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Users Guide - UC Davis Nuclear Magnetic Resonance Facility

1. 122 Chapter 9 8 5 8 6 8 7 How to Display the PID cesce knea a naa ea a ewe s LD Display Opuonss srana e dus cha ensaes Saas eas eet How to Toggle between Hertz and ppm Axis Units How to Switch on off the Spectrum Overview display How to Switch Y axis Display 0 ccc cece eens Show Display Properties Regions Files 00 0 ee eee How to Superimpose the Cursor Information How to Superimpose the Title on the Spectrum How to Superimpose the main Status Parameters on the Spectrum How to Superimpose the Integral Trails Labels on the Spectrum How to Superimpose Peak Labels on the Spectrum How to Show Individual Data Points of the Spectrum How to Display the Main Dataset Properties How to Display a List of Files of a Dataset Savin Display REGION 4 6 5 4 4 5c8 4085 od te ded CUA a MESA oe ees A How to Save the Display Region for Re display How to Save the Display Region for Baseline or Phase Correction How to Save the Display Region for Strip FT ZD DISDIAY 24 2 tice tar teenie Hed ate Rea a dears 9 1 9 2 9 3 9 4 9 5 The2D Data Widow iaiia aare e avandercd bea dbaewe awa Changing the Display of a 2D spectrum 00 0c How to Change the Intensity Scaling 0 00000 How to Swit
2. 173 ID Interactive Calibrations 003 04 has ee eae ee aa eens ewes 173 How to Switch to Calibration Mode 0 0 0 e ee eee 173 How to Calibrate a Spectrum Interactively 04 174 TD Multi ple Display sarres ta bocks pE we dla nok de ede eS gale Rane a aka 175 How Switch to Multiple Display Mode and Read Multiple Spectra 175 How to Select Deselect Datasets w2 scswsattesewavedegieccras 178 How to Remove a Dataset from Multiple Display 178 How to Display the Sum or Difference Spectra 179 How to Save the Sum or Difference Spectra 179 How to Display the Next Previous Name Expno 179 How to Toggle between Superimposed and Stacked Display 180 How to Shift and Scale Individual Spectra 180 How to Switch on off the Display of Datapaths and Scaling Factors 181 How to Return from Multiple Display mode 182 How to Set the Colors of the 1 24 Dataset 000000 cee 182 1D Interactive Baseline Correction 0 0 0 0 cece eee eens 182 How to Switch to Baseline Correction Mode 04 182 How to Perform Polynomial Baseline Correction 183 How to Perform Sine Baseline Correction 00005 183 How to Perform Exponential Baseline Correction 184 How to Preview the Baseline Corrected Spectrum 184 How to Reset the Baseli
3. 62 60 58 56 54 52 F2 ppm How to Switch on off the Projection display r Click the following toggle button in the upper toolbar 4f j Switch the projection display on off pr With the projections displayed a 2D dataset looks like this x Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid F1 ppm 120 6 4 2 F2 ppm In this example the F1 projection is selected as indicated by the filled blue square 146 2D Display whereas the F2 projection is not selected A selected projection can be rescaled using the toolbar rescale buttons of function keys If you right click inside the pro jection area of the data window the following popup menu appears External Projection Internal Projection Baseline At Center baseline At Bottom Clicking External Projection opens the a dialog box where you can specify or search for a 1D dataset and display this as a projection of the current 2D dataset Clicking Internal Projection calculates and displays the positive projection and displays it along with the 2D spectrum Clicking Baseline at Bottom or Baseline at Center allows you to put the projec tion baseline at the respective positions Various other projection features are available To access them click Processing Calculate projections proj This will open the dialog box shown in Fig 9 11 2D Display 147 CT x Options C
4. Start Edie Options Clicking Options will open the following dialog box Acquisition 261 TT x Temperature monitor optians scale kelvin Update rate s 30 OK Cancel Figure 15 5 15 4 Tuning and Matching the Probehead Tuning and matching of conventional probeheads non ATM is performed with the wobble procedure To start this 1 Enter wobb on the command line This opens the wobble window see Fig 15 6 262 Acquisition Figure 15 6 The buttons of the wobble toolbar have the following functions Change the number of wobble steps wbst Change the wobble sweep width wbsw ea I Change the wobble frequency it Switch to the next channel nucleus if available Gi Stop the wobble procedure Stop the wobble procedure and close the wobble window 2 Turn the tuning and matching knobs on the probehead until the wobble curve is exactly in the middle and its minimum reaches the zero line Automatic tuning and matching of ATM probeheads can be performed with the command atma Acquisition 263 15 5 Locking The lock display can be opened by clicking the Ea button in the toolbar or enter ing Lockdisp on the command line The lock display window will appear see Fig 15 7 0 x SS Wseeee s Figure 15 7 Here you can view the lock signal either during the lock in procedure or as shown above after lock in has been successful At the
5. and b 1 Note that the element a 0 is listed separately Acquisition 2T PA ShapFour Coefficients o s al Coefficient al Coefficients bi Coeficients OK Apply Save cancel Figure 15 18 Here you can enter the desired coefficients and then click Save to store the coefficients for later usage You will be prompted for a filename which will be stored as lt user home gt topspin hostname shapetool Apply to display the shape while keeping the dialog box open for possible further changes OK to display the shape and close the dialog box With the coefficients above you have created a Rsnob shape To save it Click E enter a Name e g myrsnob Title Flip Angle and the Type of Ro tation see chapter 15 9 5 and click OK 15 9 7 How to Analyse Shapes The Shape Tool interface offers several functions to analyse shapes Most of these functions are only meaningful for RF shapes To access these functions t Click Analysis 278 Acquisition in the TOPSPIN menu bar This will open the pull down menu shown in Fig 15 19 Calculate Bandwidth for Excitation bandw2 Calculate Bandwidth for Inversion band 2i Calculate Bandwidth for Refocusing wiw bandwry Special Bandwidth Calculations b Calculate gammab max calch1 mo Calculate gammabi max for Adiabatic Shapes calch1 adial Calculate Bloch Siegert Shift bsiegerts Calculate average Power Level ralcpay Integrate Shape
6. 005 4 Trouble SHOOUnS srssiussenii ti hea da ede nie edd aces 43 Sl eneral Tipsand Ticks a2 occu eaen DSE LEN eee TSA 43 3 2 History Loe Files Stack Traces i i ieencd tected ohdae aadat aaa 43 3 3 How to Show or Kill TOPSPIN processes 00 0c eee 47 3 4 What to do if TOPSPIN hangs 0 eee ees 47 3 5 How to Restart User Interface during Acquisition 48 Dataset Eh An oui sass cise werd ig dk aan SiS are HS Gea Wee a 49 4 1 The Topspin Browser and Portfolio 20 0 0 eee eee 49 How to Open the Browser Portfolio 20 0 cc cee eee 51 How to Open the Browser Portfolio in a separate window 51 How to Put the Focus in the Browser Portfolio 51 How to Select Folders in the Browser 0 0 0 0 51 How to Expand Collapse a Folder in the Browser 52 How to Expand a Folder showing Pulse program and Title 52 How to Add Remove a Top Level Data Directory 53 How to Open a New Portfolio 2 0 eneee ian ee ees 53 How to Save the current Portfolio 0 0 0 cc eee eee 54 How to Remove Datasets from the Portfolio 54 How to Find Data and Add them to the Portfolio 54 How to Sort Data in the Portfolio 0 0 0 0 cece eee 54 How to Add Remove or Interpret Alias Names 55 AD Credung Wales 24s sng tous cana ene eee be oe ee eee Ree 56
7. 163 How to Perform 90 90 or 180 Zero Order Phase Correction 163 How to Reset the Phase to the Original Values 163 How to Change the Mouse Sensitivity 0 0 0 00 163 How to Return from Phase Correction Mode with without Save 164 11 2 1D Interactive Intecration s 4403i442 be etadedeekteteied dekete Ga 164 How to Switch to Integration Mode 0 000 eee 165 How to Define Integral Regions 0 0 0 cee eee eee ee 166 How to Select Deselect Integral Regions 040 166 How to Read Integral Regions from Disk 0000 167 How to Perform Interactive Bias and Slope Correction 168 How to Set the Limit for Bias Determination 169 How to Change the Mouse Sensitivity 0 0 0 00 cece 169 How to Calibrate Normalize Integrals 20 0 eee 169 How to Scale Integrals with respect to Different Spectra 170 How to Delete Integral Regions from the Display 170 How to Scale Selected Integrals 0 0 0 0 cc eee ees 171 11 5 11 6 How to Move the Integral Trails Up Down 172 How to Cut Integral Regions rimpianta eng ai 172 How to Save Inteoral Recions s 2 2c3 264 0 tensed taddema diate wes 172 How to Undo the Last Region Operation 000 173 How to Return from the Integration Mode with without Save
8. Click the Change button to the right of the Command line font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font Click Apply A om Fb UO N m How to Change the Font of the Status Line Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Status line font object Click OK to store the new font 1 2 3 4 Select the desired name style and or size in the appearing dialog box 5 6 Click Apply 18 4 Command Line Preferences How to Resize the Command Line By default the TOPSPIN command line shows one command the command that is User Preferences 323 currently entered e g apk However you can resize the command line to show the currently entered com mand plus the last and second last command e g em apk You can toggle between the two different command line sizes as follows e Click View Resize command line Or e Right click in the command line and click Resize command line How to Set the Minimum and Maximum Command Line Size By default the size of the command line can be toggled between 1 and 3 You can however change this minimum and maximum value respectively To do that 1 Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Specify the Minimum visible command lines gt
9. a Some buttons will turn green when they are clicked As long as a button is green it is active Furthermore the browser portfolio is split in two parts as shown in Fig 11 9 examid 130 3 1 Cobiot examid 130 2 1 Tipio examid 130 1 1 Cobiol quest Figure 11 9 178 1D Interactive Manipulation The additional lower part shows e which datasets are displayed in the active data window e which datasets are selected these are highlighted How to Select Deselect Datasets To select a dataset r Click in the corresponding area in the data window or Click the small square at the upper right of the spectrum or Click the corresponding entry in the lower part of the browser portfolio In the lower part of the browser portfolio you can r Click one dataset to select it or Hold down the Ctrl key and click multiple datasets to select them or Hold down the Shift key and click two datasets to select these two and all datasets in between When you select a dataset the corresponding small square is filled see Fig 11 8 and its entry in the lower part of the browser is highlighted see Fig 11 9 Note that e no spectrum selected all spectra selected e scale shift buttons of the data window toolbar only work on selected spectra To deselect a dataset r Select a different dataset To deselect all datasets r Click the following button 4 Deselect all datasets How to Remove a Dataset from Multiple Dis
10. integral 1 21307940 16 1 6664 Integral 2 20864697 28 1 5945 A Object Integral abs Intec Integral 4 131427635 19 10 0425 Integral T 20492465 62 1 5658 L integral 6 10685317028 12 01 6307 examid_ 1H 1 1 Cibin guest 2 0 x rocPars AcquPars Title PulsProg Peaks Integrals Sample aj 0 5 1 0 rel 8 0 7 5 7 0 65 ppm Figure 8 6 This displays the integral list upper part of Fig 8 6 By default this shows the following items Object the integral number Integral abs the absolute integral value Integral rel the relative integral value Peaks the number of peaks within the integral range Range F1 from the left edge of the integral range 116 1D Display Range F1 to the right edge of the integral range Please note the difference between the following items Display the spectral region around an integral To display the spectral region around a particular integral r Right click the desired integral This will open the popup menu shown in Fig 8 7 Collapse Expand all Collapse all Show SHectruin b Delete In correlated window Deine as reference Calibrate by reference Copy Export Import Table properties Figure 8 7 Here you can choose from the following options tS Show spectrum In correlated spectrum selected integral the entry that has been clicked last Integral 3 in Fig 8 6 If you right click an en
11. 1 Put the cursor at the upper left corner of a peak picking range 1D Interactive Manipulation 189 2 Left click hold and drag the mouse to the lower right corner of the range The peak picking range will be marked green The minimum and maximum intensity are set and the peaks in the range are picked and displayed 3 Repeat step 1 and 2 for each peak picking range to be defined 4 Click the green button to leave the Define peak picking range mode Note that the parameters MI and MAXI are set to the lowest minimum and the highest maximum intensity respectively of all ranges How to Change Peak Picking Ranges 1 Click the following button button turns green im Change peak picking ranges 2 Put the cursor on one of the edges of the peak picking range The cursor turns into a double headed arrow 3 Left click hold and drag the peak range edge to its new position 4 Optionally repeat step 2 and 3 for the other edge and for other peak ranges 5 Click the green button to leave the Change peak picking range mode How to Pick Peaks in Peak Picking Ranges only Peaks in a peak range are automatically picked when the range is defined If peaks have been deleted from a rang they can be picked again as follows 1 Right click in the data field 2 Choose Pick Peaks On Ranges from the popup menu Alternatively you can enter pp1 on the command line This command can be en tered in Interactive peak picking mode or in the
12. 100 Tes 1e4 Figure 15 8 The individual functions BSMS control panel are described in detail in the Acqui sition Reference manual 266 Acquisition 15 7 Interactive Parameter Adjustment GS Several parameters can be adjusted interactively while observing the acquired FID To start this rs Enter gs on the command line A split window will appear showing e the FID display see Fig 15 9 e the GS parameter adjustment dialog see Fig 15 10 NZ 2000 0 2000 0 2 04 06 08 10 12 1 4 5 Figure 15 9 The buttons of the FID display are the same as for the acquisition command zg see paragraph Fig 15 8 The GS parameter adjustment dialog offers tabs at the top of the window to select power frequency delay etc The selected parameter is shown in the middle of the window The slider at the right of the window allows you to change the selected parameter The current value can be viewed and modified in the field below the slider The sensitivity of the slider can be set in the field Sensitivity above the Acquisition 267 SquarePower Frequency l Delay Receiver RetPhase Offset Pulse i a sensitivity h 1 r adjust max 3138 51 Offset Oi Hz min 3038 51 3088 51 DAYE Save all Restore Restore all stop s a Figure 15 10 slider The effect of the change can be viewed in the FID display the right part of the window This can be manipulated w
13. 300 Configuration Automation How to Change the NMR Administration Password The NMR Administration password can be changed as follows Under Windows 1 Login as NMR Superuser or Administrator 2 Open a Command Prompt 3 Enter lt x gt perl bin perl lt x gt prog bin installnmr lt x gt lt NMRSUPERUSER gt where lt x gt in the TOPSPIN installation directory 4 Enter the old password and new password as requested Under Linux 1 Login as NMR Superuser or root 2 Open a Shell 3 Enter lt x gt prog bin installamr lt x gt lt NMRSUPERUSER gt where lt x gt in the TOPSPIN installation directory 4 Enter the old password and new password as requested If you don t know the old NMR Administration password you can still define a new one In that case you have to delete the file lt x gt conf nmradminpassword before you run the installnmr script 16 2 Configuration The main configuration steps are performed by the commands cf and expin stall They can be started from the e Command line e Options Spectrometer tools menu e Spectrometer Setup menu However the Spectrometer menu is only available after c f has been performed Configuration Automation 301 once choosing Installation for spectrometer How to Perform a Default Configuration on a Datastation A default configuration can be used on a datastation It is automatically performed no cf required during the installation of
14. Il Reset the mouse sensitivity How to Return from Phase Correction Mode with without Save To return while saving the phase correction to the current dataset r Click the following button EJ Save execute and return sret This will perform the following tasks Execute phase correction command pk Save the current phase correction values Leave the phase correction mode To return without save r Click the following button a Return discarding any changes ret To return while saving the phase correction to the source 2D dataset r Click the following button EL Save to 2D s2d This is only applicable on rows or columns extracted from 2D data The phase values will be saved to the 2D dataset from which the current 1D data set was extracted 11 2 1D Interactive Integration Integration of 1D data can be done automatically with the commands abs and 1i or interactively as described in this paragraph 1D Interactive Manipulation 165 How to Switch to Integration Mode r Click the indicated button in the upper toolbar jhe JP at Sati ts or enter int on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 2 examid_1H 1 1 C bio1 quest q _ O x T da folja BA Atlan lxel le2 z a gt a Mouse Sensitivity 1 0 m 4 08 ppm lee4 36 Hz f T 15 10 5 0 ppm Figure 11 2 Data window in integration mode
15. lo 4 sa380 Spectral zm E H Figure 5 1 At the left of the parameter editor window you will see a list of parameter sec tions The processing parameter editor supports the following functions Parameter Handling 81 x Enter part of a parameter name in the search field and click r Click a parameter section e g Phase at the left of the dialog box The sec tion becomes highlighted and the corresponding parameters will appear in the right part of the dialog box r Click in a parameter field e g PHCO to set the parameter value rs Hit the Tab key to jump to the next parameter field c Hit Shift Tab to jump to the previous parameter field t Use the scroll bar at the right of the dialog box to move to parameters fur ther up or down in the dialog box How to Undo the Last Processing Parameter Change r Click the following button 1 Undo last parameter change How to Display Processing Status Parameters r Click the following button g Show processing status parameters Note that the command dpp opens the parameter editor and automatically shows the status parameters How to Change Processed Data Dimensionality r Click the following button 123 Change data dimensionality This changes the number of parameter columns and value of the processing pa rameter PPARMOD The parameter editor does not allow you to modify status parameters Processing status parameters reflect the status of the proce
16. 31 Show F3 F1 plane 10 3 Using the Tab bar The 3D data window is a tabbed pane This means its contents depends on the currently active tab in the Tab bar The individual tabs are basically the same as for 1D and 2D display see chapter 8 4 When you click the ProcPars or AcquPars tab you will find a parameters column for each of the three dimen sions F3 F2 and F1 The Fid tab allows you to display the 3D raw data as a series of 1D FIDs The Peaks tab will display the 3D peak list with a column for the chemical shift in each of the three dimensions Similarly the Integrals 160 3D Display tab will display the 3D integral list Peaks and integrals only appear if they have been calculated commands pp and int respectively When the integral list shows peaks with a column for the chemical shift in each of the three di mensions appears Like in 2D a stored or exported 3D integral list can be im ported see Fig 9 4 Chapter 11 1D Interactive Manipulation The upper toolbar of the 1D menu offers various buttons for interactive manipula tion If you click such a button the active data window will switch to the corre sponding mode An interactive manipulation mode is data window specific 1 e it only applies to the active window 11 1 1D Interactive Phase Correction Manually acquired spectra can be phased corrected automatically with commands like apk or apks or interactively in phase correction mode 11 1 1
17. 4 922190 20 345053 e 4 H 4 Figure 9 5 How to Set Acquisition Parameters r Click the AcquPars tab eda The 2D acquisition parameter editor contains a column for each of the two di mensions F2 and F1 Note that not all parameters exist in both dimensions see Fig 9 6 2D Display 14 exam2d HC 1 1 Cobo guest el es Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid o s A Experiment F2 F1 Frequent width Experiment Receiver PLILPROG hmacgpat Current MUCU AG mod DOL Acquistti Durations FnkiODe oF Acguisti Power TD fi O24 fi 20 Size of f Frograr MHS fa of Figure 9 6 How to Display the Peak list t Click the Peaks tab examz2d_HC 1 1 Cjbio guest spectrum ProcPars AcquPars Title PulsProg Peaks Integral OF2 ppr OF 1 pr Intensity Annotation r 2405 1285 2951 32061761 56 pk1 4 2692 4 4625 9039344 24 pk2 5 7906 59 4354 9562402 76 pk 5 367 56 3070 6569930 29 pk Figure 9 7 This displays list of peaks if these have been calculated command pp The list is basically the same as for 1D spectra The only difference is that there are two columns for the two dimensions now and an extra column for peak annotations v F2 ppm the chemical shift in the F2 direction v F1 ppm the chemical shift in the F1 direction 142 2D Display Annotation the peak annotation T
