian parameters from the last data set to become active 9 12 Bayesian Analysis P 239 9 12 8 Bibliography 1 Bayes Rev T Philos Trans R Soc London 53 370 1763 reprinted in Biometrika 45 293 1958 2 Bretthorst G Larry Bayesian Analysis I Parameter Estimation Using Quad rature NMR Models J Magn Reson 88 pp 533 551 1990 3 Bretthorst G Larry Bayesian Analysis II Model Selection J Magn Reson 88 pp 552 570 1990 4 Bretthorst G Larry Bayesian Analysis III Applications to NMR Signal Detection Model Selection and Parameter Estimation J Magn Reson 88 pp 571 595 1990 5 Jaynes E T in Papers on Probability Statistics and Statistical Physics R D Rosenkrantz Ed Reidel Dordrecht The Netherlands 1987 6 Jaynes E T Bayesian Spectrum and Chirp Analysis in Maximum Entropy and Bayesian Spectral Analysis and Estimation Problems C R Smith and G J Erickson Eds p 1 Reidel Dordrecht The Netherlands 1989 7 Jaynes E T How Does the Brain do Plausible Reasoning in Maximum Entropy and Bayesian Methods in Science and Engineering G J Erickson and C R Smith Eds Vol 1 pp 1 24 Kluwer Academic Dordrecht The Netherlands 1988 8 Jeffreys H Theory of Probability Oxford Univ Press London 1939 Later editions 1948 1961 reprinted in 1985
341. rs LIMITS and ADJUST as if LIMITS reg and ADJUST CX If the room needed for the region plots exceeds the length of the over view spectrum then the next regions are put to the right of the ones already plotted again up to the length of the overview spectrum The overview spec trum thus acts like a page If there are still more regions to be plotted they are put to the right of or underneath the ones plotted thus far depending on the room they need vertically Paper feed is done as for LAYOUT separat 10 4 Page layout for auto expansions edgx P 267 X1 are the expanded plots O is the overview spectrum LAYOUT top of one Case 1 height of overview plot gt height of region plots XI X2 X3 X4 X5 LAYOUT top of one Case 2 height of overview plot lt height of region plots Xl X2 X3 X4 X5 X6 LAYOUT top of more Xl X2 X3 X4 X5 X6 O X6 Figure 10 7 The three layouts of auto expansion plots with overview spectrum The 1D Output Menu P 268 e top of more Like top of one except that all regions are plotted next to each other and the overview spectrum is plotted underneath each group of plots Thus each sheet of a single sheet plotter has the overview spectrum 10 4 7 Further differences between plot and plotx 10 5 10 6 The parameters CLIP MIRROR and ROTATION are not
342. rs with maxed you need to define a point spread function PSF the region of interest in the NMR spectrum Output gt Define plot region menu a second and third data set for the output files command edc2 The two data sets will contain the following results second data set deconvolution result third data set mock data The mock data set is the multiplication of the deconvolution result with the PSF The mock data are most useful for controlling the quality of the deconvolution i e how similar are deconvolved and original data The deconvolution result contains all single peaks after the deconvolution maxent run Check the settings of the following parameters e Number of iterations Can be set to any number But the default value 99 is usually sufficient to lead to convergence given that the PSF is realistic If the number of iterations does not lead to convergence the PSF is probably unrealistic The Analysis Menu P 230 Step results If STEPRES is set to yes output information is written to disk after each iter ation Mock data Set the flag to yes if you want to write the mock data to the third data set The positive negative toggle There are two possible settings positive only peaks with a positive amplitude will be deconvolved pos neg peaks with a positive and negative amplitude will be deconvolved SIGMA SIGMA has a default value of 0 In this case MEMSYS5 determines
343. rward or backward linear prediction can be applied to the data by setting the parameter ME_mod LPfr LPbr Linear Prediction will be described in detail in a later section Processing Parameter WDW window type Data are digitally filtered with the parameter WDW determining the type of filter no no filter EM exponential multiplication GM gaussian multiplication SINE sine multiplication QSINE multiplication with squared sine TRAP trapezoidal multiplication USER user defined window function SINC sinc multiplication TRAF traficante window multiplication TRAFS traficante window multiplication These filters function exactly like the 1D window functions In the case of USER the user himself must provide the window function in the form of an Fid file of a 1D data set This data set can be created using the com The Process Menu for 2D data P 158 7 3 7 7 3 8 7 3 9 7 3 10 mand edc with TD set according to the desired size The Fid file must be provided by the user and must contain the user s window function Now before starting the transform the program must know where to find the window function Enter it as second data set via the command edc2 Processing Parameter PKNL non linear phase mode For AMX ARX type spectrometers if the F2 processing parameter PKNL is set to the value true a 5th order phase correction is performed after xf2 to compensate phase errors introduced by the Butterworth filters For AVANC
344. ry u exp stan nmr lists mac The command edmac displays all macros in this directory in a dialog box from where the desired one may be selected The command edmac may also be entered on the keyboard followed by the name of the desired macro or followed by an argument containing wildcard characters see edpul and how to change the default text editor for details Table 5 5 shows an example The charcacter signals the beginning of a comment Otherwise each line corresponds to a XWIN NMR command which is specified exactly the way it would be entered on the command line Parameter lists edlist Parameter lists are text files containing a series of values for parameters which may 5 3 Open Other Files P 87 dir select data set lb 0 5 set line broadening parameter LB sil6K set transform size SI ef perform exponential multiply and transform Table 5 5 Example of a macro file vary during an experiment This command allows you to create a new list and to edit or view an existing one XWIN NMR locates parameter lists in the directory u exp stan nmrNists lt list type gt The command edlist displays all lists in this directory in a dialog box from where the desired one may be selected See Table 5 6 for the available list types list type contains vd delay lists vp pulse lists fl frequency lists AVANCE fl f2 f3 frequency lists A X vt temperature lists ve lo
345. s The default achieved by setting TDeff 0 is to use all data TDoff The first TDoff points of the FID can be ignored in the Bayesian analysis This is particularly useful for data sets with distorted baselines SI The size of the resulting model FID or other output see BAYOUT is set with this parameter BAYNSIG It is often very advantageous to provide a noise sample for the Bayesian analysis as this allows a more accurate estimation of the magnitude of the noise and thus helps greatly with deciding on the presence of more signals in signal detection If BAYNSIG is set to a value greater than zero the program will first look for a file noise in the same directory as the current data set FID file fid If there is no file noise then the program will take the last BAYNSIG points of the FID and use them as a noise sample BAYOUT This parameter defines the way in which the result of the analysis is output as a model FID BAYOUT FID as a spectrum obtained from the model FID via Fou rier transform BAYOUT spectrum as zero width lines at the frequency posi tions and with heights approximately equal to the integral BAYOUT lines or no data output at all BAYOUT none BAYAOPT Signal detection is performed at different decay rates starting with the values set for BAYAOPT which should be set to the width of one of the narrower lines in the data A default value is automatically calculated from the available resolution of