18. In the title bar you can Left click hold amp drag to move the window Double click to maximize the window Right click to open the title bar menu Access the minimize maximize and close buttons at the right Access the title bar menu button at the left How to Use the Menu bar The menu bar contains the following menus File performing data file handling tasks Edit copy amp paste data and finding data View display properties browser on off notebook Spectrometer data acquisition and acquisition related tasks Processing data processing Analysis data analysis Options setting various options preferences and configurations Window data window handling arrangement Help access various manuals Experienced users will usually work with keyboard commands rather than menu commands Note that the main keyboard commands are displayed in square brackets behind the corresponding menu entries Furthermore right clicking any menu entry will show the corresponding command 30 The TOPSPIN Interface How to Use the Upper Toolbar The upper toolbar contains buttons for data handling switching to interactive modes display settings and starting acquisition Buttons for data handling 1S e Bee 3d The functions of the individual buttons are Create a new dataset Ctr1 n new Open a dataset Ctrl1 o open F Save the current dataset Ctrl1 s sav Sei Email the current dataset smai1 am
19. Multiplet Ticks M JRK Cancel Figure 14 18 Distance lines the default number of distance lines in the multiplet dialogs Capture range the search range for maximum intensity of peak position in manual mode Drift range the maximum difference in data points between line distances within one multiplet Min Intensity The minimum intensity of a peak compared to the reference peak to be accepted as a multiple line Min Delta J the minimum ratio of the difference in chemical shift of the coupling groups and the coupling constant Below this value the coupling constant in the Report box is indicated with a question mark to suggest pos sible second order effect Labels Vertical displays multiplet labels 90 rotated All toolbar functions are also available from a popup menu which appears when you right click in the data window see Fig 14 19 Analysis 253 Save and close Define Multiplet By Region Define Multiplet Manually Define Multiplet By Free Grid b Couple Existing Multiplets Define Multiplet by Coupled Grid ohit Single Line Define Multiplet identifier Delete Multiplet Designate Multiplet Connect Multiplets Disconnect Multiplets Molecule Operations b Figure 14 19 When you have finished multiplet analysis you can save your work and exit from multiple mode as follows Save multiplet analysis EJ Save multiplet analysis and quit Quit multiple analysis mode The multipl
20. TOPSPIN Users Guide Copyright C 2005 by Bruker BioSpin GmbH All rights reserved No part of this publication may be reproduced stored in a retrieval sys tem or transmitted in any form or by any means without the prior consent of the publisher Part Number H9469SA1 V2 January 31st 2005 Product names used are trademarks or registered trademarks of their respective holders Bruker software support is available via phone fax e mail Internet or ISDN Please contact your local office or directly Address Bruker BioSpin GmbH Software Department Silberstreifen D 76287 Rheinstetten Germany Phone 49 721 5161 455 Fax 49 721 5161 943 E mail nmr software support bruker biospin de FTP ftp bruker de ftp bruker com WWW www bruker biospin de www bruker biospin com Chapter 1 Chapter 2 Getting Started s 600 4s2eiie rs ieee eee a E aa 15 Ll Document CONVENUIONS s i5 5 06 25 40 odwad edad etewe eat eed bused 15 FOnUC On VENOMS uirri tean a eure eke ak ene ae aa 15 Pile directory Convenvuions lt Acstnaee tenn naked heehee seen s 15 Wser Achom COnvenuOns ci0 cpAauataces en aA ane ahaa ae desae 15 2 TOPSPIN OVENI EW asarira A a debe Ss Cie T ees 16 PUNCHUONANCY snus atlas ase eau ana a RANA GA 16 Available Documentation 00 ccc ccc cece ERN G ENA 17 Ld TOPSPIN NCCNSE lt 2 beni acre RE Ed He eB G eed aes dee Aes 17 Lae Sarup TOPSPIN s jn oct eda nc er oe hel ede eee awe eed Swe 18 IS CO
21. To put the baseline at the bottom of the data window 1 Right click in the data window 2 Choose in Baseline At Bottom from the popup menu see Fig 12 11 This works both in the scan submode or on a grabbed row column 12 3 2D Interactive Calibration A 2D spectrum can be calibrated automatically with the command sref or inter actively as described below How to Switch to 2D Calibration mode r Click the corresponding button in the upper toolbar Id 3d 4 LAY The Tab bar of the active data window will be replaced by a toolbar see Fig 12 14 2D Interactive Manipulation 207 WW exam2d_Hc 11 Cibo guest O x F2 ppm Figure 12 14 Data window in calibration mode A The yellow button indicates that the data window is in calibration mode How to Perform 2D Calibration In calibration mode 1 Left click in the data window at the reference peak The following dialog box will appear Poj calibrate xj Spectrum calibration frequency F2 ppr F1 per Ti 24417 JK Cancel Note that the units for F2 and F1 Hz or ppm correspond to the axis units of the display 2 Enter the F2 and F1 frequency you want to assign to the reference peak 3 Click OK 208 2D Interactive Manipulation The spectrum will be calibrated and re displayed The calibration button will turn grey again 12 4 2D Chemical Shift Distance Measurement How to Measure a 2D Chemical Shift Distance
22. e Parameter Index alphabetical list of parameters with help option e Acquisition Reference Guide acquisition commands parameters and files e Processing Reference Guide processing commands parameters and files including Linear Prediction Relaxation T1 T2 and Deconvolution e Installation Guides TOPSPIN Windows Linux Release letter e Programming manuals AU Macro and Python Programming e Application manuals High resolution Solids LC Diffusion e Accessory manuals operation of VTU MAS ACB Cortab ATM e NMR Guide NMR Guide knowledge base 1 3 TOPSPIN license TOPSPIN requires a license for startup A license can be ordered online from www bruker biospin de NMR nmrsoftw licenses index html If your PC controls a spectrometer TOPSPIN will start up without a license Fur thermore you can use TOPSPIN for developer purposes with restricted functional ity In this case you have to start it from a Windows Command prompt or Linux shell as follows topspin developer 18 Getting Started 1 4 Startup TOPSPIN Under Windows r Click the TOPSPIN icon on the desktop Or c Start TOPSPIN from a Command Prompt as follows 1 Click Start Run enter cmd and click OK 2 In the Command Prompt a Entercd lt tshome gt b Enter topspin where lt tshome gt is the directory where TOPSPIN is installed Under Linux 1 Open a Linux Shell or Terminal Window 2 In the Shell Terminal a Entercd lt tshome gt b
23. tory e NM indicates the start of the second icon column e NM2 the text to appear underneath of the icon The sign is mandatory e CMD the command to be executed when the icon is clicked This can be a regular TOPSPIN command a macro or an AU or Python program e TIP the tooltip to be displayed when the cursor is held over the icon Note that the sign is mandatory Before you can start a user defined guide you must edit the file cmdtab user prop and define the corresponding command in the file for example mytiguide EM J MC N CL tutor TutStarter ME startTuto rial AR MyT1T2Toolbar My T1 T2 Tutorial Here e MyT1T2Toolbar is the toolbar identifier as it is used in the file toolbar _user prop e My T1 T2 Tutorial is the title as it appears at the top of the guide If your guide is a Bruker modified guide you can also redefine the origi nal Bruker command 1 e specify t 1guide instead of myt lguide Note that the original Bruker guide is then no longer accessible If you want to access a user defined guide from the TOPSPIN toolbar you have to create a new toolbar button To do that right click in an empty area of the toolbar and define a button in the appearing dialog Index Symbols 2 command 31 37 104 135 8 command 31 104 135 2d command 30 3d command 30 all command 32 105 137 basl command 182 bmp files 22 bzip files 23 66 cal command 174 co command 148 dec
24. 1 Click the following button button turns green 1 Chemical shift distance measurement 2 Click hold the left mouse button at one peak position and drag the mouse to another peak position The distance in ppm will be displayed 3 Right click in the data window to quit distance mode button turns grey exam2d_HC 1 1 Cjbioi guest oj x Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Struct Le Distance measurement S iFZ 2 34 ppm 702 72 Hz Fl 18 96 ppm 1431 19 Hz Distance 19 10 ppm 1594 40 HE 12 10 8 6 4 2 F2 ppm Figure 12 15 Data window in distance measurement mode 12 5 2D Integration TOPSPIN provides automatic 2D integration Before you do this you must first per form peak picking using the pp command Automatic 2D integration can be started as follows 2D Interactive Manipulation 209 us click Analysis Integration int This opens the following dialog box PA Integration _int2d C Auto integrate all peaks in the peak list absolute threshold Required parameters Relative threshold G hile1 o 0n3892632 Absolute threshold 262783 0 JRK Cancel Help Figure 12 16 Here you can choose between integration using a relative or absolute threshold and set the required parameters Integral regions are only determined for picked peaks The calculated integrals will be marked in the data field with the letter I and c
25. 153 Chapter 10 3D Display crrerisicierces cae ea oe awGixaeaeeeadeeaeaa 155 LOM Plane Display Mode v c 05 0 Sue oer Bee ae ENG A ead whe Se aces 155 How to Switch to 2D Plane Display 0 0 0 0 cee eee 156 How to Display various Plane Orientations 156 How to Display various Plane Positions numbers 157 LOZ Cube Display MOG svi toned wees ewe Anar Oe Ee aoe bk 157 How to Display the 3D Cube tie ced dew deS owed a eae eae s 157 How to Rotate the 3D Cube aac ci5c00 62405 breno biago Peace Paws 158 How to Scale Up Down the 3D Cube 0050 158 How to Reset the Cube Size and Orientation 158 How to Switch Depth Cueing on off 0 0 0 0 00 159 How to Display a Cube Front or Side view 004 159 OSs Usma the Tab bat css is dak tate tie Sess oes a oN am amp dat aah 159 Chapter 11 1D Interactive Manipulation cccccccccccees 161 11 1 1D Interactive Phase Correction 0 0 0 cece ees 161 How to Switch to Phase Correction Mode 0 000005 161 How to Perform a Typical 1D Interactive Phase Correction 162 How to Set the Phase Pivot Point 0 0 0 0 eee eee 162 How to Perform Default Zero Order Phase Correction 163 How to Perform Interactive Zero Order Phase Correction 163 How to Perform Interactive First Order Phase Correction
26. 198 How to Perform 90 90 or 180 Zero Order Phase Correction 199 How to Reset the Phase to the Original Values 199 How to Change the Mouse Sensitivity 0 0 0 199 How to Show the Next Previous Row or Column 199 How to Arrange Rows or Columns 00 0c eee eee 200 How to Return from Multi 1D Phase to 2D Phase Display 200 How to Return from 2D Phase Mode 0000 200 12 2 2D Multiple Display and Row Column Handling 200 How Switch to Multiple Display mode and Read Multiple Spectra 201 How to Align Multiple 2D Spectra 0 0 0 0 cee eee 203 How to Scan Rows Columns 0 0 00 0 ee ees 203 How to Grab a Row Column 0 0 0 cece ees 204 How to Extract a Row Column 0 0 00 00 cece ee eee 205 How to Copy Contour Levels from First to Other Spectra 205 How to Switch on off 2D contour display 000 205 How to Position the Baseline of the Row Column 206 123 2D Interactive Calibration 24 25 da k5d a ara adds oe dw oes 206 How to Switch to 2D Calibration mode 08 206 How to Perform 2D Calibration 0 0 00 00 00000 e ee 207 12 4 2D Chemical Shift Distance Measurement 208 How to Measure a 2D Chemical Shift Distance 0 208 2 2D meas ane eet a aed amp ae ache a
27. Dialogs f Icons Save spectral window colors as a new color scheme DAVE aS Window settings Background color Ue eels Color of 1st 1D spectrum a Directory path names Acquisition status bar Color of 2nd 1D spectrum Change Acquisition Color of 3rd 1D spectrum Co Change Lock display Color of 4th 1D spectrum DO chance Color of axes a Change Figure 18 1 Click the cathegory of which you want to view change certain objects It will become highlighted and the corresponding objects will be displayed at the right part of the dialog box For example if you click Spectrum the spectrum objects will appear at the top of the dialog box The rest of this paragraph will describe some examples of setting various user preferences How to Define the Startup Dataset TOPSPIN allows you to define the dataset to be displayed after startup To do that 1 Open the Windows Explorer and navigate to the user properties directory enter hist in TOPSPIN to identify this directory 2 Open the file autostart prop and enter the desired startup command with the following format _VERSION 1 0 cmd lt arbitrary name gt lt topspin command gt Note that the file normally exists and the first line is already there User Preferences 315 Example _VERSION 1 0 cmd read spectrum re examld 13C 1 1 c bruk ts guest The above lines would cause TOPSPIN to display the dataset C bruker ts data guest nmr exam1d_13C 1 pdata 1 after startup Note
28. E The yellow button indicates that the data window is in integration mode Some buttons will turn green when they are clicked As long as a button is green it is active If integral regions have already been determined for example with abs or with a previous interactive integration these regions are displayed in the data window along with the integral values You can remove them change them or add to them as described below 166 1D Interactive Manipulation How to Define Integral Regions To define integral regions interactively 1 Click the following button button turns green 4 Define integral region interactively 2 Put the red cursor line at one edge of a peak or multiplet 3 Left click hold and drag the cursor line to the other edge of the peak or mul tiplet 4 Do step 2 and 3 for all regions to be defined 5 Click the green button to leave the define region mode button turns grey To define integral regions via a dialog box 1 Click the following button d Define region via dialog 2 In the appearing dialog box edd Exact coordinates of integrated area F1 fpr From 43 To fa O JRK Cancel Enter the exact values for the region limits 3 Click OK to define the selected region How to Select Deselect Integral Regions To select deselect all displayed integral regions r Click the following button Select Deselect all regions To select a single integral region 1D
29. E x 2 Click hold button A and move the mouse until the red line coincides with the first point of the spectrum 3 Repeat step 2 with the buttons B C D and E until the red line coincides with the entire baseline of the spectrum How to Perform Sine Baseline Correction 1 Click the following button button turns green 184 1D Interactive Manipulation E Perform sine baseline correction A red horizontal line will appear as well as the equation describing the sine function f x A B sin C x D 2 Click hold button A and move the mouse until the red line coincides with the first point of the spectrum 3 Repeat step 2 with the buttons B C and D until the red line coincides with the entire baseline of the spectrum How to Perform Exponential Baseline Correction 1 Click the following button button turns green Perform exponential baseline correction A red horizontal line will appear as well as the equation describing the ex ponential function f x A B exp C x 2 Click hold button A and move the mouse until the red line coincides with the first point of the spectrum 3 Repeat step 2 with the buttons B and C until the red line coincides with the entire baseline of the spectrum How to Preview the Baseline Corrected Spectrum Before actually performing the baseline correction you can preview the result by displaying the difference between the uncorrected spectrum and the red correction line To d
30. EL E kll LL o 135 F2 ppm Figure 12 2 c Click the 4 button to display the full spectrum d Zoom in on the next peak and add in the same way as the first one e Zoom in on the next peak etc Fig 12 3 shows an example of three selected peaks 196 2D Interactive Manipulation exam2d HC 1 1 Cobio quest 5 x wie cfl a r F1 ppm 100 140 12 10 8 amp 4 2 F2 ppm Figure 12 3 2 Click the button CT to phase correct the columns F1 A new data window called Phase 2D will appear showing the columns of the selected peaks see Fig 12 4 Figure 12 4 2D Interactive Manipulation 197 Note that the toolbar and the right click popup menu offer the full 1D phase correction functions By default all columns are selected as indicated by the filled blue squares JJ The red vertical line indicates the default pivot point in the upper column 3 A typical way to perform phase correction is e Click hold the Q button for zero order correction and move the mouse until the reference peak of the first column is exactly in absorption mode e Click hold the 1 button for first order correction and move the mouse until the reference peak in other column is exactly in absorption mode e Click the zJ button to execute save and return see Fig 12 5 O x 1 R mila j j l al pe 0 40 ph 63 356 phl 180 80 olumn 899 9748 ppm Figure 12 5 12
31. Enter the desired data directory lt dir gt and click OK Your data directory will now appear in the browser In order to display data from the Browser proceed as follows 1 Expand your top level directory lt dir gt in the browser to the level of the data name expno or procno 2 Select the desired item and drag it into the data area How to Define Alias Names for Data 1 Open the dataset for which you want to define an alias name 2 Click the Alias tab at the top of the data browser 3 Right click in the browser and choose Define alias for data in selected window Alternatively you can enter the command dalias on the command line How to Open Data in Other Ways TOPSPIN provides various other ways of displaying data You can for example use the portfolio instead of the browser Furthermore you can use command line commands like re rew rep and dir Details on these features can be found in chapter 4 3 and in the Processing Reference Manual 1 7 How to Display Peaks Integrals together with the Spectrum When a spectrum is displayed you can superimpose its title parameters integrals and peaks as follows 1 Move the cursor into the data window that contains the spectrum Getting Started 21 2 Right click and choose Display Properties in the popup menu 3 Check the desired items and click OK Please note that the selected items are only shown if they are available For exam ple peaks and integral
32. Figure 4 3 How to Open the Browser Portfolio r Click View Browser Panel On Off Ctr1 d The browser or portfolio will appear depending on which one was used last How to Open the Browser Portfolio in a separate window The browser or portfolio can be opened in a separate window as follows us Click Options Preferences set click Window settings and check Dis play dataset browser in a separate window You must restart TOPSPIN for the change to take effect How to Put the Focus in the Browser Portfolio rs Hit the F2 key Or r Click inside the browser or portfolio How to Select Folders in the Browser To select a particular folder 0s Left click the folder button or cS Hit the arrow up down keys while the focus is in the browser To select multiple folders 52 Dataset Handling 0S Hold the Ctr1 key and left click multiple folders to select them or 0S Hold the Shift key and left click two folders to select these two and all in between How to Expand Collapse a Folder in the Browser To expand a collapsed folder r Click the button to the left of the folder button or Double click the folder button or Hit the Right Arrow key while the folder is highlighted or Right click the folder button and choose Expand fully from the popup menu to fully expand the folder To collapse an expanded folder r Click the button to the left of the folder button or Double click the folder button or Hit the Left Arrow
33. Figure 9 3 Here you can select various display properties region setting and file properties If you choose Display Properties a dialog box see Fig 9 4 will appear 2D Display 139 TT x Please select the components to be displayed together with the spectrum fit available Cursor information m Title I Status parameters E Integrals lw Integral labels mj Peak labels m Contour levels bar E Show projections m Visible projections C F Fa F1 F2 Figure 9 4 Here you can set various display options including parameter integrals peaks contours and projections 9 4 Using the Tab bar The 2D data window is a tabbed pane This means its contents depends on the cur rently active tab in the Tab bar The individual tabs are basically the same as for 1D display see chapter 8 4 There are however some differences which are dis cussed below 140 2D Display How to Set Processing Parameters us Click the ProcPars tab edp The 2D processing parameter editor contains a column for each of the two di mensions F2 and F1 Note that not all parameters exist in both dimensions see Fig 9 5 exam2d_HC 1 1 Cbio guest Oj o s iA Reference F2 F1 Preguen Window Feference Phase S fi 024 fi 024 Size ofr Baseline SF MHz 500 1 300000 fi 25 7577890 Spectror Fourier OFFSET ppm 9 570 fi oF 823 Low fiel Peak CEDER SR Hz fo 00 o oo Spectrur sealers Z HZpPT Hz
34. From Top From Front F2 From right F 1 shitt To Center Shift To Bottom Properties Files Figure 9 15 How to Rotate a 2D Spectrum in Oblique Mode Click hold one of the following button and move the mouse up down a Rotate around x axis amp Rotate around y axis How to Switch between Displaying Positive and Negative levels Click the following multi state button in the lower toolbar Switch between positive negative and both contours 1t Chapter 10 3D Display 10 1 Plane Display Mode 3D data can be displayed as 2D planes or as a 3D cube By default the first F3 F1 plane is displayed see Fig 10 1 The plane orientation and number is shown The cube in the lower left corner graphically indicates which plane is displayed The full 2D display functionality is available see chapter 9 156 3D Display 0 x M ezam3d 1 1 Cibio guest Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals 4 F1 ppm 2 Plane 5 4 3 2 F3 ppm Figure 10 1 How to Switch to 2D Plane Display If the 3D cube is displayed you can switch to 2D plane display by clicking one of the following buttons Switch to 2D contour display Switch to 2D image display A Switch to 2D oblique display How to Display various Plane Orientations Click one of the following buttons 12 Show F1 F2 planes 3D Display 157 23 Show F2 F3 planes 31 Show F3 F1 planes How to Display various Pla
35. How to Create a New Dataset 2 0 0 cece nee 56 AS JOpeM ne Dale aii ci os peana Carne ka he Re Oe bee Oe eee eRe eee 57 How to Open Data Windows Cascaded 0 000 eee eee 58 How to Open Data from the Browser 0 0c eee eee ees 59 How to Open Data from the Portfolio 00 00000 60 Chapter 5 How to Automatically Select the first expno procno of a dataset 60 How to Open Data from the Topspin menu 005 61 How to Open Data from the Explorer Konqueror or Nautilus 63 How to Open Data from the Command Line 64 How to Open Special Format Data 0 0 0 0 eee eee 65 How to Open a ZIP or JCAMP DX file from the Windows Explorer 66 Ad Savins Copyin Dates vo 254 6605 4 4406460 054 Ne ead aa ana ss 66 How to Save or Gopy Data aisee oud ee cA ive Given eee Be wees 66 How to Save an Entire Dataset wi diale nk Jae kidw a Ga vee oe aes 67 How to Save Processed Data sceite restre aenedsndneees eouess 68 How to Save Acquisition Data 0 0 0 cece ee eee 68 How to Save Processed Data as Pseudo Raw Data 68 AS Dellus Alas uctacw oes anwar aoe cewek oe eae 68 How to Delete a Specific Dataset 0 0 0 0 ccc eee 68 How to Delete Types of Datasets 0 0 0 0 0 cee eee eee 69 4 6 Searching Pindin Data xi s 0 ties Gs der des Ge Lee vate Se ees 71 Howto Find Data kd ios aes awe alee a ath e
36. Panel button definitions LAYOUT format rows columns hgap vgap PAN LAYOUT 15 35 8 8 PAN BUTTONS Prints EXPORTS SSEND TO PAN COLORS BLUE1S BLUE1S BLUE1 PAN CMDS prnt exportfilesS smail PAN TIPS Print the spectrum lt br gt as it appears on the screens Export the dataset lt br gt to png jpg bmp etc Send the dataset by email Note that e The Close button and Tips switch are automatically created You don t need to specify them e The TOGGLE button is typically but not necessarily used to call another button panel In this example it calls the panel bproc2d e Items must be separated with the character button items with e A V followed by end of line continues an item on the next line e Tooltips may use html tags for text formatting e Commands may be specified as single commands like em or as com posite commands like em nft npk Note that in the latter case the com mands must be separated by n 19 6 Adding User Defined Buttons to the Toolbars The upper and lower toolbar at the top of the TOPSPIN window can be extended with user defined buttons They can be assigned to any TOPSPIN command macro AU program or Python program To create a user defined button take the following steps 1 Right click at an empty area of the toolbar 2 In the appearing popup menu click User Extensions 335 Add User Defined Button Reactivate All lInvisibleiInactive Buttons A
37. find to open the Find data window see Fig 4 22 Dataset Handling ES Searching will he performed in all data directories marked inthe data directories list below MAME ExXPMo PROCMO USER Title Pulse Frog Dimension D 204 50 Data type pectra Date trom mindy Date till raridade Data directories JRK Reset mask Cancel Help Figure 4 22 2 Specify the search criteria Note that e Dataset variables are searched that contain the specified string e Search is restricted to data created between the specified dates Note that the acquisition date is evaluated The Reset mask button resets the default criteria 3 Click OK to get a list of data that fulfil these criteria see Fig 4 23 Dataset Handling 73 0 x Search result 11 Data Sets am2d HO 1 1 C bio ques examZd HC pexam2d_ HC Cibiog gues to to to wn oo i bh Pe Cibi gues 4 bio leyxamzd HC jexam2d HH 1 1 mm ee to eI oS OO Display Properties Save selection Select all Add to portfolio Replace portfolia Cancel Figure 4 23 Note that the current search criteria are preserved until you exit TOPSPIN How to Display one of the Found Datasets In the search result window see Fig 4 23 1 Click one dataset to select it Optionally click Properties to view the datasets properties 2 Click Display to display the selected dataset in the curren
38. first order 1D 163 mode 30 mode 1D 162 mode 2D 194 pivot point in 1D 162 values 1D 164 zero order 1D 163 PHCO parameter 81 163 198 PHC1 parameter 163 199 pivot point in 1D phase correction 162 in 2D phase correction 197 pk command 164 plane display in 3D 156 plot data from the menu 95 data from the Plot Editor 97 data from the Processing Guide 97 layouts 22 plot command 22 96 97 Plot Editor 22 96 Plus key 37 polynomial baseline correction 183 port numbers 309 portfolio 20 36 49 54 60 74 202 file 54 in multiple display mode 177 position of a Topspin window 219 position of a Topspin window 218 position the baseline of a row column in 2D 206 positive 2D levels 153 pp command 114 127 208 PPARMOD parameter 81 84 108 ppl command 189 ppm axis units 124 144 pps command 187 preferences 29 313 pre scan delay 301 preview the baseline corrected spectrum 184 previous commands 33 dataset in browser 37 parameter field 81 83 plane in 3D 157 row column in 2D phase correction 199 zoom 32 105 137 print 1D peak list 114 active window 22 96 colors 317 data from the menu 95 data from the Processing Guide 97 integral list 97 metafiles 99 peak list 98 the current dataset 36 print command 30 36 95 97 114 printer colors 317 prnt command 96 probehead solvent dependent parameters 84 proc_Id AU program 90 process data 22 29 from the command line 87 from the Processing Guide 88 with AU programs 90 with comp
39. on the command line to create the AU program lt name gt How to Edit an Existing AU Program 1 Double click the AU program name in the AU program dialog box Or Click the Edit button to edit the highlighted AU program 2 Modify the AU program according to you wishes 3 Click Save to store the AU program under the name shown in the title bar 4 You will be prompted to compile the AU program click OK Alternatively you can enter edau lt name gt on the command line to edit the AU program lt name gt How to Execute an AU Program 1 Select the AU program in the AU program dialog box 2 Click the Execute button Alternatively you can enter lt name gt or xau lt name gt on the command line to execute the AU program lt name gt If the AU program has not been compiled compilation is automatically per formed before the execution starts How to Delete an AU Program 1 Select the AU program in the AU program dialog box 2 Click File Delete or click the Delete button Configuration Automation 305 How to Show Comments short descriptions in the AU Program List To switch on off the comments in the AU program list w Click Options Comment on off in the AU program dialog box A comment is a short description of the AU program which is also part of the AU program header Chapter 17 Remote Control 17 1 Remote control TOPSPIN supports remote control of your spectrometer over the local network or o
40. selecting a dataset from the browser puts the focus in the browser To put the focus on the command line r Hit the Esc key or n Click inside the command line How to Retrieve Previously Entered Commands All commands that have been entered on the command line since TOPSPIN was started are stored and can be retrieved To do that Hit the T Up Arrow key on the keyboard By hitting this key repeatedly you can go back as far as you want in retrieving previously entered commands After that you can go forward to more recently en tered commands as follows ce Hit the 4 Down Arrow key on the keyboard How to Change Previously Entered Commands 1 Hit the Left Arrow or gt Right Arrow key to move the cursor 2 Add characters or hit the Backspace key to remove characters 3 Mark characters and use Backspace or Delete to delete them Ctrl c 34 The TOPSPIN Interface to copy them or Ctr1 v to paste them In combination with the arrow up down keys you can edit previously entered commands How to Enter a Series of Commands If you want to execute a series of commands on a dataset you can enter the com mands on the command line separated by semicolons e g em ft apk If you intend to use the series regularly you can store it in a macro as follows cS right click in the command line and choose Save as macro 2 3 Command Line History TOPSPIN allows you to easily view and reuse all commands whic
41. you can super impose an arbitrary number of 1D or 2D spectra Getting Started 1 10 How to Print or Export the Contents of a Data Window How to Print Data A TOPSPIN data window may contain various objects like an fid a spectrum ex pansions of a spectrum superimposed spectra spectrum components such as pa rameters peaks integrals cross sections etc Whatever the content of the data window is it can be printed as follows type Ctr1 p or click File Print se lect Print active window in the appearing dialog box and click OK The other options in this dialog box enable you to use or create plot layouts De tails on this can be found in the Plot Editor manual Just type plot to start the Plot Editor and open the manual from its Help menu The colors of the printed data can be chosen in the User Preferences dialog box Just enter the command set or click Options Preferences and click Printer in the left part of the dialog box How to Copy a Data Window to Clipboard Under MS Windows you can easily copy the data window contents to other ap plications To do that type copy or click Edit Copy This will copy the data window contents to the clipboard After that you can paste the clipboard contents to any Windows application How to Store Export a Data Window as Graphics File The clipboard and metafile formats are resizable vector formats In addition to this TOPSPIN allows you to save the contents of a d
42. 0 Specify the Maximum visible command lines gt Minimum visible Click Apply nN Aa Ww N 18 5 Disabling Enabling Toolbar Buttons Menus and Commands How to Hide the Upper and Lower Toolbars Right click in an empty area of one of the toolbars and choose Hide the toolbars 324 User Preferences from the appearing popup menu see Fig 18 7 Wake this button invisible Wake this button inactive Reactivate all invisible or inactive buttons Add user defined button to end of toalbar Remove this user defined button Hide the toolbars Type SHIFT ESC to reset Figure 18 7 How to Hide the Menubar Right click in an empty area of the Menubar and choose Hide the menubar from the appearing popup menu To restore the toolbars c hit the keys SHIFT ESC How to Disable Remove Toolbar Buttons Buttons of the upper or lower toolbar can be disabled or removed as follows 1 Right click a toolbar button 2 Choose one of the entries Make this button invisible to remove the button from the toolbar t Make this button inactive to disable the button it will appear greyed To restore the complete toolbars click t Reactivate all invisible or inactive buttons to restore the default toolbar How to Disable Remove Menus or Commands By default all existing TOPSPIN commands can entered from the menu and or from the command line You can however selectively disable remove commands or menus This is typically d
43. 0 0 0 cece ees 26 The TOPSPIN Interlace o 02i02556 iineea dias acee tates weet 27 2 1 Whe Topspin Wind OW icere tenri ee ES Ae enh edie a S9e ode 2d How to Use Multiple Data Windows 0 000 ce eee 28 How to Use the Tile Dar lt i 205 eck Rake cha ORE E EEE Geers 29 How to Use the Menu Dar s 2i0chssr ees Enee AEE E nR 29 How to Use the Upper Toolbar 0 0 cee eee eee 30 How to Use the Lower Toolbar 000 31 22 Command Line Usao E cc cnc ceed ee baa eae nee hao kao 33 Chapter 3 Chapter 4 How to Put the Focus in the Command Line 33 How to Retrieve Previously Entered Commands 33 How to Change Previously Entered Commands 33 How to Enter a Series of Commands 000 ce eee eee 34 2 3 Command Wine HAStOry sieraed rare bene ok we ee A A RA 34 2 4 Starting TOPSPIN commands from a Command Prompt 35 2 5 Function Keys and Control Keys 0 0 0 e eee eens 36 26 sel an TOpSpit22 ty eaten et E a a chs hoe Leek ei was ee denies 39 How to Open Online Help documents 0 0000 eee 39 Howto Gel LOOlIpS 2 44 tuokieaeeice thane 6 hse cs ease eens 39 How to Get Help on Individual Commands 40 How to Use the Command Index 0 cece eee eee 40 21 User Defined Functions Keys rerasrnerea an EEEE EEA 41 2 8 How to Open Multiple TOPSPIN Interfaces
44. 1 2 2D Interactive Phase Correction Details How to Scale or Shift Individual Rows Columns To select one row or column r Click in the corresponding part of the data window The selected row column will be marked with a filled blue square J whereas un selected rows columns will be marked with an unfilled blue square _ Selecting 198 2D Interactive Manipulation a single row column allows you to shift and scale it separately from the other rows columns as shown in Fig 12 6 WW Phase 2D exam2d_HC 1 1 Cxbio guest O x Ale o 1 Ri 90 wima eo nje m jA gl EES pivot 1265 44 ppm Fhase increment 0 20 ph 63 356 phl 150 80 SIL 644 i JE a BIT Column 899 9748 ppm Figure 12 6 To select all rows or columns r Click the following button thy Select all rows or columns How to Perform Smooth Phase Correction To perform zero order phase correction 1 Click hold the following button it turns green and move the mouse 0 Zero order phase correction until the reference peak of the first row column is exactly in absorption mode 2 Release the mouse button turns grey The parameter PHCO will be set accordingly To perform first order phase correction 1 Click hold the following button it turns green and move the mouse 1 First order phase correction 2D Interactive Manipulation 199 until the reference peak of the second and further rows columns is
45. 15 29 and click OK 8 Click and click Save Shape enter a Name and Title set the Flip Angle Acquisition 293 to 90 and the Type of Rotation to excitation Now you have created a shape that can be used in a WET experiment Ey Manipulate command x Alignment C Beginning at Phase 0 thee Fhase 0 at Middle of Shape fy ly Iz I2 f Ending at Phase 0 z gt l Reference Frequency Wo Reference Frequency specified f Reference 01 from current Data Set Reference First Frequency in List Options M Frequencies taken from Frequency List With additional Phase Setting With additional Scaling Parameters fi 0000 0 Length of pulse usec ffreglist Mame of Frequency List OK Apply cancel Figure 15 28 294 Acquisition Manipulate command offs Reference fi 053 80 Reference Frequency Freqency List Oif to Reference 3759 74 1905 94 6775 99 692219 8712 96 6959 16 OK cancel Figure 15 29 Example 2 Two step Procedure to a Selective Experiment 1 Determine the width of the region to be excited Let s assume this is 40 Hz nN Aa Ww N Read acquire a 1D reference spectrum Create a new dataset Read the pulse program selgpse Enter ased and set all acquisition parameters for selgpse except for the shaped pulse parameters 6 Enter stdisp to start the Shape Tool interface 7 Click Shapes Classical Shapes Gauss 8 In the param
46. 2D 135 interactive 1D baseline correction 182 1D calibration 173 1D data manipulation 161 1D integration 164 1D peak picking 187 1D phase correction 161 1D signal to noise calculation 222 2D calibration 206 2D data manipulation 193 2D phase correction 193 data manipulation 23 30 316 modes 30 parameter adjustment 82 266 processing 87 Processing Guide mode 90 interface fonts 319 internal projection 21 Internet Browser 64 intrng file 168 171 173 IP address of a remote system 308 IUPAC standard 24 J JCAMP DX format 24 65 66 67 Jeol spectrometer 66 Jmol molecule structure viewer 122 JNMR data 66 K KDE konqueror 75 keyboard commands 29 kill command 47 Konqueror 76 130 L Left Arrow key 33 37 52 Levenberg Marquardt algorithm 239 li command 115 164 Liouville equation 25 lipp command 115 lippf command 115 list 142 1D integrals 115 2D integrals 142 2D peaks 141 AU programs 303 baseline points 186 Bruker AU programs 304 color schemes 318 data files 74 128 EXPNOS PROCNOS 60 found data 72 integrals 97 173 macros 25 opened datasets 50 parameter sets 57 peaks 98 127 190 peaks 1D 110 plot layouts 96 solvents 57 user defined AU programs 303 local host 309 network 307 Topspin interface 307 lock parameters 85 signal 263 lock command 264 lock display colors 317 mode 263 window 218 258 260 263 lockdisp command 258 263 lock in procedure 263 Lorentzian deconvol
47. 300 compile AU program 304 components of a spectrum 22 composite commands 88 configuration commands 18 customized 301 default 301 directory 301 name 301 of a datastation 18 of a firewall 309 of a spectrometer 18 of TCP IP communication ports 309 of the acquisition status bar 259 of the tab bar 316 of the Topspin menu 325 password 299 consistency check 76 contour display 194 of 2D spectra 148 of 3D planes 156 contour levels 134 149 control keys 36 convdta command 67 conventions in this document 15 convert data to JCAMP DX 67 data to text 67 data to ZIP 67 copy amp paste data 29 64 66 copy command 22 30 99 1 4 copy data 66 CORBA 309 corba conf file 309 C program 90 create an AU program 25 91 304 330 an empty data window 59 data window color scheme 318 dataset 30 macro 25 330 new data window 19 new dataset 56 268 plot layouts 22 97 Python program 26 331 set of user preferences 313 user defined command 25 user notebook 329 C statements 25 Ctrl key 52 54 60 71 74 104 135 176 178 Ctrl c key 33 36 114 Ctrl d key 27 36 51 Ctrl f key 36 Ctrl F3 key 41 Ctrl F5 key 41 Ctrl F6 key 41 Ctrl n key 30 36 56 268 Ctrl o key 30 36 61 65 Ctrl p key 22 30 36 97 114 Ctrl s key 23 30 36 67 68 Ctrl v key 34 36 Ctrl w key 36 cube display 155 cubic spline baseline correction 185 cursor information 127 customized configuration 301 cut integrals 172 D data are
48. 71 73 data 71 field in the parameter editor 81 83 result window 73 select AU program 304 color scheme 318 data 49 data in multiple display 176 178 data window 213 default printer 301 expno procno combination 60 first expno procno 60 folders in the browser 51 font 320 321 322 integral regions 166 168 lock signal color 318 multiple datasets 60 74 multiple folders 51 peaks in 2D phase correction 194 plot layout 96 printer 96 remote system 308 row column in 2D phase 197 spectra in 2D multiple display 203 spectrum color 317 spectrum print color 317 Topspin window 219 selective excitation 25 semi automatic peak picking 190 processing 88 sensitivity of the GS slider 266 of the mouse 163 169 185 199 serial command 91 serial processing 91 Server ID 307 set 1D acquisition parameters 108 2D acquisition parameters 140 2D processing parameters 140 colors for multiple display 182 contour levels 149 lock parameters 85 phase pivot point 162 processing parameters 79 processing parameters 1D 107 routing parameters 85 user preferences 314 set command 106 313 SFO1 parameter 259 Shell 18 1 14 shift 1D data down 106 1D data smoothly 106 1D data to the extreme left 106 1D data to the extreme right 106 1D data to the left 106 1D data to the right 106 1D data up 106 1D 2D data 32 37 2D data down 137 2D data smoothly 137 2D data to the left 137 2D data to the right 137 2D data up 137 data in multiple windows 103
49. Enter topspin where lt tshome gt is the directory where TOPSPIN is installed 1 5 Configuration After the installation of TOPSPIN it must be configured once TOPSPIN may be used in two different ways on a computer which controls a spectrometer The command cf must be executed once to configure the spectrometer hard ware Just type this command and follow the instructions on the screen At the end of the dialog further configuration commands like expinstal1I are of fered and can be started from there on a computer which is used as datastation The only configuration command to be executed is expinstal1l1 This allows Getting Started 19 1 6 you to install pulse programs AU programs lists etc Just type this command and follow the instructions on the screen selecting Installation for Datastation default Note that the commands cf and expinstal11 can be started from the command line or from the Options or Spectrometer menu However the latter menu is only available after c has been performed once choosing Installation for spectrome ter After the configuration has finished TOPSPIN is ready to be used The configura tion only needs to be repeated when you have installed a new version of TOPSPIN or if your spectrometer hardware has changed More details on configuration can be found in chapter 16 2 and the descriptions of cf and expinsta11 in the Acquisition Reference Manual How to Display Spectra
50. In this chapter opening data in standard Bruker format is described Opening other data formats is described in chapter 4 Please note that a standard Bruker dataset is a directory tree rather than a single file lt dir gt data lt user gt nmr lt dataset name gt lt expno gt pdata lt procno gt e g c bruker topspin data guest nmr exam1d_13C 1I pdata 1 How to Open Data from the Menu Open the File menu and click Open A dialog box appears Select the first op tion the Browser type File Chooser and click OK A file browser appears Navi gate to your data directory and expand it to the level of names expnos or procnos double click a directory to expand it Select the desired item and click Display The selected dataset replaces the contents of the currently selected active win dow If no data window was displayed a new one will be created Alternatively you can first create a new window by clicking Window New Window Al t w n and then open a dataset from the file browser in that window The file browser can also be opened by entering reb on the command line 20 Getting Started How to Open Data from the Browser TOPSPIN has data browser which by default displays the top level data directory lt dir gt with Bruker example data You can add your own data directories local or remote as follows 1 Move the cursor into the browser area 2 Right click and choose Add New Data Dir in the popup menu 3