346. s as a function of frequency and decay These findings are then automatically passed to the parame ter estimation routine for optimizing the parameters Initially the original FID data are searched for positive evidence of frequencies All maxima that are found with values greater than a certain threshold are immedi ately used for setting up a model of this many decaying sinusoids If there are only positive maxima below the threshold then only the highest BAYNADD maxima will be used to set up the initial model This model is then optimized with respect to its parameters and the model s probability is calculated This probability is compared to the probability of the previous model which initially is the constant model and if its value is higher then the new model is accepted The model FID is calculated and subtracted from the original data This residual is then used as input to the next signal detection pass If on the other hand the new model s prob ability is not greater than that of the previous model then this model is rejected If there were more positive evidence maxima in the previous signal detection pass the next highest BAYNADD frequencies are tried in a new model This cycle con tinues until either no more positive evidence maxima are found in a signal detec tion pass or until none of the found evidence maxima would lead to a model with a higher probability than that of the previous model Files The parameters
347. s in the range 1 to 1 Otherwise if e ASSFACX gt 1 If h2 lt hmax ASSFACX then the second largest signal becomes the reference signal If not the largest signal becomes the reference signal e ASSFACX lt 1 Every region is plotted twice once with the largest and once with the second largest signal as a reference The second largest signal is only searched for outside an interval around the largest signal This interval is to be specified by the processing parameter ASS 10 4 Page layout for auto expansions edgx P 265 10 4 5 WID in Hertz The vertical scaling factor of a region is assigned the greatest integer with which the intensity of the reference signal can be multiplied without exceeding the size of the plot s data window The room available is given by the difference DHEI SZERO DHEI IZERO for integrals These parameters must be set with edgx The scaling factor can never become smaller than one even if DHEI was set too small On the other hand this factor will only become so large that the noise will not exceed 3 cm The scaling of the integrals is determined by the largest integral value in this region which is not greater than the integral plot reference signal of the over view spectrum A parameter ASSFACI which exists for the overview spectrum is not available for the integrals of the regions Parameter Lists Auto expanded regions cannot contain parameter lists However XWIN NMR plots the text of
348. s left and right of inegration intervals will then be used to determine the baseline The P at the beginning indicates ppm units H for Hertz units could also be used A W at the begin ning would force the plotting or integral list command to consider the entire spectrum as a single integration interval No ranges need be specified in this case 3 intrng Figure 5 7 set up by the user Each interval is assigned a scaling factor by the user When plotting or printing numeric integral values based on this range file they will be scaled such that their weighted sum will have the result The File Menu P 92 P 1 0 low field high field weight 9 438358 8 547455 2 0 8 273884 7 523723 4 0 7 423863 7 144994 2 0 Figure 5 7 Example of an intrng file set up by user specified in the first line 1 0 in this example 4 base_info Figure 5 8 The first line contains the function code for the baseline 0 12311 1666 3 153728e 07 5 040096e 03 1 909280e 00 1 627358e 03 8 669 147e 07 Figure 5 8 Example of an base_info file fucntion the user had selected to perform the manual baseline correction e g O0 polynomial the following two lines are file offsets defining the region to which baseline correction should be applied The next lines contain the values of the coefficients A B C D E for example A Bx Cx 2 Dx 3 Ex 4 in the polynomial case 5 baslpnts Figure 5 9 The first line cont
349. s newer than 930101 if CEXPNO 1000 10 bconv creates an output file using the following naming convention lt NAME gt lt EXPNO mod 1000 gt S lt PROCNO mod 1000 gt Otherwise a TOMIKON 3D image file will be created and the following nam ing convention is used lt NAME gt lt EXPNO mod 1000 gt lt PROCNO mod 1000 gt S Flexible conversion with Bruktran Introduction The Bruktran program command btran provides a flexible method to convert data from an Aspect 2000 3000 referred to as Aspect in this description into the XWIN NMR data format You can convert data from any station and any user You can also individually specify the destination disk or user for the converted data Bruktran also allows you to rename files thus enabling you to make use of the 14 characters available for a filename Renaming can be done either automatically or for each set of files with the same experiment name To rename files automati cally the program needs to know the filename formats for both the Aspect filename and the XWIN NMR filename Using these formats it is possible to extract a group of characters from the Aspect filename check these characters against a The File Menu P 120 list of expanded tokens and place the expanded token in the XWIN NMR filename Automated renaming is only really useful for those users who name their Aspect files in a specific manner Other features of the program include date stamping of a filename wh
350. screen Select one or two additional rows if you want to look at several rows simultaneously while phasing and move them to the 1D windows 2 and 3 Phase the rows just as with 1D spectra and apply these phase parameters to the whole 2D spectrum For the F1 dimension use colums instead of rows We now present these steps in more detail 1 Select a suitable region of the 2D spectrum When you enter phase correction mode the 2D spectrum displayed at the upper left part of the screen is shown in compressed form since it is impossible to have a fully resolved spectrum in a small display area As soon as you move the row to a 1D window it is loaded from the data file and may therefore appear different from the compressed row in the 2D window If you expand the 2D spectrum sufficiently before you select a row then they should apper the same The program informs you if the expan sion is still too small The Info box below the 2D spectrum says Attention 2D is compressed in this case 2 Select a row Click on the row button Position the horizontal line as desired and click the middle mouse button The row at this position will be displayed Click the left mouse button the leave row selection mode You can scale the row using the 2 and 2 buttons below the row button and you can increment or decre ment the row number with the and buttons 3 Move the row to a 1D window Click on the mov button The program will extract the selected row
351. see example in Fig ure 15 2 n is the number of loops to be performed A loop must be terminated by the end command The predefined integer variable Joopcount is the loop counter associated with times n with values from 0 to n 1 The commands times2 n and times3 n are additonal loop commands with loop counters loopcount2 and loopcount3 Their use is intended for nesting 15 9 Calling other AU programs The AU command xau paropt would execute the AU program paropt from the current AU program Arbitrary nesting of this kind is legal xaua and xaup would execute the AU program specified in the acquisition parameter AUNM or the processing parameter AUNMP of the current data set respectively While xau and xaua will not return until the called AU program has finished its task xaup returns immediately after AUNMP is started as background task This feature is used by the AU program stan_sx responsible for controlling automated spectrometer oper ation using a sample changer xaup starts processing the last measured sample but does not wait until processing is complete instead immediately continues measur ing the next sample A special form of xaup is xaupw which is identical to xaup except that is does not return until execution of AUNMP is complete 15 10 Terminating an AU program The commands quit and quitmsg message are intended for the legal termination of an AU program The latter one outputs a message string upon ter