51. List Options Frequencies taken from Frequency List vith additional Phase Setting With additional Scaling Parameters 13000 0 Length of pulse usec fi Humber of Frequencies OK Apply cancel Figure 15 24 A dialog box will appear see Fig 15 24 where you can set the required param eters The Alignment radio buttons allow you to define the position of phase 0 the be ginning middle or end of the shape The Reference Frequency radio buttons allow you to choose whether the refer ence frequency e is not used e is set to Ol of the associated dataset Acquisition 285 e is Set to the first entry of the frequency list The Option Frequencies taken from Frequency List will automatically be checked The Options check boxes allow you to set e Frequencies taken from a Frequency list The Parameter Name of Fre quency List will automatically appear Frequency lists can be set up from the TOPSPIN interface with the command edlist or interactively by click ing the H button e With additional Phase Setting With additional Scaling O 100 the relative amplitude for each excita tion region The overall amplitude will be divided by the number of fre quencies For example for 3 frequencies with equal scaling factors each frequency will contribute 33 The Parameters fields e The Length of Pulse e The Number of Frequencies or when the Option Frequencies taken from a Frequency list is ch
52. Processing Processing Guide The Processing Guide window will appear as an integral part of the current data window 2 In the Processing Guide window a Uncheck Automatic mode b Click Open data set and click OK to open a dataset manually e g from the browser or click Browse to open the File Chooser c Click Window function Fourier Transform ete For each step a dialog box will appear where you can enter options parameters etc For details on these items please refer to the corresponding commands in the Processing Reference Guide 6 3 Processing Data with AU programs Data processing can be performed by using AU programs An AU program is actu ally a C program which contains TOPSPIN commands macros and or C language statements Various standard AU programs are delivered with TOPSPIN A typical 1D processing AU program is proc_1d A simplified version of this AU program iS EF APK SREF ABS AUTOPLOT QUIT It executes the commands ef apk sref abs and autoplot To run this AU Data Processing 91 program just enter proc 1d on the command line You can create your own AU programs with the command edau Note that an AU program must end with QUIT or QUITMSG your message and that all statements must be specified in capital letters For more information on AU programs please refer to the AU pro gram reference manual Click Help Programming AU programming As an alternative to AU programs
53. User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset Print Associated Command Figure 19 4 The button definitions are stored in the file toolbar user prop which resides in the subdirectory userdef ined of the user properties directory To locate this directory enter the TOPSPIN command hist A dialog box will show the contents of the history file Near the top of this file you will see an entry User properties directory For icon image buttons the formats gif jpg jpeg and png are supported Standard TOPSPIN toolbar icons have a size of 16 16 pixels If your own icons have a different size they are automatically rescaled and displayed at the standard size Adding User Defined Menus to the Menubar The menubar at the top of the TOPSPIN window can be extended with user defined menus They can be assigned to any TOPSPIN command macro AU program or Python program They are specific for the dimensionality of the active dataset To create a user defined menu take the following steps 1 Open a dataset of the desired dimensionality 2 Right click at an empty area of the menubar 3 In the appearing popup menu click 338 User Extensions User_defined Menus User Defined Menus Hide the menubar Type SHIFT ESC to reset 4 In the appearing dialog box see Fig 19 5 a Click Add Menu and specify the Menu Name in the appearing dialog b Click Add Men
54. Y offset to previous window Use standard values instead of those above ho JRK Cancel Figure 4 10 5 Here you can specify the data window sizes and offsets as fractions of the maximum window sizes 6 Click OK to close the dialog box How to Open Data from the Browser In the browser r Left click hold a data name expno or procno and drag it into the data area The data will be displayed in a new data window or Left click hold a data name expno or procno and drag it into an open data window The data will replace the currently displayed data or Left click hold a data name expno or procno and drag it into an empty data window created with Alt w n or Left click hold a data name expno or procno and drag it into a multiple dis play data window The data will be superimposed on the currently dis played data or Right click a data name expno or procno and choose Display from the pop up menu the data will be displayed in the current data window or Right click a data name expno or procno and choose Display in new win 60 Dataset Handling dow from the popup menu the dataset will be displayed in a new data win dow or Hold the Ctrl key and left click several datasets to select them or hold the Shift key and left click two datasets to select these two and all in be tween Then right click one of the selected datasets and choose Display from the popup menu A new window will be opened showing the
55. a list box for each parameter see Fig 15 26 EA Define Parameter Table x Parameter Table BE Length of hard pulse PLi x Power level of hard pulse Piz Length of shaped pulse sri gt Power level of shaped pulse SPNaM1 Mame of shaped pulse Pi x Length of ref shaped pulse s3 gt Power level of ref shaped pulse SPNaM3 Mame of ref shaped pulse FaiuisT Mame ot trequency list OK Cancel Figure 15 26 Make any changes you want and click OK The acquisition parameters of the as sociated dataset can be set viewed from the TOPSPIN interface by clicking Ac quPars or entering eda How to Change the Shape Storage Directory To change the shape storage directory r Click Options Set path to Shape Directory Acquisition 291 Set path to shape directory l x Select path Use default path to shape directory Path to shape directory OK cancel Figure 15 27 In the appearing dialog box you can select the default path or select and specify a different path Note that a shape base directory must be shape and a gradient base directory must be gp Opening and saving shapes gradients will access the specified directory How to select the Associated Dataset To set the dataset associated to the Shape Tool interface r Click Options Select associated dataset A list of open datasets will appear Select the desired dataset and click OK 15 9 10 Examples of using the Shape To
56. acquisition parameter editor r Click the AcquPars tab in the Tab bar of the data window or r Enter eda on the command line Fig 5 2 shows an example of the acquisition parameter editor with the Experi ment parameters displayed examid_1H_1 1 Chio guest Ox Spectrum ProcPars AcquPars Title PulsFrog Peaks Integrals al Structure Fid o s e A Experiment Experiment Width PULPROG kao o oo Current pulse Receiver AG mod bens J Acquistion tr koong TD lsss8 Size of fid Durations NS ha of scans DS ot dummy s O T Power Figure 5 2 The processing parameter editor supports the following functions c Enter part of a parameter name in the search field and click r Click a parameter section e g Experiment at the left of the dialog box The section becomes highlighted and the corresponding parameters will appear in the right part of the dialog box n Click in a parameter field e g TD to set the parameter value r Hit the Tab key to jump to the next parameter field o gt Hit Shift Tab to jump to the previous parameter field 84 Parameter Handling t Use the scroll bar at the right of the dialog box to move to parameters fur ther up or down in the dialog box How to Undo the Last Acquisition Parameter Change r Click the following button 1 Undo last acquisition parameter change How to Set Pulse Program Parameters r Click the followin
57. and choose Display Properties dopt 2 Check Show data points in the appearing dialog box and click OK 3 Expand the spectral region where you want to see individual points 1 These are the status parameters that also appear on the plot 128 1D Display How to Display the Main Dataset Properties cs Right click inside the data window and choose File Properties An information box as displayed in Fig 8 13 will appear x examid 1H 1 1 CAbio guest Dimension ProctAcgu fi DrD Pulse program zg 30 Acquisition date fos apr 2001 09 33 36 Nuclei F1 1s NUCI 1H SFO MHz 300 1 91853796133 solvent epe Acquired data available ves Processed data available Yes TITLE Proton AY 300 Automation Cyclosporin Figure 8 13 Note that this is status information which cannot be changed How to Display a List of Files of a Dataset ns Right click inside the data window choose Files Fig 8 14 shows the file list when the Fid tab is active i e when the raw data are displayed It is the contents of the expno directory 1D Display 129 RAR xX Directory CJbioidatarguestnmriexamd d_i Hi1 Last modified Size in bytes Dir acgu 4 acqus 5 audita tst fid formatased format termnp prosal History pulseprogram relations Scan Open cancel Figure 8 14 Fig 8 15 shows the file list that appears when the Spectrum tab is active 1 e when the processed data are displayed It is the co
58. calibration mode How to Calibrate a Spectrum Interactively In calibration mode 1 Position the red cursor line at the reference peak 2 Left click at that position 1D Interactive Manipulation 175 The following dialog box will appear EA calibrate x Spectrum calibration trequency Note that the units Hz or ppm correspond to the axis units of the display 3 Enter the frequency you want to assign to the reference peak 4 Click OK The spectrum will be calibrated and re displayed TOPSPIN will automatically leave calibration mode 11 4 1D Multiple Display The multiple display mode allows you to display multiple superimposed spec tra The spectra will be ppm aligned or Hz aligned according to the selected axis unit Each spectrum can be individually shifted and scaled allowing exact align ment of corresponding peaks in different spectra The number of superimposed spectra is unlimited Although multiple display is normally used for spectra with matching nuclei it allows you to superimposed spectra with non matching nuclei You will get a warning that the nuclei do not match Just just click OK to continue How Switch to Multiple Display Mode and Read Multiple Spectra One way to superimpose data in multiple display is to read one dataset switch to multiple display mode and add other datasets L 2 Read a 1D dataset Click the button in the upper toolbar or type md on the command line The
59. cece cece e eens 307 Mek REMO CONUOL eerren ah ae banned avhb eae dos Sade eed 307 17 2 How to Establish a Remote Connection from your PC 307 17 3 How to Configure TCP IP Communication Ports 309 17 4 How to Make a Remote Connection without a Local License 310 17 5 Security of Remote Connections 0 000s 310 17 6 How to Allow Remote Connections 00 000 ce eee 311 17 7 Note to Windows XP Service pack 2 0 eee eee 312 17 8 How to Access ICON NMR from a Remote Web Browser 312 Chapter Is User Preferentes siti o l0t esi een dcitetnce ieee ceaeees 313 ISE User PrelerenCes eika See tates a a tees S e the eek e 313 How to Define the Startup Dataset 0 0 0 0 00000 314 How to Set Automatic Startup Actions 0 000 315 How to Change the Preferred Editor 0 00000 0 315 How to Configure the Tab Bar 0 ccc ee ees 316 How to Configure the Right click Menu Function 316 3 2 Chane mo COs i030 e ha oo nae Che See aa a A 317 How to Change Colors of Data Objects on the Screen 317 How to Change Colors of Data Objects on the Printer 317 How to Change Colors of the Lock Display 317 How to Create a New Data Window Color Scheme 318 How to Read a Different Data Window Color Scheme 318 tSo Changing Fon erer Sosa dad SUR e
60. click the following toggle button in the upper toolbar 1D Display 125 ill Switch the spectrum overview display on off ov To shift the displayed region simply click hold the green area in the overview spectrum and move the mouse see Fig 8 11 How to Switch Y axis Display Click the following toggle button in the upper toolbar EJ Switch the y axis display between abs rel off y Fig 8 11 shows a data window with the spectrum overview on ppm axis units and absolute y axis display examid_1H 1 1 Cubio guest l t o x Spectrum ProcPars AcquPars Title PulsPrag Peaks Integrals Sample Structure Fid 3 0 8 5 3 0 75 ppm Figure 8 11 126 1D Display 8 6 Show Display Properties Regions Files If you right click inside the data window the following popup menu will appear Display Properti Save Display Region To Restore Display Region From Params Fis File Properties Files If you choose Display Properties a dialog box see Fig 8 12 will appear TT x Please select the components to be displayed together with the spectrum cit available Cursor information m Title M Status parameters E Integrals M Integral labels vj Feak labels a Multiplets a Show data points E Figure 8 12 Here you can check or uncheck the spectrum components that you want to be dis played in
61. data window will switch to multiple display mode Add a dataset as follows r Left click hold the dataset in the browser and drag it into the data win 176 1D Interactive Manipulation dow or r Right click the dataset in the browser and choose Display from the popup menu or r Enter re and specify the additional dataset in the appearing dialog box Another way to superimpose data in multiple display is to read multiple datasets simultaneously 1 In the browser or portfolio r Hold down the Ctr1 key and click multiple datasets to select them Or r Hold down the Shi ft key and click two datasets to select these two and all datasets in between 2 Right click any of the selected data r Choose Display from the popup menu This will show the data in the active data window if that is in multiple dis play mode or otherwise show the data in a new window Or r Choose Display in new window from the popup menu This will show the data in a new window In multiple display mode the Tab bar of the active data window is replaced by a toolbar Fig 11 8 shows three comparable 1D spectra and the sum of all three 1D Interactive Manipulation 177 examid 13 C 1 1 Cobio1 guest examld 130 3 1 Cit biol gest examld 13sec l1 Ci biol gyest examld l13C 1 1 Cit bigl gyest Figure 11 8 Data window in multiple display mode pn The yellow button indicates that the data window is in multiple display mode
62. dialog box To start the conversion select one or more parameter sets and click OK 16 4 Automation How to Install AU Programs To install AU programs you have to run the command expinstal11 see chap ter 16 2 How to Open the AU Program Dialog Box To get a list of all AU programs enter edau or 1 Click File gt Run 2 Click Execute an AU program in the appearing dialog box 3 Click OK A dialog box showing either the Bruker defined or User defined AU programs Fig 16 2 shows a dialog box with two User defined AU programs ioi xi File Options Help my aul User defined AJ program User defined AU program 2 Edit Execute Delete Cancel 3 Figure 16 2 List with two User defined AU programs Note that Bruker AU programs are only shown if the command expinstall has been executed once after the installation of TOPSPIN How to Switch to the List of User defined AU Programs w Click Options User defined in the AU program dialog box 304 Configuration Automation How to Switch to the List of Bruker defined AU Programs us Click Options Bruker defined in the AU program dialog box How to Create an AU Program 1 Click File New in the AU program dialog box 2 Enter the AU program lines in the edit field of the appearing dialog box 3 Click Save as to store the AU program under a new name 4 You will be prompted to compile the AU program click OK Alternatively you can enter edau lt name gt
63. dt Fees Be Ram ee as Sees 329 OZ INVACTOS p25 esas 8s ager as SR he ek Be dete ued Grate Sas ede All eae ace ay eet 330 WO AUPS 2 4 au hike Sie Soe Boe Sa ea ee Oa Ree aan 330 Poe Python Procrams scsi oh eee we ee eh ae ees ee 331 VOD Buton Panes sais ian cae ew a Pate Ooo a dee oar ado ar 332 19 6 Adding User Defined Buttons to the Toolbars 334 19 7 Adding User Defined Menus to the Menubar 337 19 8 Adding User Defined Guides 0 0 0 0 cece 339 14 Chapter Getting Started 1 1 Document Conventions Font Conventions abs commands to be entered on the command line are in courier bold italic ProcPars menus buttons icons to be clicked are in times bold italic fid filenames are in courier name any name which is not a filename is in times italic File directory Conventions lt tshome gt the TOPSPIN installation home directory User Action Conventions r a single user action 1 the first action of a sequence 2 the second action of a sequence 3 etc a the first action of a sub sequence 16 Getting Started b the second action of a sub sequence c etc 1 2 TOPSPIN Overview Functionality TOPSPIN is an integrated software package for Displaying NMR spectra Printing and plotting spectra Exporting displays and plots in various graphics and metafile formats Importing NMR data from files of various formats Archiving spectra in various format
64. exactly in absorption mode 2 Release the mouse button turns grey The parameter PHC1 will be set accordingly How to Perform 90 90 or 180 Zero Order Phase Correction Click one of the following buttons 4 90 zero order phase correction 4 90 zero order phase correction 180 180 zero order phase correction How to Reset the Phase to the Original Values Click the following button Reset zero and first order phase How to Change the Mouse Sensitivity Click one of the following buttons 1 Increase double the mouse sensitivity inc t Decrease halve the mouse sensitivity dec Il Reset the mouse sensitivity to 1 0 How to Show the Next Previous Row or Column To show the next row column click the following button Show next row column Note that only the selected row column is increased If all rows columns are se lected only the first one is increased To show the previous row column click the following button Show previous row column 200 2D Interactive Manipulation Note that only the selected row column is decreased If all rows columns are se lected only the first one is decreased How to Arrange Rows or Columns Click one of the following buttons Arrange rows columns horizontally Arrange rows columns vertically see Fig 12 6 Arrange rows columns vertically in a split window How to Return from Multi 1D Phase to 2D Phase Display Click the foll
65. flip angle Acquisition 281 How to Calculate the Maximum RF Field Strength for Adiabatic Pulses To calculate the RF field strength for adiabatic pulses w Click Analysis gt Calculate gammaBImax for Ad shapes calcbladia HypSec calcoladia fio610 0 Length of pulse usec Results 4 4305E05 Sweep rate on resonance Hzisec sof 42 Gammab ma pills grin Hz Calculator s o G s66 29 Gammabliepl Figure 15 22 Fig 15 22 shows the resulting parameter section for a HypSec shape The result yB1 max 27 y Q is calculated from the on resonance sweep rate Here Q is the quality or adiabaticity factor After entering the appropriate value for Q the value for yB 1 max 2r is obtained As a rule of thumb Q is set to 5 for inversion pulses However for decoupling pulses Q should be set between 2 and 3 to allow a lower decoupling power How to Calculate the Bloch Siegert Shift To calculate the phase difference due to the Bloch Siegert shift t Click Analysis gt Calculate Block Siegert Shift bsiegert3 Input parameters are the length of the shaped pulse in us yB 1 max in Hz and the offset of a theoretical signal relative to the frequency of the RF pulse in Hz The result consists of the phase difference due to Bloch Siegert shift in Degree and the corresponding frequency shift in Hz 282 Acquisition How to Calculate the Average Power Level To calculate the average power 0s Click Analysis Calculate ave
66. geometric sequence of levels 149 geometry of a Topspin window 218 219 getprosol command 84 108 gf command 88 gfp command 88 GLP 76 GMP 76 Gnome Mozilla 76 grab rows columns in 2D 204 gradient enhanced spectroscopy 25 graphic functions 331 graphics files 22 99 grid display 31 147 263 window arrangement 214 gs command 82 266 GS parameter adjustment window 266 H halt an acquisition 258 259 halt command 258 270 helium level 264 Help button 40 menu 29 39 menu of the Plot Editor 22 97 help in Topspin 39 on commands 40 help command 40 Hertz axis units 124 144 hist command 41 44 99 308 314 333 337 339 history file 337 hostname of a remote system 308 HTML page 40 I 8 I iconify all data windows 218 data window 216 iconnmr command 26 image display of 2D data 151 of 3D planes 156 import data 24 inconsistent dataset 81 initial guess 240 install AU programs 19 303 pulse programs 19 Topspin 299 installation directory 53 300 301 installnmr script 300 int command 127 Integral list 2D 142 integral bias 168 display 20 label 167 list 1D 115 regions 165 166 167 172 scaling factor 171 slope 169 trails 127 172 values 165 Integrals tab 115 142 173 integrals txt file 173 integration 1D automatic 164 167 1D interactive 164 167 mode 31 165 173 295 intensity alignment in multiple display 180 decrease 1D 104 134 increase 1D 104 134 manipulation 31 reset 1D 32 104 105 134 scaling
67. individual spectra in multiple display 21 175 180 row column in 2D phase 198 Shift key 52 60 71 74 176 178 Shift Tab key 81 83 short description of an AU program 305 shortcuts for processing 88 show command 47 SIGF1 parameter 222 SIGF2 parameter 222 signal region 222 signal to noise calculation 222 Simplex algorithm 235 239 simulatation of powder spectra 225 simulating experiments 24 sine baseline correction 183 single commands 87 slider sensitivity 266 slope correction 168 smail command 24 30 smooth 1D phase correction 198 1D scaling 32 104 1D shifting 105 1D zooming 32 104 1D 2D shifting 32 2D scaling 135 2D shifting 137 scaling of 1D integrals 171 scanning of planes in 3D 157 shifting of 1D integrals 172 solaguide command 225 Solids Line Shape Analysis 225 solvent 57 sort data in portfolio 54 sort mode 55 spec command 107 special format data 24 spectrometer frequency 259 spectrometer hardware 18 19 Spectrometer menu 29 257 spectrum display 1D 107 objects 313 314 overview 1D 124 overview 2D 144 Spectrum tab 107 124 129 split pane 27 square 2D layout 135 square brackets 29 39 102 106 sref command 87 90 173 206 stacked multiple display 180 Start button 63 startup actions 313 315 status line font 322 status parameter change 81 display 84 127 display 1D 108 stop an acquisition 258 stop command 258 270 store 2D contour levels 150 structure file 122 Structure tab 122 sum spectrum in
68. integri Integrate Adiabatic Shape integradial Integrate and compare to Reference integandcomp Simulation simulate Figure 15 19 From here you can start the analysis functions discussed below How to Calculate the Bandwidth for Excitation To calculate the excitation band width factor Aw AT w click Analysis gt Calculate Bandwidth for Excitation bandw2 For the excitation band width the V Mx7 My magnetization is used Fig 15 20 shows the resulting parameter section for a Gauss shape Acquisition 279 Gauss bangwz g0 0 Total rotation degree Results 21220 DeltaQmega Deltal factor using transy magn Calculator fi 00 0 DeltaOmega Hz 21 220 0 DeltaT usec update parameters Figure 15 20 As you can see for a 90 Gaussian shape the bandwidth factor is 2 122 The bandwidth factor is the product of the width of excitation DeltaOmega and the pulse length DeltaT This means a pulse length of 21220 usec gives a band width Aq of 100 0 Hz The bandwidth is the excitation width at the 3 dB point 1 e the point where the magnetization has dropped to 70 8 When you change one of the parameters in the parameter section the others are automatically adjusted Clicking the Update Parameters button will store the length of the shaped pulse DeltaT to the associated dataset parameter default P11 How to Calculate the Bandwidth for Inversion To calculate the inversion band width factor A
69. more powerful than AU programs They are easy to use and allow you to execute TOPSPIN commands handle NMR data and parameters generate graphics and interact with the TOPSPIN user interface via di alogs windows etc To create a Python program enter the command edpy select a file and insert your Python statements Graphics and interface features pro grammed in Python look and work the same as regular TOPSPIN features For details on Python programming click Help Programming Python Pro gramming The examples mentioned there like pycmd are delivered with TOP SPIN Just enter their names on the command line to execute them The Python dialog window is also available from the TOPSPIN menu us Click File gt Open and select Open other file Python program 1 17 How to Automate Data Acquisition TOPSPIN provides special user interfaces for automation walk up bio molecular experiments etc To open these interfaces t Type iconnmr or click Spectrometer gt ICONNMR Chapter 2 The TOPSPIN Interface 2 1 The Topspin Window The TOPSPIN window consist of several areas bars fields and buttons The main part is a split pane which consists of the data area and the browser Note that the browser can be inactive hit Ctr1 d or displayed as a separate window Fig 2 1 shows the Topspin window with two data windows in the data area and the browser as an integral part 28 The TOPSPIN Interface minimize maximi
70. on the command line The Shape Tool window will appear see Fig 15 15 This consists of a toolbar a command line and a split pane with a data section at the right and a parameter sec tion at the left Acquisition 213 ShapeTool o x mA Gauss Amoliude Parameters hooo oo Size of Shape fo Truncation Level Figure 15 15 By default a 1000 point Gauss shape is displayed with Truncation level 1 0 The TOPSPIN menu is changed showing the additional Shapes and Manipulate menus and the adjusted File Analysis and Options menus File Edit View Shapes Analysis Manipulate Options Window Help Note that all functions of the interactive Shape Tool can also be performed non interactively with the TOPSPIN command st This command must entered with the appropriate arguments on the command line while the associated dataset 1s dis played and selected For a description of the st command see us Help Application manuals Shape Tool 15 9 1 How to Open a Shape Gradient To open an existing shape gradient click the button lt 3 Open a shape or gradient select Shape or Gradient select a file from the appearing file list and click OK The selected shape gradient will appear in the data section 274 Acquisition 15 9 2 How to Use Shape Tool Display Options The Shape Tool toolbar offers the following display options 2 Display amplitude and phase 4 Display amplitude only fu Display phase onl
71. one interface its display is automatically updated in all TOPSPIN interfaces The command exit closes the current Topspin interface Interfaces that were opened from this interface remain open Entering exit in the last open TOPSPIN interface finishes the entire TOPSPIN session The position and geometry of each TOPSPIN interface is saved and restored after restart Chapter 3 Trouble Shooting 3 1 General Tips and Tricks On a spectrometer make sure the commands cf and expinstal1l1 have been executed once after installing TOPSPIN c f must be executed again if your hard ware configuration has changed Sometimes executing cf is useful in case of acquisition problems On a datastation a default configuration is automatically done during the installa tion No configuration commands are required Only if you want to use AU pro grams you must run expinstall once 3 2 History Log Files Stack Trace If you have a problem with TOPSPIN and want to contact Bruker it is useful to have as much information as possible available If TOPSPIN is still running you can view log files with the commands hist and ptrace If TOPSPIN hangs you can create a stack trace by hitting Ctr1 Linux or Ctr1 Break Windows in the TOP SPIN startup window 44 Trouble Shooting 3 2 1 History log file By default the history protocol feature is switched on This means all TOPSPIN commands will be protocolled and can be examined by entering hist on t
72. previously exported list from the current dataset Note that integration commands store the integral list in the processed data directory under the name inte grals txt Exported integrals are stored in the files lt name gt txt and lt name gt reg where lt name gt is the name specified by the user How to Display the FID t Click the Fid tab fid 144 2D Display 2D raw data consist of a series of FIDs which are displayed in a row Individual FIDs can be displayed by zooming out To do that click repeatedly Now you can shift and zoom in out the data to display different FIDs see Fig 9 10 exame2d_HC 1 1 Cubio guest ol x Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid 163 0 100 62 64 66 68 fid Figure 9 10 9 5 2D Display Options How to Switch between Hertz and ppm Axis Units in F2 and F1 r Click the following multi state button in the upper toolbar ha Switch between Hz and ppm axis units in F2 and F1 hz How to Switch on off the Spectrum Overview display r Click the following toggle button in the upper toolbar in Switch the spectrum overview display on off ov 2D Display 145 With the spectrum overview on the data window will for example look like this F E ia exam2d_HC 1 1 Cbio guest E o EEN Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid F1 ppm 60
73. region around the selected peak w Expand spectrum In correlated window to open a new data window showing the region around the selected peak Export entries of the peak list Entries of the peak list can easily be exported to Excel or any other program as follows 1 For multiple peaks Select the desired entries while pressing the Ctrl or Shift key 2 Right click an entry to open the popup menu see Fig 8 4 3 Click one of the following menu items e Copy Copy the selected peak s entry to the Clipboard Equivalent to click ing Edit Copy or hitting Ctr1 c Copied peaks can easily be pasted in any other application such as Excel 112 1D Display e Export Export selected peaks Opens a dialog box where you can specify the export file cvs txt or xml Check the box in the lower left corner to export the selected peaks only or uncheck it to export the entire list Then click Export Import a peak List A peak list from a different dataset can be imported as follows 1 Right click an entry to open the popup menu see Fig 8 4 2 Click Import 3 In the appearing dialog box navigate to the directory where the list resides and select the peak list xml or txt As such you can import a peak list from a different dataset or a previously ex ported list from the current dataset Note that peak picking commands store the peak list in the processed data directory under the name peak txt Delete remove pea
74. see Fig 11 1 1D Interactive Manipulation 163 How to Perform Default Zero Order Phase Correction 1 Right click in the data window 2 Choose Calculate phO in the popup menu see Fig 11 1 The spectrum will automatically be corrected according to the calculated value How to Perform Interactive Zero Order Phase Correction 1 Click hold the following button button turns green 0 Zero order phase correction parameter PHCO 2 Move the mouse until the reference peak is exactly in absorption mode 3 Release the mouse button turns grey How to Perform Interactive First Order Phase Correction 1 Click hold the following button button turns green 1 First order phase correction parameter PHC1 2 Move the mouse until the entire spectrum is exactly in absorption mode 3 Release the mouse button turns grey How to Perform 90 90 or 180 Zero Order Phase Correction r Click one of the following buttons gl Perform 90 zero order phase correction ph90 Perform 90 zero order phase correction phm90 180 Perform 180 zero order phase correction ph180 How to Reset the Phase to the Original Values r Click the following button Reset zero and first order phase values phr How to Change the Mouse Sensitivity r Click one of the following buttons 164 1D Interactive Manipulation 1 Increase double the mouse sensitivity inc t Decrease halve the mouse sensitivity dec
75. selected datasets in multiple display mode However if the current window was al ready in multiple display mode the selected spectra will be superimposed on the currently displayed spectra How to Open Data from the Portfolio The portfolio offers the same possibilities to open a dataset as the browser Addi tional options are cS Hit the Enter key to display the highlighted dataset in the current window examed HH 1 1 CAbio quest examed HO 1 1 CAbio quest evamid 130 1 1 Cibio quest evamid 1H 1 1 Cibio guest Figure 4 11 r Double click a dataset to display it in the current window How to Automatically Select the first expno procno of a dataset If you open a dataset from the Browser by clicking a data name there might be more that one expno and or procno available By default TOPSPIN then opens a dialog box from which you can select the desired expno procno combination see Fig 4 12 You can however configure TOPSPIN to automatically open the first available expno procno combination To do that 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Uncheck the item Display expno procno list when opening data 4 Click OK to close the dialog box Dataset Handling 61 PA examid_13C E a x This data set contains several EXPNO SPROCNO pairs corresponding to several ravv processed data file Please choose the desired one trom the list EXPHO SPROCNO dim pulsprog
76. set in a ZIP file Save data set in a JCAMP DX file Save data of currently displayed region in a text file Save parameters as a new experiment Save digital a analog fitered data Save other file Required parameters File type processed data as new PROCHO Y JRK Cancel Help Figure 4 18 2 Select an option and if applicable a file type 3 Click OK to execute the option The six options correspond to the following command line commands e wrpa copies the current data to a new data name or expno e tozip convert a dataset of any dimension to ZIP format e tojdx convert a 1D or 2D dataset to JCAMP DX format e totxt convert a 1D or 2D dataset text format e wpar write parameter set e convdta save digitally filtered data as analog filtered data e wrp wra genfid wmisc write various files How to Save an Entire Dataset 1 Click File Save Ctri1 s 68 Dataset Handling 2 Select the option Copy dataset to a new destination wrpa and click OK 3 Specify the dataset variables and click OK How to Save Processed Data 1 Click File Save Ctr1 s 2 Select the option Save other file 3 Select File type Processed data as new procno wrp and click OK 4 Enter a processing number procno and click OK How to Save Acquisition Data 1 Click File Save Ctr1 s 2 Select the option Save other file 3 Select File type Acqu data as new expno wra and click OK 4 Enter a experiment nu
77. t I t I 0 P x i 1 0 Px exp where is Intensity or Area according to the Fitting Type The best fit is cal culated by varying I 0 P and T1 in an iterative process according to the Lev enberg Marquardt algorithm Clicking and executes the commands ct1 current peak and dat1 all peaks respectively uxnmrt2 for one component T2 experiments Set the parameter List file name to the list type used during the acquisition A T2 fitting function is de fined by the function I t Px exp 5 where is Intensity or Area according to the Fitting Type The best fit is cal culated by varying P and T2 in an iterative process according to the Leven berg Marquardt algorithm Clicking and executes the commands ct2 current peak and dat2 all peaks respectively invrec satrec cptlrho expdec gaussdec lorgauss linear varbigdel var litdel vargrad vardamp these functions can be used for various experi ments with up to 6 components except for cpt1rho and lorgauss which allow only 4 and 3 components respectively They all use the simplex algo rithm and require some parameters to be set e Enter the Number of components 240 Analysis e Click the Setup button to set the Iteration Control parameters For each component the initial guess G and step rate S can be set The initial guess for I O must be selected such that the sum of all compo nents does not exceed 1 If there is only one component I
78. that you can use a single forward slash or a double backslash as path separator An example of the latter would be _VERSION 1 0 cmd read _spectrum re examld_13C 1 1 c bruk ts guest How to Set Automatic Startup Actions 1 Click Options Preferences set 2 Check or uncheck the options under Program startup actions for example Auto open last used data set Show NMR Data Processing Guide How to Change the Preferred Editor You can choose your preferred editor as it is used by commands like edau ed pul edcpd etc To do that 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Click the Change button to the right of the object Preferred text editor enter the desired Editor and its path For example for Wordpad under 316 User Preferences Windows 2000 this would look like A Editor definition x Please specife an IO name and the editor s path Editor ID wordpad Full path CAProgram FilesWindows NTWAccessorestwwordpad Remove Save cancel 4 Click Save to save the changes How to Configure the Tab Bar The default Tab bar at the top of the data window consist of Tabs to switch be tween various dataset objects like Spectrum Parameters Title etc You can how ever configure the Tab bar to contain Tabs for interactive data manipulation like phase correction integration etc These Tabs have the same function as the cor responding
79. the integral Clicking this button again rescales all integrals to their original height 172 1D Interactive Manipulation How to Move the Integral Trails Up Down To move the integrals selected and unselected up or down r Click one of the following buttons 4 The left edge of the lowest integral is put just above the baseline Theright edge of the highest integral is put at 3 4 of the window height t Shift all integral trails up down smoothly How to Cut Integral Regions 1 Click the following button button turns green Cut integral region 2 Move the red cursor line into an integral region to the position where it must be cut and click the left mouse button 3 Do step 2 for each integral region that must be cut 4 Click the green button to leave the cut integral mode button turns grey How to Save Integral Regions 1 Click the following button Save integral regions The following popup menu will appear Save Regions To intrrg Save Regions To reg Export Regions To Relaxation Module cave amp show List Figure 11 6 2 Choose one of the following entries e Save regions to intrng Save the currently displayed integral regions including the slope and bias correction values 1D Interactive Manipulation 173 e Save Regions to reg Save the integral regions to the file reg e Save amp show list Save the currently displayed integral regions including the slope and bi
80. ti Xo alT BM la gt rel 1 28 1 26 1 24 1 22 1 20 ppm Figure 14 13 To define the multiplet 1 Zoom in on the region around the desired multiplet 2 Click the button it turns green 3 Left click the peaks to be defined Note that left clicking a peak again will undefine it 4 Right click in the data window and select Define Multiplet in the popup menu The multiplet will be displayed 5 Click the t button to leave this mode In Fig 14 13 the left peak is already assigned and the cursor line is within the cap ture range of the central peak as indicated by the faint line on the peak maximum Manual analysis can also be started by right clicking in the data field and choosing Define Multiplet Manually 14 5 3 Free grid analysis In this mode you can define a multiplet by assigning one peak manually and all other peaks by free grid analysis The grid consists of a predefined number of dis tance lines Analysis 245 To define the multiplet L 2 3 Zoom in on the region around the desired multiplet Click the HH button it turns green Right click in the data window and if necessary set the number of distance lines Left click the central peak to be defined For a multiplet with an even number of peaks left click one of the central peaks The central peak will be marked Note that clicking a marked peak again will unmark it Move the mouse to the left or right unt
81. title 4d zgeg30 13C 1H DRX 300 Chola Td deptis5 C13 DEPTIS5 DRX 300 Cholac qd dept4s C13 DEPT45 DRA 300 Cholac Td dept90 C13 DEPTS0 DRAX 300 Cholac 1d jmod C13 AFT Attached Proton Test DRX 300 Cholac 1d zgigs0 C13 Inverse gated DRX 300 Cholac f Show dinvpulsproqtitle next time OK Cancel Figure 4 12 How to Open Data from the Topspin menu 1 To open a dataset w Click the lt Q button in the upper toolbar or us Click File Open open Ctr1 o see Fig 4 13 62 Dataset Handling File Edit View Processing Analysis Mew Ctrl M Oper Ctrl O Reopen Close Ctrl Y Close All Save Ctrl 5 Print Ctrl F Expor send To Run Delete Figure 4 13 2 In the appearing dialog box see Fig 4 14 xi Options ir Open NMR data stored in standard Bruker format iC Open NMR data stored in special formats C Open other file Reguired parameters Browser type IRE Dialog Cancel Help Figure 4 14 a Select the option Open NMR data stored in standard Bruker format b Select the browser type RE Dialog c Click OK Dataset Handling 63 3 In the appearing dialog box see Fig 4 15 Be n Please specify data set MAME EXPN PROCNG DIF c i USER guest CK Cancel Browse Find Help Figure 4 15 a Specify the dataset name expno etc b Click OK Note that the dataset s
82. to Measure a Chemical Shift Distance 221 14 2 1D Signal to Noise Calculation 20 0 00 0 cece 222 How to Perform Interactive S N Calculation 222 How to Delete the Signal Region or Noise Region 223 How to Edit the Limits of the Signal Region or Noise Region 223 How to Change the Width of the Signal Region or Noise Region 224 14 3 Solids Line Shape Analysisixs wesc teeusesatsadalsdds Peony e yews 225 Spectrum PreparauiOn wie nt Ute wwtetnws dase a a 2 225 Switch to Line Shape Analysis Mode 00000 00 eee 225 The simulation procedure 0 ccc eee eens 221 STM ation doS e 4 22 erer en R A nA Nr rE hae ad 232 144 Relaxation Analysis iere is 4 aro eee ead EE E E ee 235 145 Multiplet Analysis 35 225 204 cana a a e e tee ea Aaa 241 Sclectne a WiUIMIDIEt a2 ee AERE anaes BE bad wel eats we RA 247 Selecting a Level in a Multi Level Multiplet 247 Designating a Level in Multi Level Multiplets 248 Dave And Clos Ene Sida aur eeu ees cae Ae Raha a ae eee ae oF 253 ACUBINON seriean ikae nN 6B ace aaa a a E 255 ra ACquisition Guide 33 65 tana aa a eee EEA 299 15 2 Acquisition Toolbar 2 a oa anasan ee eens 257 15 3 Acquisition Status Bar s 4oi icohtde Siw seed bee Ca eeu takeess 259 15 4 Tuning and Matching the Probehead 0000 006 261 L53 tWOCKING 4 6165 fu SS ed a a Gide A ont aie ae OS ad
83. top of the lock window the following buttons are available Open the user preferences window set oon T T oF a Toggle lock monitor mode cig Lock the magnetic field lock Toggle lock display mode between single and dual color Colors can be set in the User preferences command set HH Switch grid mode between both vertical horizontal and off D Make the lock display external Put focus into TOPSPIN window 264 Acquisition a Close the lock display window Note that an external lock display window is independent from the TOPSPIN win dow You can for example minimizes TOPSPIN while keeping the lock display open The lock display can also be opened by double clicking the lock field in the acqui sition status bar see par 15 3 The lock process can be started by entering Lock on the command line This com mand is described in the Acquisition Reference manual 15 6 BSMS Control Panel The BSMS control panel allows shimming locking sample handling and helium level measurement To open this panel r Enter bsmsdisp on the command line The BSMS Control Suite window will appear see Fig 15 8 Acquisition 265 ESMS Control Suite O x Main Lock Sample amp Level Shim Autoshitn Service AUTO Phaze Power ain Lock Lock Phaze Power ain SAMPLE LIFT SFIN SHIM ra Previous Actual Absolute Step Difference Step Stepsize qp o fer pir frar 1 10