352. selected fit function NUMTERM determines the maximum number of components which can be fitted The following rule applies COMPNO maximum 12 NUMTERM After all parameters are set save your changes with SAVE and type a simfit if you want to fit the currently displayed points or b simfit all if you want to fit all peaks with one command The command nxtp see Section 9 6 4 2 switches to the next peak and updates the parameter CURSOR Important notes The simfit commands will always show the data points and the fit curve in an abso lute scaling mode The display is scaled according to the maximum and minimum of the data points of all peaks The commands nxtp ctl datl ct2 and dat2 will always show the points and the fit curve in full scale mode The display is scaled according to the maximum and min imum of the data points of the current peak For each variable from the fit equation you must enter an initial start value for the iterative refinement If you have more than one component then each variable 9 6 The T1 T2 relaxation menu P 201 9 6 4 5 appears as often as you have components The sum of all I 0 guesses should not be greater than 1 because simfit rescales all data points of all peaks to a maximum of 1 You must also enter an initial step rate with which the variables are modified A good guess for the step rate is 10 of its corresponding variable The editor defaults to this value automatically if yo
353. selected pulse program library to the working directory u exp stan nmr lists pp edpul opens a dialog window with two colums The right column shows the pro grams provided by Bruker after expinstall was done The left column lists those pulse programs that were created by the user A Bruker standard pulse program that was modified by the user is also listed in the left column Modification of a Bruker standard pulse program however requires input of the superuser password if one is defined in the system When selecting a pulse program from the right col umn the text is displayed in a dialog window In order to modify the program the command buton gt di at the lower edge must be activated and then the program be selected This brings the program into the text editor For user pulse programs left column the text is always loaded into the text editor If a new pulse program is to be created the command field New Name at the lower edge of the dialog window must be activated After entering a name for the pulse program the text editor is called and the program may be written 5 3 Open Other Files P 83 5 3 3 5 3 4 Text editor A text editor for your system is called You can specify your own editor by invok ing User Interface from the Display gt Options menu or by typing in the com mand setres Arguments and Wildcards The command edpul when entered on the keyboard can optionally take the name of a pulse progr
354. sferred without expansion from 24 bit to 32 bit per word In this case the files are not byte swapped e The data can be transferred with expansion from 24 bit to 32 bit per word These files are byte swapped during the transfer Therefore the file format is the same as for BRUKNET running in binary mode and special parameter file handling disabled When using NMRLINK the receiving computer is a PC and the files will be stored in lower case letters Renaming into upper case letters or appending a sign is not necessary because conv recognizes all different file formats correctly The conversion of A3000 extended parameter files works for data which were transferred with NMRLINK in 32 bit transfer mode The conversion also works if the data were tansferred in 24 bit mode and the extended parameter file was trans ferred in 32 bit mode If the transfer of the data was done in 32 bit and the extended parameter file was transferred in 24 bit then the extended parameters will NOT be converted This last case cannot be implemented because it interferes with the conversion of files first transferred with NMRLINK to a PC and then to a UNIX station In such a case the file name convention changes 32 bit files lose the sign at the end Configuration files The number and type of components with which a spectrometer is equipped deter mines its software configuration If you use the DISNMR software this configura tion information is sto
355. sing status parameter file procs 16 4 JCAMP DX format 1D acquisition and processed data files fid 1r Li may also be stored in text files based on the JCAMP DX format The initial part of such a file is similar to Figure 16 1 and contains the parameters followed by the data section with the fid or spec trum encoded according to the option chosen when calling the JCAMP conversion command tojdx Fore detailed information about the JCAMP format please refer to the following literature 1 JCAMP Dx A Standard Form for Exchange of Infrared Spectra in Computer in Readable Form Robert S McDonald and Paul A Wilks JR Applied Spectroscopy 42 Number 1 1988 2 Generic JCAMP DX Version 5 0 Draft 1 0 February 28 1991 Robert S McDonald JCAMP DX subcommitte 9 Woodside Drive Burnt Hills NY 12027 USA 3 JCAMP DX NMR Standard Dr A N Davies ISAS Institut fiir Spektrochemie Dortmund Germany pri vate comm 16 5 2D spectra Like 1D spectra and acquisition data 2D processed data are stored as 32 bit inte gers The spectrum real part is contained in the file 2rr the imaginary parts in the files 2ii 2ri 2ir The latter two are only present if the spectrum is phase sensitive All files are stored in the so called submatrix format The submatrix dimensions are given by the status parameters XDIM contained in the files procs and proc2s XDIM is calculated by automatically depending on the available computer mem ory so as to opt
356. so be cleared and you will lose the regions defined so far If you answer no 3 11 Spectrum integration P 51 the regions are only deleted from the screen the file contents are retained You can now define new regions which will be appended to the file The read button When you click on this button the programs invites you to enter the name of a region file It will read the region stored there and display it You can now define new regions which will be appended to the file Computing the integrals int2d int2dref These commands may be typed in or called from the Analysis menu Either com mand first invites you to enter the name of the file where the integration regions are stored int2d then calculates the integrals immediately and stores the result in the text file int2d in the current data directory int2dref before proceeding asks you to enter an integral region number and an integral value you want to assign to this region It also stores the result in int2d Both commands perform the same calcula tion int2dref in addition generates an output column in which the reference region has the specified value assigned The integrals of all other regions are scaled relative to this reference value You can use the same integral region file to integrate different 2D spectra In a region file integration regions are defined by the limiting row and column num bers as well as the corresponding ppm values When integrating spectra o
357. specified date and time For example wait_until 20 15 7 11 would continue execution at Nov 7th 20 15h Chapter 16 File Formats 16 1 Parameter Files The parameter files acqu proc and meta containing acquisition processing and plot parameters respectively are text files see Figure 16 1 Their format cor responds to the so called JCAMP DX standard It allows the inclusion of user spe cific parameters which are marked by the character sequence For this reason all parameters XWIN NMR parameters in the file are preceded by this sequence 16 2 Acquisition Data The files fid and ser contain one dimensional or multi dimensional acquisition data respectively They consist of a sequence of 32 bit integer numbers in binary format On workstations with different microprocessors an integer number may be represented by a sequence of 4 bytes ordered differently There are two common modes little endian and big endian The latter one is typical for MIPS and SPARC microprocessors the former one for Intel x86 and Bruker X32 XWIN NMR stores the byte order corresponding to the acquisition data in the acquisition status parameter BYTORDA in the file acqus which may take on the value little or big This allows XWIN NMR or other software packages to convert the data to the cor rect byte order if the endian mode of the computer where the data are to be proc P 333 File Formats P 334 TITLE Parameter file
358. sting numbers are displayed in a menu If you select one of these numbers the corresponding parameter set is loaded With new a new parameter file with the next available processing number is cre ated The new path name for this parameter file params is displayed in the header line Title The title field displays NEW_FILE to indicate that you have not yet edited the parameters When you return to the main menu after you have edited parameters the title is updated with the title specified in the Miscellaneous parameters menu see Input pages Edit During an editor session several pages of input are shown depending on the type of program For SPECPREP you can set all relevant parameters on one page For The Analysis Menu P 218 9 10 1 6 9 10 1 7 all other programs you must enter the parameters on several pages Use the buttons next page to display the next parameter page prev page to display the previous parameter page main menu to return to the main menu page comment to open the UXNMR editor of your choice The comment button allows you to write any information which you want to store together with the parameters into the params file The DAISY programs ignore these comment lines until the first line with the first character not equal to C or c is found From there on the format is fixed due to the nature of the Fortran programs This means that a comment line or line with no input somewhe
359. t shows all AU programs available as source code Select one from the list for execution If you already know the name of the program you can start it via xau lt name gt or just with lt name gt leaving off xau A compiled AU program behaves for this reason just like a normal XWIN NMR command You should avoid giving an AU program the same name as an existing XWIN NMR command If you did and typed in the command name the internal command would be executed instead of the AU program How ever you could still start the AU program by calling it via xau AU programs are like all XWIN NMR processing commands executed in the back ground This means that you can start several AU programs and they will run in parallel In order to see which AU programs are currently running execute the command Display gt Active Commands gt Show If you want to interrupt the execution of an AU program before it terminates regularly or if it hangs up for some reason invoke the command Show amp allow for killing in the same menu AU programs can also be called from within AU programs The command xau tlcalc inserted in an AU program would execute the AU program t calc Instead of specifying an explicite name between quotes a character array variable 5 12 Execute P 133 initialized with a name would serve the same purpose xaua xaup These two commands provide an alternate method of starting an AU program Its name is taken from the a
360. t for each integral range default 0 After entering proton values the display is replaced with the Component identification dialog where additional information can be entered such as identification string molecular weight and reference weight 9 8 The Simulation submenu The remaining sections of this chapter introduce a collection of simulation pro grams NMRSIM DAISY Memsys5S K Bayesian Analysis Figure 9 10 The Simulation submenu 9 9 NMRSIM NMRSIM is a program for the simulation of NMR experiments The user must specify a spin system and a pulse program in the standard Bruker pulse program language for AMX ARX or AVANCE series spectrometers Based on the numeri The Analysis Menu P 214 9 10 cal solution of the quantum mechanical Liouville equation NMRSIM applies the pulse program to the spin system and calculates the resulting Fids A wide range of NMR experiments can be simulated including selective excitation and magnetiza tion transfer HOHAHA TOCSY multiple quantum and filtered COSY heteronu clear 3D Mixtures can also be simulated NMRSIM is equipped with a pulse program display facility and a Bloch simulator It is ideally suited for both scien tific calculations and educational purposes NMRSIM stores the calculated data in XWIN NMR format When the calculation is finished the result is automatically displayed by XWIN NMR and the user can apply a fourier transform and all other XWIN NMR
361. ta and light blue dark blue violet shadings for negative data This button allows you to toggle through display modes where the negative or the positive data are turned off or where the whole color range from red to violet is assigned to the positive data Toggle the x and y axis units between Hertz and ppm If an axis unit is displayed in seconds sec rather than Hertz or ppm the acquisition data were not fourier trans formed in this dimension For example T1 experiments are acquired as a sequence of fids into a ser file like a 2D experiment However they are only transformed 3 3 2D spectrum display modes P 41 along one dimension using the command xf2 Use the calibrate button to define the origin of the axes see section Spectrum calibration 3 3 2D spectrum display modes The command buttons intensities contours serial and oblique provide different representations of the current 2D spectrum intensities The intensities of the individual spectrum points are logarithmically mapped to the available color range contours A contour map is calculated and the diffrent contour levels are displayed using diffrent colors serial Enters a special display mode where you can examine the 2D spectrum row by row or column by column or where you can examine the 2D acquisition data fid by fid This is essentially a 1D display mode oblique An oblique view of the 2D spectrum is generated You may change the viewing perspectiv
362. ta generate a new fid using the command genfid This fid can be treated with the Bayesian analysis Commands Activation of the menu field Simulation gt Bayesian Analysis allows the choice between five commands which can also be typed in bayed The parameter editor is called to set or edit the parameters for a subsequent Baye sian analysis bayx Start of the Bayesian analysis The parameters previously defined with the com mands bayed or bayedx will be used If no Bayesian analysis parameters have yet been defined the program will assume default values for the parameters and try to analyze the data with repeated signal detection passes in a black box fashion An optional argument of y or yes can be specified with the commands bayx and bayedx which has the following effect if the parameters BAYSTO2 or BAYSTO3 are set to yes then results are stored in data set 2 or 3 to be setup via the com mand edc2 However the program will first check if the data set already exists and if so ask for permission to overwrite it The argument y or yes explicitly gives per mission to overwrite data set 2 or 3 and thus prevent the popup message from appearing bayedx This is a combination of the commands bayed and bayedx First the parameter editor is called to set or edit the Bayesian analysis parameters Leaving the editor 9 12 Bayesian Analysis P 235 with SAVE will cause the actual analysis to be started using the parameters just s
363. ta area of the XWIN NMR window Click the left mouse button The cur sor is now bound to the spectrum and moves along the spectrum trace when you move the mouse Select the integral you want to make the current integral by mov ing the cursor under it and release the cursor by clicking the left button again The integral will be marked with an asterisk All button panel commands in the section current can now be applied to this and only this integral The commands slope and bias perform a baseline correction of the region before integration bias adds a constant to the spectrum while the cursor is located on this button the left mouse button is kept depressed and the mouse is moved The result on the integral is a linear correction You should use this command to correct the initial part of the integral If after that the end part of the integral is still not horizontal use the command slope analogously It adds a linear function to the spectrum before inte gration The calibrate command allows you to enter a number which is assigned to the current integral All other integrals are rescaled accordingly The delete com mand removes the current integral from the screen but not from the intrng file if the regions were already stored on disk and you can redefine it if required The 2 2 etc buttons allow you to expand the current integral on screen Manipulating and scaling all integrals All button panel commands in the section all operate
364. ta points Since XWIN NMR stores 2D spectra as a sequence of submatrices arbitrary values of STSI are not allowed The strip must consist of complete submatrices XWIN NMR therefore rounds the value entered by the user so the calculated strip is usually somewhat larger than specified The values actually used are stored after the trans formation in the status parameters see command dpp The desired strip can also 7 3 Transform of F2 rows xf2 P 157 7 3 4 7 3 5 7 3 6 be set interactivly Enter the 2D utilities menu define a region using the drag and draw button then click the set strip command button This will set STSR and STSI for both dimensions Processing Parameter BC_mod baseline correction mode The first step of processing is the baseline correction of the fid to be transformed by subtracting either a constant or a 5th order polynomial or by applying a filter according to Marion Ikura amp Bax 1989 BC_mod quad qpol qfil The latter two cases are used to suppress water signals in the center of the spectrum or off center if the processing parameter COROFFS is different from 0 BC_mod no means that no baseline correction is performed default in FI dimension which is sometimes to be preferred if the signals have not decayed strongly towards the end Further details on BC_mod can be found in the description of bc Processing Parameter ME_mod linear prediction mode Instead or in combination with zerofilling fo