84. you can also write Python programs which allow you to use TOPSPIN commands User Interface functions and Graphic func tions For more information 0s Click Help Programming Python Programming 6 4 Serial Processing using Python programs TOPSPIN allows you to process a series of datasets using serial scripts The dataset list and command s to be used can be easily setup from the TOPSPIN interface as follows Enter the command serial on the command line This will open the 1 Before you can use any Bruker AU program expinsta11 must have been executed once 92 Data Processing dialog window shown in Fig 6 2 CE x Options Process specified data set list with specified script Browse for a data set list Browse for a serial Script Edit specified data set list Edi specified serial script Create new data set list Create new serial script Required parameters Data set list Tull path Ic data_list Serial script name ser_em script location ru Shlexpletan iin Wists mac Show data sets during script execution YES z Script type Python of JR Cancel Help Figure 6 2 Here you can set up and start data processing of a series of datasets using scripts which can be TOPSPIN macros or Python programs The dialog offers you the following options Process specified data set list with specified script Process the data in the specified dataset list using the specified ser
85. 01 parameters 82 83 269 status bar 259 271 toolbar 257 Acquisition Reference Manual 19 85 264 265 302 AcquPars tab 82 108 140 269 activate a data window 213 the next data window 218 add comment to audit file 77 data to portfolio 74 directory to the browser 20 53 found data to portfolio 54 74 functionalities to Topspin 25 peak in 2D phase correction 194 peak to peak list 190 add increment in 2D levels 149 align intensities in multiple display 180 peak positions in multiple display 180 Alt F11 key 104 134 Alt F4 key 36 41 Alt F6 key 41 Analysis menu 23 29 anisotropy 225 apk command 87 90 161 apks command 161 arrange data windows 214 data windows horizontally 216 data windows vertically 215 rows columns in 2D phase correction 200 ascii files 75 130 ased command 84 108 Aspect 3000 data 65 ATM probehead 261 262 atma command 262 AU macros 25 330 331 AU program reference manual 91 AU programs 19 25 90 303 330 334 337 audit trail check 76 trail files 76 audit command 76 auditp txt file 76 automate data acquisition 26 automatic 1D baseline correction 87 1D calibration 87 173 1D integration 164 1D peak picking 187 1D phase correction 87 161 2D calibration 206 allocation of TCP IP ports 309 compilation of an AU program 304 configuration of a datastation 301 selection of the first expno procno 60 startup actions 315 tuning and matching 262 automatic mode of the Acquisition Guide 256 of the Proce
86. 1D Interactive Phase Correction Procedure How to Switch to Phase Correction Mode Click the indicated button in the upper toolbar A Jaw A or enter ph on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 162 1D Interactive Manipulation 11 1 examid_1H 1 1 Cobia guest O x Ajo 1 R mwm as ngA y CE 0 00 pivot 1 2508 ppm Phase increment 0 20 ph 0 00 phl Set Pivot Point 10 rel Calculate pho O 5 Figure 11 1 Data window in phase correction mode A The yellow button indicates that you are in phase correction mode Some buttons will turn green when they are clicked As long as a button is green it is active How to Perform a Typical 1D Interactive Phase Correction For a typical 1D phase correction take the following steps 1 Click hold the button 0 and move the mouse until the until the reference peak is exactly in absorption mode 2 Click hold the button 1 and move the mouse until the entire spectrum is exactly in absorption mode 3 Click the button bi to save and execute the phase correction and return 11 1 2 1D Interactive Phase Correction Details How to Set the Phase Pivot Point By default the phase pivot point is set to the biggest magnitude intensity of the displayed region of the spectrum To change the pivot point 1 Right click on the desired pivot point position 2 Choose Set pivot point from the popup menu
87. 2 12 shows row 669 with the 1D baseline at the center of the data window How to Extract a Row Column 1 Scan rows or columns as described above and hold at the desired position 2 Right click in the data window and choose Extract Row Column from the popup menu see Fig 12 11 3 Specify the row column number and output procno in the dialog box Note that the ROW COLUMN field is initialized with the grabbed row column or if no grabbing was done with the current row column 4 Click OK The extracted row or column is stored as a 1D dataset under the specified PROC NO and displayed in a new data window In the upper left part is this the row number and source 2D dataset is specified see Fig 12 13 exam2d_HC 1 999 C ibio guest _ olx Spectrum ProcPars AcquPars Title PulsProa Peaks Integrals Mi aj row 669 from examed HC 1 1 C bio quest Figure 12 13 How to Copy Contour Levels from First to Other Spectra Click the following button 3 Copy contour levels from the first to the other spectra Note that the contour levels are only changed on screen not on disk How to Switch on off 2D contour display Click the following button 206 2D Interactive Manipulation imi Switch on off 2D contour display How to Position the Baseline of the Row Column To put the baseline at the center of the data window 1 Right click in the data window 2 Choose in Baseline At Center from the popup menu see Fig 12 11
88. 22 NOISF2 parameter 222 notebook 329 NS parameter 258 O O1 parameter 259 O2 parameter 259 O3 parameter 259 objects of a dataset 22 102 212 313 316 317 318 of Topspin 309 oblique display of 2D spectra 151 153 of 3D planes 156 online help 39 online manual plot editor 97 Topspin 39 open browser portfolio 51 data 30 36 49 59 60 61 data from the browser 19 data from the command line 64 66 data from the Explorer 63 data from the menu 19 IconNmr interfaces 26 Linux Shell 18 new data window 214 new portfolio 53 new procno 64 online help documents 39 special format data 65 title bar menu 29 Topspin command index 40 open command 30 36 61 65 Options menu 29 overview spectrum 1D 124 2D 144 P paper format 301 paracon command 302 parameter adjustment window 82 266 change 81 84 display 20 editor 79 80 82 83 field 81 83 files 74 handling 79 name 79 82 search 108 value 81 83 parameter set 57 67 PARMODE parameter 108 paste command 30 64 66 peak alignment 21 180 display 20 fitting 24 group 24 labels 127 190 list 190 191 list 1D 110 190 list 2D 141 picking mode 187 position 221 position alignment 180 ranges 191 peak picking 1D automatic 187 1D interactive 187 mode 31 I 11 mode 1D 188 ranges in 1D 189 peak txt file 191 peakrng file 191 Peaks tab 98 110 141 phase correction 1D automatic 87 88 1D interactive 161 2D interactive 193
89. 2ii i Imaginary processed data 11i Required parameters Mame Data directory Ets 2a ser quest JRK Cancel Help Figure 4 20 1 Select a data type option For each option the corresponding command appears in the title of the dialog box These commands can also be used to delete data from the command line 2 Specify the Required parameters Note that you can use the wildcards Question mark for any single character 3 Click OK Asterix for any character and any number of characters A dialog box will appear showing the matching datasets For example if you se lect the option An entire dataset 1 Select dataset entries for deletion selected entries are highlighted Dataset Handling 71 To select multiple entries click them holding the Shift or Ctr1 key 2 Click Delete to delete the entire data directory If you select the option Acquisition data or Processed data you can choose be tween deleting the data files only and deleting the entire expno or procno direc tory respectively see Fig 4 21 4 CEE x Data director C big User guest Wild card 13 evamid 13C evamid 13C evamid 13C Delete selected EAPNO S Delete selected FILE S Cancel Help Figure 4 21 4 6 Searching Finding Data How to Find Data You can find TOPSPIN data according to various criteria To start searching do the following 1 Click Edit gt Find data Ctr1 f
90. 30 161 2D 193 user defined AU programs 303 buttons 334 337 339 commands 23 25 functions keys 41 plot layouts 96 User Interface functions 331 user preferences 313 user properties directory 41 99 314 User s guide 39 y Varian spectrometer 66 I 16 vertical scaling 104 View menu 29 49 126 virtual spectrometer 24 VNMR data 66 W walk up 26 wbst command 262 wbsw command 262 wildcards 70 window layout 218 Window menu 29 219 WINNMR data 65 wm command 23 79 wmisc command 67 wobb command 261 wobble display 260 frequency 262 procedure 261 steps 262 sweep width 262 window 261 wpar command 67 wra command 67 68 wrp command 67 68 wrpa command 23 67 68 X xau command 304 x axis rotation in 3D 153 158 xmac command 25 Y y axis display 31 125 y axis rotation in 3D 153 158 Z z axis rotation in 3D 158 zero order phase correction 1D 163 2D 197 198 zg command 258 269 ZIP data format 23 65 zoom 1D data 32 104 2D data 136 in 2D phase correction 194 reset in 1D 105 reset in 2D 137 zoom 1D 2D data 37
91. 37 data directory 19 20 49 data directory fully 52 data directory in the browser 52 individual spectra in multiple display 180 spectrum 24 experiment time 258 expinstall command 18 43 258 299 300 301 303 expl command 63 75 76 130 Explorer 49 63 75 130 expno 56 60 63 68 128 exponential baseline correction 184 window multiplication 87 88 export data 22 99 expt command 258 extend the Topspin functionality 329 external projection 21 extract a row column in 2D 205 F F1 dimension 137 144 193 F1 key 15 36 F1 F2 plane 156 159 F2 dimension 137 144 193 F2 key 36 51 F2 F3 plane 157 159 F3 key 41 F3 F1 plane 155 157 159 F5 key 41 F6 key 36 41 214 FDA 76 fid command 124 143 FID display 258 260 266 269 Fid tab 124 128 143 File Chooser 19 File menu 19 29 file size of raw data 258 files of a dataset 64 67 75 128 130 find command 36 54 71 find data 29 54 71 firewall 309 first order phase correction 1D 163 2D 197 198 fitting peaks 24 fmc command 88 focus 33 36 51 font of dialog windows 321 of the browser 321 of the command line 322 of the interface 319 of the menu 320 of the status line 322 of the tab bar 320 forward peak picking 190 Fourier transform 87 88 fp command 88 fromjdx command 24 fromzip command 23 ft command 23 87 ftf command 23 325 function keys 36 G Gaussian deconvolution 24 Gaussian window multiplication 88 genfid command 67 68 genser command 68
92. 7 221 2 5811e 009 1 9737e 008 10 000s 7 221 3 2898e 008 2 9056e 007 8 000s 7 221 7 8525e 008 6 4616e 007 5 000s 7 221 1 6289e 009 1 3101e 008 Print Export of Copy the Fitting Results To print the fitting curve r Click File gt Print To export the fitting curve as a graphics file 0s Click File Export To copy the fitting curve to the Windows Clipboard 0s Click Edit gt Copy 14 5 Multiplet Analysis TOPSPIN offers a multiplet analysis package To start this tS Click Analysis Multiplet Analysis managuide This will open the Multiplet Analysis Guide This will guide you step by step through the multiplet analysis process Alternatively you can enter the command mana which directly switches to Multi plet Analysis mode The data window Tab bar will change to a multiplet analysis 242 Analysis toolbar Fig 14 11 shows a region of an ethanol spectrum Multiplet analysis can be performed in three different ways e define multiplet by region e define multiplet manually e define multiplet by free grid For multi level multiplets the following methods are available e couple existing multiplets into a multi level multiplet e define multi level multiplet by coupled grid Multiplet analysis uses a maximum intensity search within a user defined capture range see Fig 14 18 If peak picking has been performed required for defining a multiplet by region the found peaks within the capture range are used Ho
93. AQ mod Dad Acquisition tr eae cue Th e5536 Size of fid Durations WE h E of scans Power pos oof dummy s Ei T R This opens the acquisition parameter editor see also chapter 5 1 The following extra buttons are available 1 Undo last value change Can be used to undo multiple changes JL Show pulse program parameters ased amp Status parameter display The button turns green when activated dpa g Set probehead solvent dependant parameters getprosol 123 Change raw dataset dimensionality parameter PARMODE gy Search for specified parameter Changed parameters are automatically saved 1D Display 109 How to Edit the Title Click the Title tab edti examid 13C 1 1 Cobia guest Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid Bale 1301H AY 300 Automation Cyclosporin This allows you to edit the title that appears in the data window and on the plot Save the title file under its current name H Save the title file under a new name 1 Reload the title file Undo modifications since the last save How to Edit the Pulse Program t Click the PulsProg tab edcpul1 iexamid 1H 1 1 Cobio quest Spectrurn ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid BH Alo s ne File Mame ft Shvexp stanMimrdists pp ego Finclude Avance incl gt l ze 2 230m dl Div Gee
94. Actions The plot limits and maximum intensity are set according to the Plot Editor Reset Actions right click inside the Plot Editor data field and choose Auto mation to set the Reset Actions e as saved in Plot Editor The plot limits and maximum intensity are set in the specified layout Fill dataset list e from your default portfolio The portfolio contains the current TOPSPIN dataset plus the data from the default Plot Editor portfolio from port folio saved in dataset The portfolio contains the current TOPSPIN dataset plus the data from the portfolio stored in this dataset How to Plot Data from the Processing guide Printing plotting data can be done from the Processing guide by clicking the Plot Print button If Automatic mode is checked the active data window will be printed as it appears in the screen If Automatic mode is unchecked you will get the dialog box as displayed in Fig 7 1 How to Plot Data with the Plot Editor The Plot Editor can be started from the Plot Editor or from the command line command plot The Plot Editor allows you to create layouts and plot data The complete functionality is described in the online manual which can be opened from the Plot Editor Help menu How to Print the Integral list 1 Click the Integrals tab of the data window see Fig 7 2 2 Enter print or Ctrl1 p to print it 98 Printing Exporting Data examid 1H 1 1 Cobo guest Spectrum ProcPars AcquPa
95. Correction r Click Parameters ABSF1 2 The region will be stored in the processing parameters ABSF1 and ABSF2 These are used by the commands absf and apkf How to Save the Display Region for Strip FT r Click Parameters STSR STSI The region will be stored in the processing parameters STSR and STSI These are used for Fourier Transform commands like ft and trf to perform strip FT Chapter 9 2D Display 9 1 The 2D Data Window The 2D data window consists of a data field a title bar a Tab bar and buttons Fig 9 1 shows a data window with a 2D spectrum 2D Display 134 data title bar minimize maximize close field Tab bar button button button x exam d HC 1 1 Cobia guest spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid 120 F1 ppm 6 4 2 F2 ppm Figure 9 1 9 2 Changing the Display of a 2D spectrum TOPSPIN offers various buttons to scale or shift a 2D spectrum both vertically and horizontally How to Change the Intensity Scaling r Click the button Change the intensity scaling contour levels edlev Or rs Hit one of the keys e Alt PageUp Increase the intensity by a factor of 2 e Alt PageDown Decrease the intensity by a factor of 2 e Alt Enter Reset the intensity or r Click hold the button and move the mouse 2D Display 135 Increase decrease the intensity smoothly or r Click one of the following button
96. Directory pathnames enter a directory and click OK If no structure file is found you can open one by clicking File gt Open in the Molecule Viewer 1D Display 123 The following structure file types are supported xyz mol pdb cml out mmlgp res CLE gpr hin NWO Secondary structure elements of proteins backbone cartoons ribbons can be displayed in selectable sizes and colors Mouse button effects Rotate a molecule around the x and y axis by pressing the left mouse button and moving the mouse left right or up down respectively Rotate a molecule around the z axis by pressing the middle mouse button and moving the mouse left right Zoom in or out a molecule by pressing the middle mouse button and moving the mouse up or down RASmol command scripts are supported To send a RASmol command to the currently displayed molecule enter isjmol lt RASmol command gt Here are some example isjmol zoom 400 isejmol ribbon 200 isejmol color ribbon yellow You may create Topspin macros containing RASmol commands Just enter edmac on the TOPSPIN command line and insert the RASmol commands in the appearing editor Here is an example jmol load mystructures alphahelix pdb load a structure jmol backbone 0 7 display its backbone with 0 7 Angstrom size jmol color backbone yellow change backbone color jmol background green change background color jmol zoom 200 zoom structure The avail
97. E olr E 0392 Ok Cancel The S N value is automatically recalculated and displayed 4 Click OK How to Change the Width of the Signal Region or Noise Region 1 Right click in the data window 2 Choose Change region width from the popup menu see Fig 14 2 3 Enter new width values in the appearing dialog box SS 6hxl Define sind parameters wicth Unit SIGREG a 3960 ppm NOISEREG 4 0425 ppm Ok Cancel 4 Click OK Note that as you change the width the right limit is modified correspondingly The left limit is kept The S N value is automatically recalculated and displayed Analysis 225 14 3 Solids Line Shape Analysis Solids Line Shape Analysis allows you to simulate and fit calculated spectra to various experimental 1D solid NMR spectra The following fitting models are available e Gauss Lorentz e Chemical Shift Anisotropy e Quadrupolar Central Peak of the 1 2 Transition of a Quadrupolar Nucleus e All Quadrupolar Transitions of a Quadrupolar Nucleus e The Combination of the Chemical Shift Anisotropy and Quadrupolar Inter action You can simulate powder spectra of static or rotating samples at single or double axis conditions Both rotation angles can be set The inner and outer rotating speeds are freely adjustable For rotating samples a maximum of ten rotation side bands and five DOR bands can be set You can simulate one 1D spectrum with a maximum of 25 ob
98. IN Interface Focus in a Table e g peaks integrals nuclei solvents Delete the selected entries Select the Fist entry Select the last entry Shift Home Select the current and first entry and all in between Shift End Select the current and last entry and all in between ENA Focus in a Plot Editor Open the Plot Editor Manual F5 Refresh ctr1 F6 Display next layout etre Ctr1 i Open TOPSPIN Interface O a a a a Lower the selected object Ctr T w Open the attributes dialog window Note that the function of function keys can be changed as described in chapter Det The TOPSPIN Interface 39 2 6 Help in Topspin TOPSPIN offers help in various ways like online manuals command help and toolt ips How to Open Online Help documents The online help manuals can be opened from the Help menu For example to open the manual that you are reading now t Click Help User s Guide To open the Avance Beginners Guide guide t Click Help Avance Beginners Guide To open the Processing Reference guide o gt Click Help Processing Reference Manual Note that most manuals are stored in the directory lt tshome gt prog docu english xwinproc pdtf The most recent versions can be downloaded from www bruker biospin de How to Get Tooltips If you hold the cursor over a button of the toolbar a tooltip will pop up This is a short explanation of the buttons function For example if you hold the c
99. Interactive Manipulation 167 1 Right click in the integral region 2 Choose Select Deselect from the popup menu Selected integral regions are indicated by a color filled integral label In the Fig 11 3 the two left most regions have already been selected the right most region is currently being selected examid_1H 1 1 Crbio guest l ojx Tj d folja Bl Alan nx 2 s e a Mouse Sensitivity 1 0 p mt 5 976 ppm 1793 020 Hz Calibrate f Mormalize Delete O wat Way Em 6 5 ppm Figure 11 3 How to Read Integral Regions from Disk You can read integrals regions from disk which have been stored by automatic in tegration command abs or by a previous interactive integration To read integrals 1 Click the following button Read integral regions The following popup menu will appear 168 1D Interactive Manipulation Fead intrng Fead intrng Mo Slope amp Blas Corr Read intrng Use Last Slope amp Bias Edit intrng Figure 11 4 2 From the popup menu choose one of the following entries Read initrng to read the last saved integral regions and apply the saved slope and bias correction values Read intrng no slope amp bias corr to read the last saved integral regions but do not apply the saved slope and bias correction values Read intrng use last slope amp bias to read the last saved integral regions applying the last slope
100. MMPUTANONG wc obbe ati debe dalhtae detente aes wea Me 18 L6 How to Display Spectax redis ounce Sand ectatecewndgnanesearks 19 How to Open Data from the Menu 0 0 cece eee eee 19 How to Open Data from the Browser 000 cece ee ees 20 How to Define Alias Names for Data 0 0 0 0 00 20 How to Open Data in Other Ways 0c cee eee ees 20 1 7 How to Display Peaks Integrals together with the Spectrum 20 1 8 How to Display Projections 1D Spectra with 2D Spectra 21 1 9 How to Superimpose Spectra in Multiple Display 21 1 10 How to Print or Export the Contents of a Data Window 22 How to Print Data 505 aieeaa a E a S 22 How to Copy a Data Window to Clipboard 0044 22 How to Store Export a Data Window as Graphics File 22 LIL Howto Proces Date eea nE a oie ANRE RNN R 22 I2 How toArchive Di rae aR an eee E 23 1 13 How to Import NMR Data Stored in Special Formats 24 1 14 How to Fit Peaks and Deconvolve Overlapping Peaks 24 1 15 How to Compute Fids by Simulating Experiments 24 1 16 How to Add Your Own Functionalities 0 0 00 00 25 Howto Create Macros hoege 203 nein ote tad hehe ee aa eA 25 How to Create AU automation Programs 0005 25 How to Create Python Programs 0 0 0 cece ees 26 1 17 How to Automate Data Acquisition 0