365. ted The three radio buttons all current off are equivalent to the commands status all status auto status off respectively described earlier in this chapter The advantage of the radio buttons versus the command is that the buttons allow you to view the current setting hist on hist off default setting 12 5 User Interface P 311 History If enabled all XWIN NMR given by the user are written in the file u prog lt X WIN NMR version gt curdir lt user gt history The radio buttons on and off are equivalent to the commands hist on and hist off respectively described earlier in this chapter Editor Certain XWIN NMR commands call a text editor e g for writing pulse or AU pro grams The default editor is xedit an editor of the X Windows system You may change this entry and specify your preferred editor e g SGI s jot If you decide for an editor requiring an xterm window such as the traditional Unix vi you must specify it in the form xterm e vi Please note that XWIN NMR can only start an edi tor if it is located in a directory which is part of the shell s search path ExpLoc Standard experiment files such as pulse programs and many other files are searched for by XWIN NMR in the directory u exp stan nmr If you change the ExpLoc field e g to stan2 XWIN NMR will search these files in u exp stan2 nmr This feature allows you to maintain several such directories Plotter By default this field is
366. ter may serve for this purpose The color of the text is specified by TCOLOR If TMODE o a long text line will not automatically be continued on a new line if there is not enough room but clipped instead Also the separation character TSEP has no effect The position of the text within the title window may be controlled via the parame ter TALIGN The following values may be selected e TALIGN 3 The text is written left adjusted starting at the upper left corner of the title win dow e TALIGN 2 The text is written left adjusted but vertically centered in the middle of the title window e TALIGN 1 The text is written left adjusted with the last line starting in the lower left cor ner e TALIGN 9 8 7 Analogous to 3 2 1 the text being right adjusted e TALIGN 6 5 4 Also analogous to 3 2 1 but centering each line of text horizontally i e leav ing the same distance to the left and right end of the title window 5 will cause horizontal and vertical centering positioning the text at the middle of the title window If the text considering all these parameters does not fit into the title window the program will decrease the character size This is done until a minimum still read able size is reached Then the text is clipped at the edges of the title window The Parameter Window In the parameter window with the upper left corner being defined by PXULEFT and PYULEFT in cm acquisition processing and plot p
367. tervals lies directly above the x axis window The operator can control the plot with the following parame ters ILCHAR mm character height for the digits of the integral values ILDIGIT number of digits with which to plot the greatest integral value The other values will be plotted with leading blanks ILCOLOR color for integral values 10 3 Page layout edg P 251 10 3 1 4 The integral values appear in the plot between two lines marking the correspond ing integration interval These lines will either be cut off at the upper end of the integral values window of height ILHED or they will be continued from there to the zero line of the spectrum depending on the parameter ILONG yes continue no clip XWIN NMR provides the capability of generating integral plots on which the numeric integral values are scaled relative to the previous plot in order to be able to compare the values of different spectra While relative scaling of the integral traces on a plot is enabled by setting the plot parameter HEI 1 relative scaling of the numeric values is achieved by setting the processing parameter INTSCL 1 In detail INTSCL can be set as follows INTSCL gt 0 The numeric values are scaled individually for each spectrum plotted The user can influence the absolute value by adjusting the first line in the intrng file see description INTSCL 0 The integrals on a plot will obtain the same numeric values as the user defined in th
368. tf3 pu2 The option p may be given together with the options decribed earlier Their sequence does not play a role The 3D transform commands may also be invoked from AU programs Two argu ments are required The first one specifies whether to store the imaginary parts and the second one corresponds to the p option described above Example tf3 y pu 8 3 Phase correction tf3p tf2p tflp The purpose of tf3p tf2p tflp is to apply an additional phase correction to a trans formed 3D spectrum provided the required imaginary parts are available The storage of imaginary parts can be selected when giving the transform commands Alternately the imaginary part can be generated from the real 3D spectrum by means of a Hilbert transform commands tht3 tht2 tht1 Details about phase correcting a 3D spectrum can be found in the chapter 3D Data Processing Tutorial 8 4 Baseline correction tabs3 tabs2 tabs1 The commands tabs3 tabs2 tabs1 are the 3 dimensional analoga to the 2D com mands abs2 and abs and the 1D command absf Please refer to the chapter 3D Data Processing Tutorial for a more detailed dicus sion 8 5 Calculate projections r23p r13p r12p The commands r23p r13p r12p calculate the F2 F3 F1 F3 and F1 F2 projections of the real part 3rrr of the current 3D spectrum respectively The result is stored as 8 6 Hilbert transform tht3 tht2 tht1 P 179 a 2D spectrum under
369. the Add button When you are finished setting up the list click on OK Now whenever you click on one of the entries in the directory field e g on usr people guest XWIN NMR will search for a subdirectory named data and will dis play all data sets of all users located there User Click on a user id to display all data set NAMES of this user in the Name column Name Click on a name in this column to display all experiments stored under this name in the Expno column Expno Click on an experiment number to display all processed data sets belonging to this EXPNO in the Procno column 5 5 2 Command buttons Append Click on this button to append the selected highlighted data set USER NAME EXPNO PROCNO to the end of portfolio Insert Similar to Append but inserts the selected data set before the highlighted portfolio entry Remove Remove the highlighted portfolio entry Apply Click on this button to make the highlighted portfolio data set the current XWIN NMR data set and display it Alternatively double click on the desired portfolio data set The File Menu P 98 5 5 3 Commands in the File menu Load Load a portfolio stored via the Save commands Save Store the portfolio contents in a file of your choice Save as default Store the portfolio contents in the file default por which is located in the subdirec tory xwinnmr of your home directory Reset Resets the contents of the data set windows Unit Use
370. tion recovery cptirho ICP Tirho TIS expdec exponential decay T2 or TI rho lgaussdec Gaussian decay lorgauss combined Lorentzian Gaussian decay linear linear varbigdel diffusion variable Big Delta varlitdel diffusion variable Little Delta vargrad diffusion variable Gradient Two different fitting algorithms are available The first algorithm estimates the start parameters from the data points This algorithm only works where one single component is the source of the intensity of the data points The commands to fit these types of experiments are ct1 dat1 ct2 and dat2 Command FCTTYPE Number of Equation Components ctl datl uxnmrtlt2 1 t I 0 P exp t T1 ct2 dat2 uxnmrtlt2 1 t I 0 exp t T2 The second algorithm is a Simplex method This algorithm can fit data where one or more than one component contributes to the intensity of the data points The fit command is always simfit and the following fit equations are currently imple mented 9 6 The T1 T2 relaxation menu P 189 FCTTYPE Number of Equation Components uxnmrtlt2 1 4 E t I 0 P exp t T1 knvrec 1 4 E t I 0 1 2A exp t T1 satrec 1 6 E t I 0 1 exp t T1 cptirho 1 4 Iit I 0 1 TIS T Irho exp t T Irho exp t TIS expdec 1 6 E t I 0 exp t T lgaussdec 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 t A B t varbigde
371. to define a region proceed as follows 1 Move the cursor into the data window and click the left mouse button 2 Position the cross hair to the upper left corner of the region to be integrated 3 Click the middle button to fix the upper left corner or the left button to quit 4 Move the second cross hair to the lower right corner of the region 5 Click the middle button to fix the lower right or the right button to delete The defined region is shown as a rectangle Now click the left mouse button A popup window will offer you the following choices a a a a These codes control how integration of this region is to be performed by the int2d command If a is selected all intensities in the area are added to give the integral If is selected only the positive intensities added If is selected only the neg ative intensities added If a is selected you will get two results from the int2d command the first corresponds to option a the second to option Similarly a gt and a provide additional combinations The a option delivers three results The chosen option is written aside the rectangle of a region and is stored in the region file along with the region boundaries The clear button This button allows you to remove all integration regions from the screen You will be asked whether to override the region file If you answer yes the file contents will al
372. tput are omitted a menu is brought up in which the missing entries must be entered In this menu you can terminate the conversion with the Abort button fromjdx input file o The file input file is converted to an XWIN NMR data set If the file name is omitted you will be asked for it in a dialog window The data set to be created is stored in the path DU data USER nmr lt input file gt EX P NO pdata PROCNO If the JCAMP file has the suffix dx the XWIN NMR data set is stored without this suffix The experiment number and the processing number are determined with the following procedure e Ifthe option o overwrite was specified EXPNO and PROCNO are both set to 1 Any existing data set is overwritten e Ifthe option o was not specified EXPNO and PROCNO are initially set to 1 If the JCAMP data set contains a fid the EXPNO is incremented until an unused number is found If the JCAMP data set contains a spectrum the PROCNO is incremented The File Menu P 128 5 11 3 5 11 3 1 In this way the lowest possible EXPNO or PROCNO is assigned to the new data set During the conversion an error logging is performed Any errors are logged into the file jcerr lt input file gt in the current directory Even if the file seems to be suc cessfully converted there could have been errors which are logged to this file After successful conversion the converted data set becomes the current data set From VNMR The command
373. trng where it should get the name intrng After calling wmisc the available file types intrng base_info baslpnts peaklist reg are displayed Select the type intrng The program will then show all files which are already present in the directory u exp stan nmr intrng If you select one of those it will be overwritten by the intrng file of the current data set Alternately you can specify a new name e g intrng 1 5 6 8 Copy miscellaneous files from rmisc The meaning of miscellaneous files is presented in the description of the command edmisc The purpose of rmisc is to copy a saved miscellaneous file from the direc tory u exp stan nmr lt misce file type gt to the current data directory rmisc is the inverse command to wmisc 5 7 Delete Data Files The Delete menu Figure 5 14 provides commands to delete data files parameter files and other files used in XWIN NMR The delete commands display a dialog box where the data sets or other files to be deleted can be marked by clicking on them In order to actually delete the marked files the Execute button at the bottom of the dialog box must be activated When deleting data sets other than parameter files etc the bottom of the dialog box contains a button MODE which is a toggle command for the two delete modes delete data parameters and delete data only Remember that an XWIN NMR data set is a directory structure containing data and parameter files If the
374. ttle infor mation about couplings for instance but with a relatively high overall intensity can be reduced in their importance by setting the statistical weight to a value less than 1 0 9 10 3 Requirements for the installation of the DAISY package To run the DAISY program the following files must exist directory program name data type contents function u prog daisy mkux executable converts data formats specprep executable SPECPREP dsym executable DSYMPLOT dcym executable DCYMPLOT ds1 executable DAVSYM1 ds2 executable DAVSYM2 del executable DAVCYM1 dc2 executable DAVCYM2 usr bin specux shellscript starts SPECPREP dsymux shellscript starts DSYMUX dcymux shellscript starts DCYMUX dslux shellscript starts DS1 ds2ux shellscript starts DS2 dclux shellscript starts DC1 dc2ux shellscript starts DC2 u prog daisy doc english text help files u exp stan nmr lists sym text character tables u exp stan nmr lists symnew text character tables It is possible to store the executables anywhere on the disk if the corresponding The Analysis Menu P 226 shellscripts are modified accordingly The character tables are part of the UXNMR program and are automatically stored in the correct directories 9 10 3 1 References For more information please check the manual pages in the directory u prog daisy doc english or refer to the literature published by the authors of the DAISY program package See for instance G Haegele M E
375. u enter edg edg or edgw to change several parameters and exit from the parameter editor to save the new val ues In order to preview the effect of the changes click on the Restart button located in the top bar of the preview window and the plot will be redrawn Particu larly in the case of 2D plots you may have to wait a few seconds until the contour search is finished During this time the cursor shape changes to a clock In order to terminate the preview window click on its Quit button A preview win dow always belongs to the data set from which the preview command was given If you leave a preview window for a particular data set open and change the current data set you may execute another preview command The result is that two pre view windows will be open at the same time containing the plot of the two data sets This procedure may be continued even with more data sets although it might not be very useful The plot parameter CLIP type clip on the keyboard or set it in edg may take on the two values yes or no If set to yes which is the default all parts of a plot not fit ting on the paper will be clipped If set to no those parts will be drawn on addi tional pages Assume for example the coordinates of the plot title are set in edg such that the title would lie outside the paper If CLIP is set to yes the plot would not contain the title text and you may wonder why During previewing a plot we therefore rec
376. u set the step rate to a value bigger than its corresponding variable During the iterative refinement the step rate is adjusted according to the change of the variable If you set the step rate of a parameter to 0 then the variable is not iterated kept constant This feature can be used for instance if you want to fit a two compo nent system with the combined Lorentz Gauss function But for the first compo nent the Gaussian contribution is 0 and for the second component the Lorentzian contribution is 0 In the EDGUESS menu set the parameters as follows GC1IL 0 5 SC1IL 0 05 GCITL 0 1 SCITL 0 01 GC1IG le 20 SC1IG 0 0 GCITG 0 5 SCITG 0 0 GC2IL le 20 SC2IL 0 0 GC2TL 0 5 SC2TL 0 0 GC2IG 0 5 SC2IG 0 05 GC2TG 0 05 SC2TG 0 005 Wrong guesses can lead to completely wrong parameters This is an inherent SIM PLEX problem Always check the RSS root mean square and SD standard devi ation values after a simfit run If you are in doubt about the fit change one guess or more by at least a factor of 5 and repeat the fit If your results remain the same change the guess or guesses by a factor of 5 in the opposite direction repeat the fit and compare all three results Usually the match between the points and the fitted curve will allow you a good judgement of the quality of the fit simfit asc Fit data from the ASCII file tlascii You have to set the same parameters as described for simfit see