101. N measurement mode 2 Move the mouse into the data window 3 Left click hold and drag the mouse from one edge of the signal region to the other edge A horizontal double headed arrow will indicate the signal region 4 Left click hold and drag the mouse from one edge of the noise region to the other edge A horizontal double headed arrow will indicate the noise region 5 Right click any position in the data window The popup menu as shown in Fig 14 2 will appear Analysis 223 Uit Clear NOISEREG Clear SIGREG Edit Regions Change Region Widths start S N Calculation Enter Zoom Figure 14 2 Choose Start S N calculation The other entries allow you to redefine or clear the regions After the noise calculation has finished the result will appear on the screen How to Delete the Signal Region or Noise Region To delete the current signal region 1 Right click in the data window 2 Choose Clear SIGREG from the popup menu see Fig 14 2 To delete the current noise region 1 Right click in the data window 2 Choose Clear NOISEREG from the popup menu see Fig 14 2 How to Edit the Limits of the Signal Region or Noise Region 1 Right click in the data window 2 Choose Edit regions from the popup menu see Fig 14 2 224 Analysis 3 Enter new limit values in the appearing dialog box SS h x Define sino parameters From pom To ppm Slo REG i Bara Lo isisi NOMEREG
102. O is usu ally set to 1 The step rate is usually set to about one tenth of the initial guess If the step rate of a variable is set to zero then this variable is not changed during the iterations Clicking gt and gt gt executes the commands simfit current peak and simfit al11 all peaks respectively View the Fitting Results When the fitting procedure has finished the fitting curve 1s displayed in the data section and a Brief Report appears in the parameter section see Fig 14 10 The latter consists of e the calculated relaxation value e the fitted parameters e the standard deviation SD For further examination of the result click one of the following buttons Show the fitting result of the previous peak area Show the fitting result of the next peak area Switch x axis to linear scaling Fo Switch x axis to logarithmic scaling AC Switch x axis to quadratic scaling amp Export integrals to dataset TEMP and exit Show an extended report including the fitted intensity or area distribu tion This consists of the same information as the brief report plus a ta ble with the intensity or area distribution Example Dataset C bio data guest nmr titest 1 pdata 1 INTENSITY fit Analysis 241 I t I 0 P exp t T1 12 points for Peak 1 Cursor Point 7 221 ppm Results Comp 1 I O 1 215e 000 P 2 211e 000 al 19 449s SD 36856 003 tau ppm integral intensity 30 000s
103. PIN installation directory with the Bruker example datasets To suppress this feature click Options Preferences set click Program startup actions and uncheck Show TOPSPIN default data direc tory in data browser How to Open a New Portfolio 1 Right click inside the portfolio 54 Dataset Handling 2 Choose Open portfolio from the appearing popup menu see Fig 4 6 3 Navigate to the folder that contains the portfolio files 4 Select the desired portfolio file extension prop 5 Click Open How to Save the current Portfolio 1 Right click inside the portfolio 2 Choose Save portfolio from the appearing popup menu see Fig 4 6 3 Specify a folder and filename in the appearing dialog box The filename must have the extension prop 4 Click Save How to Remove Datasets from the Portfolio To remove a single dataset from the portfolio 1 Right click the dataset 2 Choose Remove from portfolio from the popup menu see Fig 4 6 3 Click OK in the appearing alert box To remove multiple datasets from the portfolio 1 Hold the Ctr1 key and left click several datasets to select them or hold the Shift key and left click two datasets to select these two and all in between 2 Right click any of the selected datasets 3 Choose Remove from portfolio from the popup menu see Fig 4 6 4 Click OK in the appearing alert box How to Find Data and Add them to the Portfolio 1 Click Edit gt Find dat
104. Pulse are shown Depending on the application these set tings have to be modified accordingly You can use the same shape for each region of all different shapes In the latter case the check box Use same Shape for all Regions must be unchecked How to Add Shapes To add multiple shapes r Click Manipulate Add Shapes addshapes A dialog box will appear where you can select up to 10 shapes from the available shape files Acquisition 287 A minimum of two shapes must be selected Note that the selected shapes re place the current shape The file size of each shape is shown in the Size column Note that if the sizes differ the desired alignment must be selected For each added shape you can specify a scaling factor between 0 and 100 in the Scaling column The Scale resulting shape radio button allows you to rescale the resulting shape e to 100 e to the average of the individual scaling factors The alignment of the added shapes may be with respect to the Beginning of Shape the Center of Shape or the End of Shape If Arbitrary Alignment is se lected the start point must be entered for each shape in the Start column In other cases the Start entry 1s deactivated How to Perform Single Sine Modulation To perform an amplitude modulation such that the pulse excites at two symmet ric sidebands offset with opposite phase r Click Single Sine Modulation sinm2 and set Offset frequency to be relative to the
105. PulsePrag Peaks Integrals Sample Structure Fid We periment PULPRO ts zg30 T Current pulse Atl mod ban Acquistion mo TD e5536 Size of fid MS f Bi of scans DS 2 of durri Sc TCO f Loop count fot Wicith Su prn 20 5630 Spectral width SH Hz le T2039 Spectral width At 53084660 Acquistion tirri FIDRES Hz o 0941 g0 Fid resolution FvW Hz g0000 00 Filter m BE 4 Figure 15 12 a Optionally click L to show the pulse program parameters only b Click the E button to read the prosol parameters Or Set the relevant parameters manually As an alternative to step 2 you can set the acquisition parameters interactive ly in the GS window see par 15 7 To start the acquisition e Click p in the upper toolbar or enter zg on the command line The FID display window will appear 270 Acquisition FID protona 1 1 C guest Acquisition POLPROG zg30 NUCL 1H ail 20 567 mW h 6172 04 TD 644356 EXPERIMENTS l l SCANS 2 16 RES TIME lme9s lms4e Figure 15 13 The buttons in the toolbar have the following functions Iw Show FID in shuffled mode li Show FID in unshuffled mode horizontally arranged i Show FID in unshuffled mode vertically arranged Iw Show FID in unshuffled mode interleaved ki Switch between FID and spectrum ul Switch to spectrum data window Gi Stop the acquisition stop m Halt the acquisi
106. Required parameters LAYOUT fe jos2 xwep Apply Use plot limits Fill data set list from Plot Editor Reset Actions az saved in Plot Editor C from portfolio saved in data set trom vour defaut portfolio JRK Cancel Help Figure 7 1 2 In the Print dialog box a Select Print active window prnt b Click OK Before printing starts the operating system print dialog box will appear Here you can for example select the printer name and the printer properties The Print dialog box see Fig 7 1 contains two further options Print with layout start Plot Editor plot If you select this option and click OK the Plot Editor will be started This option is equivalent to entering plot on the TOPSPIN command line Print with layout plot directly autoplot Selecting this option activates the Plot Editor layout list box Select the desired layout and click OK to print Standard layouts are delivered with TOPSPIN They use the Windows default printer User defined layouts use the printer defined in the Plot Editor On a 1D dataset only 1D layouts are listed on a 2D dataset only 2D layouts are listed etc For the last two options the following Required Parameters are available Printing Exporting Data 97 Use plot limits e from screen CY The plot limits and maximum intensity are used as they are on the screen processing parameter F1P F2P and CY respectively from Plot Editor Reset
107. Right click any position in the data window 2 Choose Delete All from the popup menu see Fig 11 14 How to Return from Cubic Spline Baseline mode with without Save To return while saving the baseline points r Click the following button Hj Save baseline points and Return retsab To return while discarding any changes r Click the following button a Return Discarding any changes ret Alternatively you can right click in the data window and choose Save amp Quit or Quit respectively 11 6 1D Interactive Peak Picking Peak picking can be performed automatically with the commands pps or interac tively in the peak picking mode 188 1D Interactive Manipulation How to Switch to Peak Picking Mode r Click the indicated button in the upper toolbar DE or enter pp on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 15 examid_1H 1 1 Cbio guest oj x M EERE dom S al ERA 0 97 ppm 483 04 Hz CY 20 00 rel MAXI 19 50 rel MI 0 00 rel 10 15 20 1e6 5 0 10 g 6 4 2 ppm Figure 11 15 Data window in peak picking mode The yellow button indicates that you are in peak picking mode a Some buttons will turn green when they are clicked As long as a button is green it is active Note that the E button is automatically activated i e you are in Define peak picking range mode How to Define New Peak Picking Ranges
108. Set the 2D Contour Levels r Click the following button in the lower toolbar Edit contour levels edlev 1v This will open the following dialog box shown in Fig 9 13 Contour levels can be entered manually or they can be calculated Manual setup This allows you to create an arbitrary sequence of levels 1 Enter the level values in the fields 1 2 at the top of the dialog box 2 Click Apply to update the display or OK to store the levels update the display and close the dialog box Calculation This allows you to easily create a geometric or equidistant sequence of levels 1 Click one of the following items Multiply with increment to create a geometric sequence of levels e Add increment to create a equidistant sequence of levels 2 Enter the desired Base level Level increment and Number of levels 3 Click Fill to display and activate the sequence 4 Click Apply to update the display or OK to store the levels update the display and close the dialog box The Contour level sign allows you to select positive levels negative levels or both 150 2D Display PN exam2d_HC 1 1 C bio guest 2253560 0 2253560 0 4056408 0 4056408 0 7301 534 4 7301 534 4 fi 3142761 9 a 3142761 9 23656974 z 23856971 5 425625456 42562548 6 76648567 5 76648587 5 fi ar 967457 5 a af 967457 5 248341 423 6 248341 423 5 Required parameters Calculation method ie Wiultigply with increment A
109. TOPSPIN on a new computer a new disk or in a new TOPSPIN installation directory The default configuration name is Bruker_default_av500 and corresponds to a Avance 500 MHz spectrometer For manual or interactive data processing the automatic default configuration is sufficient If however you want to use AU programs you must execute expin stall once selecting Installation for Datastation Default How to Perform a Customized Configuration on a Datastation If you want to configure your datastation according to a spectrometer other than default you must first copy the configuration directory lt tshome gt conf instr lt instrum gt from that spectrometer to the datastation Here lt tshome gt is TOPSPIN home the directory where TOPSPIN 1s installed Note that this can be different on the spectrometer than on the datastation lt instrum gt is the configuration name After copying the configuration directory you have to perform expinstall1 as follows e Click Spectrometer gt Setup Experiment installation or enter expin stall on the command line Follow the instructions on the screen In successive dialog boxes check select the options below and click Next to continue e Installation for Datastation Customize e High Resolution Systems e The configuration name as it was copied from your spectrometer e The items you want to install e Select the desired printer and paper format for the parameter sets e The spe
110. The new data window will become the active window and will by default cover the entire data area hiding possible existing data windows To open a dataset in the new window drag a dataset from the browser or from the Windows Explorer into the new window or click File gt Open see also chapter 4 3 How to Arrange Data Windows If the data area contains multiple data windows you can arrange them in various ways All the arrange commands arrange the windows left to right and or top to bottom in the order in which the windows have been active The currently active data window will therefore be positioned at the top and or left of the data area To arrange the data windows as a grid 0s Click Window Arrange as a Grid Depending on the number of windows they will be arranged vertically and or horizontally see Fig 13 3 Data Window Handling 215 Pojexam1d_13C 2 1 C bio guest Spectrum ProcPars AcquPars Title PulsFrog Peaks Integrals Molecule Fidi a ll Figure 13 3 To arrange data windows in stack see Fig 13 4 t Click Window Arrange in Stack Fajexam2d_HC 1 1 Czibio quest Title PulsPrag Peaks Integrals Molecule Fia 5 Figure 13 4 216 Data Window Handling To arrange data windows side by side see Fig 13 5 t Click Window Arrange Side by Side Figure 13 5 To cascade data windows see Fig 13 6 c Click Window Cascade Wy exam2d_HC 1 Sp
111. Windows t Click Window Iconify all How to Maximize all Data Windows c Click Window Maximize all The active window will be displayed on top all other windows are hidden How to Activate the Next Data Window t Click Window Next window F6 The windows title bar will become highlighted 13 2 Window Layouts A data window layout defines the position geometry and window type of one or more TOPSPIN windows The following windows types are available e data windows e lock display window e acquisition display window e BSMS display window e temperature unit window How to Save the Current Window Layout 1 Click Window Save layout 2 In the appearing dialog box Specify the layout File name extension prop and click Save Layout How to Read a Window Layout 1 Click Window Read layout 2 In the appearing dialog box Specify or click the layout File name and click Read Layout Windows are arranged according to the following rules Data Window Handling 219 e Each currently displayed window type gets the position and geometry to the corresponding definition in the layout e Ifa window type is displayed but not defined in the layout it keeps its current position and geometry e Ifa window type is defined in the layout but not displayed the layout definition is ignored e Multiple data windows are arbitrarily assigned to the available data window definitions How to Swap Data Windows W
112. a Ctr1 f find 2 Specify the search criteria and click OK 3 Select dataset s and click Add to portfolio How to Sort Data in the Portfolio 1 Right click inside the portfolio Dataset Handling 55 2 Choose Sort mode from the popup menu see Fig 4 6 3 Click Alphabetical to sort data in alphabetical order Or Click Recent first to sort data by date of last open Display Display In Mew window Copy File Properties Files Sort Mode Alphabetical pen Portfolio Recent First save Portfolia Remove From Fortfolio E Figure 4 6 How to Add Remove or Interpret Alias Names To add an alias name 1 Click the Alias tab in the browser 56 Dataset Handling 2 Right click in the Alias table to open the popup menu see Fig 4 7 Display Display In Mew Window File Properties Files Define alias for data in selected window List selected alias List all aliases Remove selected aliases List available alias commands Figure 4 7 3 Click Define alias names for data in selected window 4 Enter an alias name in the appearing dialog box and click OK Note that alias names must begin with a letter To remove an alias name 1 Right click the alias name 2 Click Remove selected aliases from the popup menu see Fig 4 7 Furthermore the popup menu offers entries to display the dataset list its prop erties and print the full dataset specification 4 2 Creating Data H
113. a 20 27 59 64 66 211 214 217 compression 24 dimensionality 28 81 84 108 directory 49 53 71 field 33 101 106 133 object colors 317 data window 19 27 29 59 64 66 2D 133 3D 155 color scheme 318 contents 22 99 creation 59 handling 29 211 in 1D peak picking mode 188 in 1D phase correction 162 in 2D calibration mode 207 in 2D multiple display mode 201 in 2D phase mode 194 in baseline correction mode 183 in calibration mode 174 in integration mode 165 in multiple display mode 177 in S N measurement mode 222 in spline baseline correction mode 186 objects 22 popup menu 126 138 printing 95 reopen 102 tab bar 1D 106 tab bar 2D 139 tab bar 3D 159 toolbar 21 dataset active 213 colors 182 dir 19 directory tree 19 63 expno 19 50 56 files 75 130 handling 25 49 last 2D 30 last 3D 30 last used 315 name 19 50 56 64 procno 19 50 56 procno directory 63 properties 73 128 selection in multiple display 178 specification 63 213 title 57 top level directory 50 user 19 50 56 variables 68 datastation configuration 301 dcon command 24 326 dconpeaks txt file 24 deconvolution 24 default color scheme 318 command line size 322 configuration 301 find criteria 72 menu font 320 pivot point in 1D phase correction 162 pivot point in 2D phase 197 plane in 3D display 155 port numbers 309 printer 96 Tab bar 316 zero order phase correction 163 define cubic spline baseli
114. a remote connection as described in chapter 17 2 Note that without a local license e TOPSPIN on the remote system must run with a licence e Local data cannot be accessed 17 5 Security of Remote Connections All data transferred during a remote control session is by default encrypted This ensures that nobody can see data or commands by observing and recording your Remote Control 311 17 6 network traffic TOPSPIN uses the Secure Socket Layer SSL technology for encryption which is also used for secure web sites SSL needs digital certificates on both sides of a connection to achieve a valid authentication After a TOPSPIN installation default certificate files are provided to secured connections There is a chance however small such connections are attacked by a malicious person who also has the same default certificate files If for this reason you want to create your own set of certificate files you can do this by executing a script that is installed in lt tshome gt prog server make new certificates and follow the instructions given there To start a remote connection the new certificate files must be installed on BOTH machines How to Allow Remote Connections For security reasons remote access to a PC is by default prohibited for all sys tems To open a PC for remote access 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Click the Change button to the ri
115. able RASmol commands are described in the Jmol Help menu Multiple molecules or multiple aspects of one molecule can be displayed simultaneously To do that just open multiple data sets or open the same dataset in multiple data windows and click on the Structure Tab in each window 124 1D Display How to Display the FID t Click the Fid tab fid examid_1H 1 1 Cibio guest _ O x Spectrum ProcPars AcquPars Title PulsPrag Peaks Integrals Sample Structure Fic 1 2 3 4 s displays the raw data If these do not exist the text No raw data available ap pears The following additional buttons appear at the right of the lower toolbar j Show FID in shuffled mode Iw Show FID in unshuffled mode If you open a new dataset the Spectrum tab 1s activated no matter which tab was selected before If you switch to any interactive manipulation mode for example to phase correction mode the Tab bar is replaced by a toolbar for that mode 8 5 1D Display Options How to Toggle between Hertz and ppm Axis Units Click the following toggle button in the upper toolbar ha Toggle between Hz and ppm axis units hz How to Switch on off the Spectrum Overview display The spectrum overview shows the entire spectrum at the top of the data window It is useful when only a certain region of the spectrum is displayed In the over view the displayed region is marked as a green area To switch on the spectrum overview
116. alculate positive projection Calculate negative projection Calculate sum Calculate disco sum Read positive projection Read negative projection l Update rovesicols trom display Required parameters Projection sum of rows Display projection fon 2D First rowicol fi Last rowcol fi 0 Destination PROCMO 999 Disco reference colton fi Cancel Help Figure 9 11 From here you can calculate positive negative sum and disco projections and ei ther show them with the 2D spectrum or display them in separate data window as a 1D data For more details on the corresponding commands as shown in the header of the dialog box please refer to the Processing Reference Manual How to Switch on off the Grid display r Click the following multi state button in the upper toolbar HH Switch between no grid axis aligned grid and fixed grid gr Fig 9 12 shows an example of axis aligned grid display 148 2D Display exam2d_HC 1 1 Cobio guest Ol x spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid 8 6 4 2 F2 ppm Figure 9 12 Axis aligned grid display How to Display a 2D Spectrum in Contour Mode r Click the following button in the upper toolbar Switch to contour display mode co In contour mode a spectral region looks like this 50 48 46 F1 ppm 5 4 5 2 5 0 4 8 F2 ppm 2D Display 149 How to