377. u want to use this file The handling is the same as for the case vdlist c Enter vclist if you want to use this file The handling is the same as for the case vdlist d Enter dw if you want to use the dwell time DW for automatic calculation of the x coordinates e Enter auto if you want to use individual time values as x coordinates In this case the parameters X_START and LISTINC must be set f Enter any filename in which the x coordinates are stored The file must reside in the acquisition data directory DRIFT Enter the number of drift points The maximum of a peak will be picked if it lies within DRIFT points of the position specified for the point picking START Enter the row number on which you want to define the point positions where later the peak maxima will be searched Normally you will set START to 1 INC Enter the row increment for the point picking Normally you will set INC to 1 which means that the data points are picked from the rows in ascending order 9 6 The T1 T2 relaxation menu P 193 X_START Enter the start value of the x axis Usually you will set X_START to 0 but you can introduce an offset by setting X_START to a value greater than 0 X_START is used only if LISTTYP auto LISTINC Enter the increment between two adjacent data points LISTINC is used only if LISTTYP auto After you have set all relevant parameters leave the editor with SAVE and exe cute the command rspc This will r
378. uencies of all frequencies above the evidence threshold BAYELEV are added to a new model at once If fewer than BAYNADD frequencies are found above the evidence threshold then all those are added at once Frequencies below the threshold BAYELEV are always added one at a time to check the new model s probability Even if the frequencies are added one at a time only BAYNADD frequencies may be added to a model and accepted in one signal detection pass Once BAYNADD frequencies have been added to the model successfully a new signal detection pass will be per formed BAYNPAS If BAY_ANA is set to sig_detection the maximum number of consecutive signal detection passes with intermediate model optimization is set by the parameter BAYNPAS 9 12 7 Bayesian Analysis in AU Programs The module for Bayesian analysis can also be called from within automation AU programs and will work exactly as described above However the Bayesian param eters in the file baypar are handled separately from the other XWIN NMR parame ters and can thus not be accessed via the AU commands fetchpar and storepar The commands fetchbaypar and storebaypar must be used for the Bayesian parameters instead The syntax is exactly the same as for the corresponding commands fetch par and storepar see the chapter on AU programs Example storebaypar BAYAOPT 5 0 The commands uselastpars and usecurpars in AU programs also work with the Bayesian analysis paramete
379. uisition data set ser file the spec trum is stored in the directory of the current data set in the files 2rr 2ri 2ir and 2ii 2rr is the real part which is displayed on the screen or output to the plotter The other files contain imaginary parts with 2ri and 2ir only occuring for phase sensi tive spectra There are various commands for the calculation of magnitude spectra which have the following effects xf2m The contents of 2rr and 2ir are substituted pointwise by Qrr J 2rr 2ir 2ri J 2ri2 2ii2 xflm The contents of 2rr and 2ir are substituted pointwise by 2rr J 2rr 2ri 7 9 Power Spectrum xflps xf2ps xfbps P 165 2ir J 2ir2 2ii2 If the command xf2m has been applied before the final result is thus Qrr J 2rr2 2ir 2ri2 2ii2 xfbm This command has the same effect as xf2m followed by xflm so that the result equals the last formula above 7 9 Power Spectrum xflps xf2ps xfbps These commands are analogous to xflm xf2m xfbm except that the square root is not taken for the calculation of the power spectrum 7 10 COSY Type symmetrization sym syma These commands symmetrize the data points on both sides of the spectrum diago nal which runs from below left to above right The command sym replaces the larger of two symmetrical points with a point which has the same magnitude as the smaller point while syma does the same thing but the replaced point retains
380. um display between contour mode intensity display mode and oblique view mode These operations are screen operations only and do not modify the data file You must click on a button to execute a function Some operations require that you keep the left mouse button pressed while the cursor is located in the command button field and then move the mouse When you move the cursor over the com mand buttons without clicking their function is displayed in the status line at the bottom of the XWIN NMR window 1 Multiply magnify data by 2 lower the cutoff level 2 Divide data by 2 raise the cutoff level 3 Reset the vertical scaling of the data to the default value 1 Multiply data by 8 lower the cutoff level 2 Divide data by 8 raise the cutoff level 3 Vertically scale data arbitrarily lower or raise the cutoff level depending on the direction of the mouse movement You must keep the left mouse button pressed and then move the mouse until the desired scaling is reached This button is only active in intensity display mode not in contour or oblique view mode Scaling is achieved by changing the color lookup table In contour or oblique view mode the contours or the oblique projection must be recalculated These processes are time consuming and cannot be performed in real time 1 Display complete spectrum 2D Data Processing Tutorial P 40 2 Display last zoomed expanded region 3 The purpose of this button is to draw a box
381. urier transform and phase correction depending on the values set for the processing parameters BC_mod WDW FT_mod and PH_mod This command is essentially intended for the experiments performed by the more experienced oper ator trf operates on the acquisition data and generates a processed data set leaving the Fid unchanged The parameters may have the following values Hilbert transform ht The dispersion relations or Kramers Kronig relations see for example R R Ernst G Bodenhausen and A Wokaun Principles of nuclear magnetic resonance in one and two dimensions Clarendon Press Oxford 1987 apply to the real and imaginary parts files Zr and i of a spectrum They state that the real and imagi The Process Menu for 1D Data P 148 BC_mod effect no bc baseline correction will not be executed single subtract bc constant from single detection data quad subtract be constant from quad detection data spol subtract bc polynomial from single detection data qpol subtract be polynomial from quad detection data sfil Bax Maion bc filter for single detection data qfil Bax Maion bc filter for quad detection data Table 6 2 WDW effect no no filter function used EM exponential multiplication GM gaussian multiplication SINE sine multiplication QSINE multiplication with sine squared TRAP trapezoidal multiplication SINC sinc multiplication TRAF traficante window multiplication TRAFS traficante window
382. value of Evidence indicates the most probable and most reliable and therefore hopefully best result e CSIGMA CSIGMA is the statistical noise value determined by MEMSYSS It must be set in maxed if you want the exact comparison of two runs using two different PSFs The Analysis Menu P 232 A more detailed evaluation of the MEMSYSS result can be obtained by running xline 9 12 Bayesian Analysis 9 12 1 Introduction In the past years many alternative methods of data analysis have received increased attention in the field of Nuclear Magnetic Resonance NMR spectroscopy Some of these methods try to avoid the disadvantages of the Fourier Transform trunca tion artefacts implicit periodicity and of the accompanying routine processing apodization filters by extracting all the information of interest directly from the acquired time domain data without tampering with the data first This is a very important principal difference because most NMR spectra do not reflect as accu rately as possible what has actually been measured because of all the data manipu lations that have taken place in order to arrive at the spectrum The Bayesian analysis module in XWIN NMR is based on Bayes Theorem from probability theory and not only allows to fit different time domain models to the raw acquisition data but also to reasonably answer such questions as Can a signal be detected in the data and how well and How many decaying si
383. variable delay list of a T1 experi ment Set the parameter ZLIST VDLIST If the z axis should be labelled with seconds set ZUNIT to sec The program transforms the units in the VDLIST auto matically to the units specified in ZUNIT Then set STKZ1 and STKZ2 to the VDLIST range to be plotted e g 0 3 5 sec STKZ1 is the spectrum drawn first at the bottom of the page STKZ2 the last one STKINC must be set to 0 for this application STKXZ This is the x offset of two spectra on the page It must be specified in cm per z unit according to the parameter ZUNIT STKYZ This is the y offset of two spectra on the page It must be specified in cm per z unit according to the parameter ZUNIT It must have the same sign as STKZ2 minus STKZ1 STKINC This parameter defines the row increment in the z dimension i e it selects which rows of the 2rr file are to be plotted starting at the first row If the value is 0 indi vidual rows may be specified in the array parameter ZARR if ZLIST 0 If 0 and ZLIST gt 0 an application of the type above STKZ1 2 is to be plotted If STKINC is 1 the row index is given by ZUNIT and ZAXIS must be disabled ZARR IF STKINC 0 and ZLIST 0 you may specify the list of rows to be plotted In all The 2D Output Menu P 298 other cases ZARR is calculated from the other parameters ZLIST Select list type ZARR VTLIST VDLIST VPLIST VCLIST If ZARR is selected the row array ZARR must be set manually
384. with the following the name as it would appear in the XWIN NMR data tree the XWIN NMR user directory the rename flag whether the name specified in a is used whether the file is to be converted Each of these items can be edited individually for each entry in the preview table e Hard Copy Flag With this parameter set the contents of the current BRUKNET directory are listed on the default printer e Date Format Flag This parameter indicates the format in which the date is pre sented in the renamed file The following formats are available YYMMDD DDMMYY MMYY The File Menu P 122 For date strings to appear in the XWIN NMR filename the XWIN NMR file format string must contain between two and six 0 s Bruktran Preview Mode Using The Preview Mode The preview mode is enabled by setting the Preview enabled flag to on in the Edit Program Options window and then by selecting the Convert Rename enabled flag in the main menu Preview allows the user to inspect and edit the results of the renaming routine as well as changing the destination directory the renaming select flag and the conversion select flag The Preview Window The layout of the Preview window shows the current BRUKNET data directory the station and the user as specified in the program options Each entry in the table corresponds to one or more files with the same experiment name Each entry con tains the following e Aspect filename without the
385. ws you to define the integration regions manually Select the command Manual integration from the Analysis menu or simply click on the inte grate button of the button panel at the left side of the XWIN NMR window The screen will change to the layout presented in Figure 2 4 The upper part of the button panel is identical to the standard layout and allows you to shift and scale the data on screen In addition there are three special sec tions headed by current all and mouse The command buttons in these sections work on the current integral marked by the user on all integrals on the screen and on the mouse sensitivity respectively Before discussing them we ll explain how to define integration regions Defining integration regions Move the cursor into the data area of the XWIN NMR window Click the left mouse button The cursor is now bound to the spectrum and moves along the spectrum trace when you move the mouse It can be released from there by clicking the left button again Clicking the middle button will mark the current position the mark can be removed using the right button Clicking the middle button a second time at a different cursor position will define the area between the mark and the current cursor position as the integration region and the corresponding integral trace is displayed along with the value of the area under the integral This procedure can be continued for all desired regions Click the left button to
386. y faster AZFW gt 0 will give a better fit of the peak edges and of the region between the signals or signal groups 4 Set up the so called second data set using the command edc2 The result of the deconvolution which is the sum of iterated Lorentzian or Gaussian lines will be stored there Since this data set is displayed above the current data set in Dual Display mode you can compare the two spectra after termination of Idcon gdcon or mdcon by simply clicking on Dual display in the Display menu Usually one uses the next available PROCNO for the second data set while taking over the remaining parameters NAME EXPNO DU and USER from the current data set It is convenient to store a series of deconvolutions by incrementing the PROCNO numbers This facilitates comparing the spectra using the Incr PROCNO commands in the Display menu of the dual display routine 5 Upon termination of a fit XWIN NMR will output the result the position inten sity integral of the iterated lines Set up the parameter CURPRIN using the command edo to define the output device for the fit result CUR PRIN screen output to screen CURPRIN lt printer gt output to specified printer CURPRINT lt file path name gt output to a file 6 Now you are ready to start deconvolution with Idcon or mdcon Caclulation speed depends on the selected spectral region and of the number of lines therein The iteration cycles are displayed on XWIN NMR s status line info
387. y mode base line is the baseline trace which may be real time adjusted in manual baseline mode Background was already described above Please note that these colors do not influence plot colors which must be defined separately when setting up the plot layout Chapter 13 The Windows Menu The Windows menu contains XWIN NMR commands which generate new windows Figure 13 1 The Windows menu independent of the main XWIN NMR window They may remain on screen simulta neously with other windows of this type and with the main XWIN NMR window Since XWIN NMR is a multi tasking program the commands are executed in paral P 313 The Windows Menu P 314 13 1 lel For example if a data acquisition is in progress and the lock and the amplifier control windows are open the contents of all three windows are refreshed at the same time and the user may at any time move the mouse into one of the windows and execute a command Command panel cpan The command cpan in the Windows menu allows you to display a command but ton panel whose contents and layout may be tailored according to your require ments The command panel consists of an arbitrary number of buttons that you may label with your own text You must set up a panel file where you specify the button labels the corresponding XWIN NMR command and a help text The name of the panel file is default Its must be located in the subdirectory xwinnmr lt hostname gt cmdpan
388. ysis Menu P 204 either with simfit or with simfit asc Here is an example you can try to fit Enter the following lines in the file t ascii SIMFIT 2 0 1 99 48 0 5 90 44 1 0 81 39 2 0 64 33 3 0 48 23 4 0 34 17 6 0 10 6 8 0 10 5 10 27 13 15 0 55 26 20 0 73 38 40 97 50 Use the following parameter setup in edt to fit the above data points IFCTTYPE tnvrec COMPNO I Click on EDGUESS and enter the following guesses GC110 11 0 SC1I0 D 1 GC1A 1 0 SCIA 0 1 GCIT1 1 0 SCIT1 0 1 Leave the editor and type simfit asc The display should be the same as the one shown in Figure 9 8 Type nxtp and then simfit The display should be the same as the one shown in Figure 9 9 Important notes Simfit and simfit asc cannot be used alternatively if a baslpnts and a tlascii file exist and the two files contain different numbers of peaks 9 6 The T1 T2 relaxation menu P 205 If you have placed the t ascii file into a processing data directory where you previ ously used pd pdO or pft2 to pick points then the simfit asc command will over write all auxiliary files created by these commands With the command pd pdO or pft2 you will on the other hand overwrite the auxiliary files created by the simfit asc command This does not really present a problem you can switch between different ways of picking points this way But be aware of this alternat

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