117. an be listed by clicking the Integrals tab Fig 12 17 shows a region of peaks after peak picking Fig 12 18 shows the same region after 2D integration Here you can see the integral labels and areas in this case yellow The area color can be set in the user preferences command set as Color of 3rd spectrum 210 2D Interactive Manipulation exam2d HC 1 1 Chio guest 6 0 5 8 5 6 5 4 5 2 5 0 F2 ppm Figure 12 17 6 0 5 8 5 6 5 4 5 2 5 0 F2 ppm Figure 12 18 Chapter 13 Data Window Handling 13 1 Data Windows The TOPSPIN window has a data area that may contain multiple data windows The size of the data area depends on the overall size of the TOPSPIN window and on presence of the Browser and or Processing Guide Fig 13 1 shows the TOPSPIN window with the Browser and three data windows 212 Data Window Handling FA Bruker TOPSPIN 1 3 on nmr datastation as Administrator aloj xj E e OEE E ee ee E Dangah ee sat A t Ti 2 7248 8 FWAR A Me e gt ii Browser PFolio Alias F h e Bruker La J to Figure 13 1 Note that the three data windows show different data objects 1D processing parameters a 1D spectrum and a 2D spectrum How to Move a Data Window t Click hold the title bar and move the mouse How to Resize a Data Window 1 Move the cursor to the window edge until it becomes a double headed arrow 2 Left click hold that position and move the mouse Dependin
118. and bias correction values Edit intrng to edit the file intrng that contains the integral regions and slope and bias correction values Changes in this file are automatically shown on the screen How to Perform Interactive Bias and Slope Correction To perform interactive bias correction 1 3 Select the integral s that you want to correct right click in the region If no integral is selected bias correction will work on all integrals Click hold the following button it turns green and move the mouse b Integral bias correction until the integral bias is correct Release the mouse button turns grey To perform interactive slope correction 1 Select the integral s that you want to correct right click in the region 1D Interactive Manipulation 169 If no integral is selected slope correction will work on all integrals 2 Click hold the following button it turns green and move the mouse Integral slope correction until the integral slope is correct 3 Release the mouse button turns grey How to Set the Limit for Bias Determination r Click the following button Limit for bias determination How to Change the Mouse Sensitivity r Click one of the following buttons 1 Increase double the mouse sensitivity inc t Decrease halve the mouse sensitivity dec Il Reset the mouse sensitivity How to Calibrate Normalize Integrals Calibrating integrals means se
119. aring dialog box and click OK SS tC Please se lectthe system you wantto connect to This requires a properly configured TOPSPIM be running on that system Remote systems can be setup inthe Preferences panel see Options menu Under the Miscellaneous item Remote system lied Cancel Figure 17 1 Now you are prompted for a user and password on the remote computer Remote Control 309 17 3 eS s i Please enter the name and password forthe TOPSPIN session on the remote computer This connection is secure User guest Password n OK cancel Figure 17 2 The TOPSPIN browser will show the data directory tree of the remote system You are now ready to acquire process or analyse remote data How to Configure TCP IP Communication Ports The communication between various parts of the TOPSPIN program is based on TCP IP technology and uses a high level protocol known as CORBA an acronym for Common Object Request Broker Architecture This concerns communication between the TOPSPIN interface on the one hand and various other objects like e g the command interpreter and servers for datasets and hardware control on the other hand CORBA allows these objects to run on the local host or alternatively on a remote host in the network Each component automatically allocates two TCP IP ports for its services One for local network traffic and another one for SSL secured remote connection
120. as correction values and show the integrals on the screen How to Undo the Last Region Operation r Click the following button x Undo the last region operation How to Return from the Integration Mode with without Save To return and save the integrals to the current dataset r Click the following button Hj Save integrals and return sret As such you will e save the integral regions and corresponding slope and bias corrections to the file int rng e save the integral regions slope and bias corrections and integral val ues to the file integrals txt This file is displayed when you click the Integrals Tab e leave the integration mode To return without save r Click the following button 4a Return discarding any changes ret 11 3 1D Interactive Calibration A 1D spectrum can be calibrated referenced automatically with the command sref or interactively as described below How to Switch to Calibration Mode r Click the indicated button in the upper toolbar 174 1D Interactive Manipulation 4A SoM ail AN or enter cal on the command line The Tab bar of the active data window will be replaced by a toolbar examid_13C 1 1 Cbio quest ojx A a Ems O 005 ppm O 35756 He 75 40469965 MHz DEFINE REFERENCE FREQUENCY Define Lett click inside data window 0 2 0 1 0 0 0 1 ppm Figure 11 7 Data window in calibration mode A The yellow button indicates that the data window is in
121. ata window in a graphics file of selectable type e g png jpg jpeg bmp emf and wmf To do that click File gt Export The resolution of such a screen dump equals the resolution of your screen Note that when you import a graphics file into another program resize it you loose information Therefore we recommend to resample rather than resize graphics 1 11 How to Process Data Since this manual is not a general NMR text book we assume here that you are familiar with terms like window multiplication Fourier Transform phase correc tion etc Getting Started 23 1 12 Any Fid or a spectrum displayed in a TOPSPIN window can be processed by e typing a command on the command line e g ft e invoking a command from the Processing or Analysis menu e g Process ing Fourier Transform e entering an interactive data manipulation mode by clicking a tool button e g T e entering a user defined command usually an AU or a Python program see Help Programming Processing and analysis commands require certain parameters to be set correctly Most commands in the Processing or Analysis menu like wm and ft f open a dia log box showing the available options and required parameters for that command Other commands such as em ft start processing immediately Before you use them you must set their parameters from the parameter editor To do that enter edp or click the ProcPars Tab of the data window If
122. browseDataTree C bio dataiquestnmriexarm d_13C M4 indata DIRECTORY i 2 13 15 36 29 244 browseDataTree C bio dataiquestnmriexarm d_13Cindata DIRECTORY ai 2 13 15 36 29 274 brovwseDataTree Cbio dataiquestnmriexarmn d_13Ceindata DIRECTORY li 2 13 15 36 29 264 brow seDataTree C bio dataiguestnmriexarm d 130r indata DIRECTORY ai 2 13 15 36 29 504 brow seDataTree Cbio dataiquestnmriexarm d_13Caindata DIRECTORY oi 2 13 15 36 29 514 brow seDataTree C bio dataiquestnmriexarm d_13C indata DIRECTORY a 2 13 15 36 29 394 9 jgetDiscFuncByldent C hiotdatatquest nimrfexarn d_ 13C Jodatan ZAPOA _T Z T Documents and Settings Administrator topspin nmr datastation prop ir otacol txt Cott S61 Siprogicurdir Administrator history Cott abl Siprogicurdir Administratarinistory traffic tt Sb SiprogicurdirAdministratar stdout dataserver 1504 Figure 3 1 Here TOPSPIN log messages from various log files are displayed time sorted 46 Trouble Shooting Messages from different log files are shown in different colours The color assign ment and location of the files is shown in the lower part of the dialog window ptrace supports the following functions Search keywords To search the displayed log files for a certain keyword just enter it in the text bar at the top of the window and hit Enter Anchor specific entries To anchor an entry double click in the first column of the entry The en
123. built in website which can be activated to allow remote access to ICON NMR from any web browser which is networked to the spectrometer workstation Experiments may be cancelled submitted the run may be paused or halted and spectra in PDF format are available from the browser win dow No added software apart from ICON NMR is required and configuration is performed via the standard ICON NMR Configuration window For security a SSL HTTPS connection is supported Pocket PC Internet Explorer is also sup ported for full spectrometer control via Windows Mobile 2003 TM or equivalent PDF files of spectra may also be viewed on this platform making the mobile pocket spectrometer a reality Chapter 18 User Preferences 18 1 User Preferences TOPSPIN can be tailored to your preference in many respects This ranges from star tup options to spectrum objects menu settings remote connections etc Every standard user can create his her own set of preferences To set user preferences e Click Options Preferences set A dialog box will appear with at the left side the categories that can be tailored 314 User Preferences see Fig 18 1 15 x Program startup actions Program startup actions Spectrum Auto open last used data set Contour plot Show TOPSPIN default data directory in data browser Spectrum tithe Spectrum Spectrum Cursor r Tabbed pane layout Spectrum parameters aa Change spectral window color scheme Forts
124. buttons in the upper tool bar see chapter 11 and 12 but are easier to access You can configure the Tab bar as follows 1 Click Options Preferences Click Spectrum in the left part of the User preferences box Click the Change button to the right of the object Tabbed pane layout Check the desired Tabs uncheck the others Click OK nan amp WwW N How to Configure the Right click Menu Function By default right clicking a pull down or popup menu either displays or executes the corresponding command line command This can be configured as follows 1 Click Options gt Preferences 2 Click Miscellaneous in the left part of the User preferences box 3 Check uncheck the item Right click on a menu item shows associated command 4 Click OK User Preferences 317 18 2 Changing Colors How to Change Colors of Data Objects on the Screen nnd grd The color of various objects in a data window on the screen like 15t and spectrum axis parameters etc can be changed To set these colors 1 Click Options Preferences set 2 Click Spectrum in the left part of the User preferences box 3 Click the Change button to the right of the object you want to change e g Color of 1st10 spectrum P Change 4 Select the desired color in the appearing dialog box and click OK 5 Click Apply How to Change Colors of Data Objects on the Printer The color of data objects on the printer is independent from the
125. carrier frequency How to Perform Single Cosine Modulation To perform an amplitude modulation such that the pulse excites at two symmet ric sidebands offset with the same phase w Click Manipulate Single Cosine Modulation cosm2 and set Offset frequency to be relative to the carrier frequency How to Create a Shape with a Linear Sweep To create a shape with a phase modulation according to a linear frequency sweep 0s Click Manipulate Linear Sweep sweep and set the pulse length and sweep width Then specify the Q factor to obtain the value for yB 1 max 27 Q is the quality or adiabaticity factor which as a rule of thumb Q is set to 5 for inversion pulses and between 2 and 3 for decoupling puls 288 Acquisition es How to Create a Shape with Const Adiabaticity Sweep To create a shape with a phase modulation according to a constant adiabaticity sweep t5 Manipulate Const Adiabaticity Sweep caSweep and set the pulse length and sweep width Then specify the Q factor to obtain the value for yB 1 max 27 Q is the quality or adiabaticity factor which as a rule of thumb Q is set to 5 for inversion pulses and between 2 and 3 for decoupling puls es How to Calculate a Shape with Amplitude to the Power x To create a shape with an amplitude to the power of a specified exponent tS Click Manipulate Power of Amplitude power and enter the desired exponent How to Scale the Amplitude To
126. cedure The simulation procedure consists of the following steps Set Optional parameters In the Main panel you find some parameters which you can normally leave un changed See the section Simulation Details below for more information If a simulation on the current dataset has already been done and stored you can read this by clicking Open If not you will start from scratch and setup the simulation as described below Define the Model Click the Spectrum panel and select the Model according to your experiment You can refine the experimental conditions by checking one of the following 228 Analysis boxes e All for all quadrupolar transitions e DOR for performed double rotation experiments e Sync for rotor synchronized experiments When a parameter is greyed this means it cannot be changed for the se lected model or it is related to one of the other checked parameters Define Rotation Parameters From the Spectrum panel set the values for e MASR rotation speed of the single axis MAS VAS experiments or DOR outer axis speed e DORR inner rotation speed in DOR experiment and set their checkmark if they must be optimized during the simulation Set the value for e SBands the number of side bands on one side of the central transi tion Define the Spectral Region Typically non overlapping experimental peaks are fitted in separated simula tions Before each simulation the region to which it is appl
127. ch on off Square 2D layout aaaea How to Zoom a 2D spectrum in out 0 eee How to Shift a Spectral Region in the F2 direction left right How to Shift a Spectral Region in the F1 direction up down Show Display Properties Regions Files 000000 00s Using the Tab Dat y ca3 iced eared ga e ote eek Ca wee Cee Rade ads How to Set Processing Parameters 00 cece eee eens How to Set Acquisition Parameters 0 0 0 cece eens How to Display the Peak list 0 0 ce ee ee nee How to Display the Integral list 2 0 0 0 0000 How to Display the FID 3 2 343 rro tai ees A ee hes 2D Display OPONE 2424 Jo 5 2 05 0ar Cora ose Sone Petar ses How to Switch between Hertz and ppm Axis Units in F2 and F1 How to Switch on off the Spectrum Overview display How to Switch on off the Projection display 040 How to Switch on off the Grid display 0 0 0 0 eee How to Display a 2D Spectrum in Contour Mode How to Set the 2D Contour Levels 0 0 0 0 cee eee How to Store interactively set Contour Levels How to Display a 2D spectrum in Image Mode 151 How to Display a 2D Spectrum in Oblique Mode 151 How to Rotate a 2D Spectrum in Oblique Mode 153 How to Switch between Displaying Positive and Negative levels
128. ck the corresponding button in the upper toolbar as indicated below id 3d A4 i iA S or enter ph on the command line The Tab bar of the active data window will be replaced by a toolbar Fig 12 1 194 2D Interactive Manipulation shows an example of an unphased 2D inverse spectrum 0 x AL B ct Bh a 4 a Click the right mouse button to select the peaks for phase GOLLEGELON g pr E p F1 ppm 7 120 12 10 8 6 4 2 F2 ppm Figure 12 1 Data window in phase correction mode 4 Ei R 1 Switch to phase columns mode to display columns of selected peaks Eb The yellow button indicates that you are in phase correction mode Toggle the contour display on off Switch to phase row mode to display rows of selected peaks Fl Save the phase values to the 3D data from which this 2D was extracted Return How to Perform a Typical 2D Interactive Phase Correction In this example we will perform F1 phase correction columns only Take the fol lowing steps 1 Select two or more peaks in different parts of the spectrum To do that a Zoom in on a peak by drawing a box around it To do that click hold the left mouse button and move the mouse see Fig 12 2 b Right click at the peak position and choose Add from the popup menu 2D Interactive Manipulation 195 examed HC 1 1 Cobia quest Ox PRLE Click the right mouse button to Select the peaks for phase correction d r
129. color of the cor responding object on the screen To set print colors 1 Click Options Preferences set 2 Click Printer in the left part of the User Preferences box 3 Click the Change button to the right of the object you want to change e g Color of title i Change 4 Select the desired color in the appearing dialog box and click OK 5 Click Apply How to Change Colors of the Lock Display The colors of lock display objects can be changed as follows 1 Click Options Preferences set 2 Click Lock display in the left part of the User preferences box 318 User Preferences 3 Click the Change button to the right of the object you want to change e g Color 2 Change 4 Select the desired color in the appearing dialog box and click OK 5 Click Apply How to Create a New Data Window Color Scheme To create a new data window color scheme 1 Click Options Preferences set 2 Change any color of the objects Spectrum Spectrum title Spectrum cursor or Spectrum parameters 3 Click Apply 4 Click Spectrum in the left part of the User preferences box 5 Click the button Save as to the right of the object Save spectral window colors as a new color scheme and enter a new name in the appearing dialog box 6 Click OK How to Read a Different Data Window Color Scheme 1 Click Options Preferences set 2 Click Spectrum in the left part of the User preferences box 3 Click in the list box to
130. command 164 169 185 199 dopt command 127 dx files 66 emf files 22 fIr command 137 f2r command 137 gif files 337 gr command 147 hr command 32 105 hz command 124 144 im command 151 Inc command 164 169 185 199 int command 165 Jpeg files 22 337 Jpg files 22 337 keep command 32 105 137 ls command 151 lt command 153 lv command 149 md command 21 175 ov command 125 144 ph command 39 161 193 ph180 command 163 ph90 command 163 phr command 163 png files 22 99 337 pp command 188 pr command 21 145 prop files 54 218 ret command 164 173 182 185 187 191 retsab command 187 s2d command 164 sd command 33 106 137 sino command 222 s command 32 106 137 sl0 command 32 106 sr command 32 106 137 srO command 32 106 sret command 164 173 185 191 st command 151 su command 33 106 137 tif files 99 txt files 130 vr command 32 104 135 winf files 22 99 y command 125 zi command 32 105 136 zl command 32 105 137 ZO command 32 105 136 ZX command 32 105 136 2 command 31 37 104 135 8 command 31 104 135 command help 40 Numerics 180 degree phase correction 1D 163 2D 199 90 degree phase correction 1D 163 2D 199 90 degree phase correction 1D 163 2D 199 2 A abs command 87 90 164 165 167 182 absd command 182 absorption mode 162 163 197 198 199 acqu command 258 acquisition commands 258 260 mode 3
131. ctions and Graphic functions It is created with edpy The Python program below reads a region of the real part of a spectrum and the corresponding region of the imaginary part and displays both The simplest form of DISPLAY_DATALIST is used from TopCmds import import math region 80 72 define region in ppm open testdata don t display testdata exam1d_13C 1 1 c Bruker topspin guest 332 User Extensions RE testdata n read real and imaginary points of the region reals GETPROCDATA region 0 region 1 imags GETPROCDATA region 0 region 1 data const PROCDATA_IMAG if reals None or imags None EXITQ set up list of data to be displayed and respective axis info list dataList reals imags display the data in the list DISPLAY_DATALIST dataList For more information on writing Python program rs Click Help Programming Python programming 19 5 Button Panels A button panel is a window with user defined buttons for executing TOPSPIN com mands AU programs Python programs or macros It appears as an integral part of the active data window and acts on that Bruker delivers a few standard button pan els like bnmr and bnmrsel To create your own button panels you can modify one of these or write them from scratch In this description we will create a very simple button panel with some 1D processing commands and print export buttons see Fig 19 2 1D Proces
132. ctrometer frequency acquisition mode and pre scan delay In the last dialog box click Finish The installation of the selected items will start 302 Configuration Automation now Wait until this process has finished For more details on expinstal11 please refer to the description of this com mand in the Acquisition Reference manual 16 3 Parameter set conversion The command paracon changes the basic frequency in parameter sets This allows you to use parameter sets which were created on a spectrometer with a dif ferent frequency It opens dialog box shown in Fig 16 1 xl Parameter set conversion Select parameter sets for conversion from the list on the right Use the che boxes to select bruker or user define parameter sets Use the match field to apply wildcard to the list of parameter sets Use cf to set parameters Basic frequency 300 16 M Bruker defined parameter sets User defined parameter sets Watch lPROT IY Case insensitive match Avallable parameter sets PROT T PROTON PROTON 26 PROTON 36 PROTONCOMNLF PROTONEXP PROTONMNLF PROTONMLFESP PROTONNF PROTONNREXP PROTONMRLF PROTONT 1 PROTONINtO SElect all select none Cancel Ok Figure 16 1 Configuration Automation 303 Here you can setup a list of available parameter sets You can select Bruker and or User defined parameter sets and use a match string The matching parameter sets appear in the right part of the
133. ctrum Click fF to switch to integration mode Click to define regions around the peaks to be excited Click Lj to save these regions and return Create a new dataset Read the pulse program selgpse IA nm amp WW Enter ased and set all acquisition parameters for selgpse except for the shaped pulse parameters 8 Switch back the reference spectrum 9 Enter stdisp to start the Shape Tool interface 10 Click Shapes Classical Shapes Gauss 11 In the parameter section enter 296 Acquisition Size of shape 1000 Truncation level 1 12 Click Options Define Parameter Table e Set Length of shaped pulse to P12 e Set Power level of shaped pulse to SP2 e Set Name of shaped pulse to SPNAM2 13 Click Manipulate Calc Shape from excitation Region region ie Manipulate command region Dataset evamid 1H 1 1 Clbio guest a Lise same Shape for all Regions Carrier Frequency 01 1853 80 Hz Lett Limit i Right Limit Shape I Flip Angle rlinitial Phase 263410 209209 Gauss igo o o 611 96 177 38 Gauss 180 0 0 0 Alignment with respect to 7 pType of 180 Degree Pulse Beginning of Shape thee Center of Shape he ly i End of Shape lz gt Iz Refocussing OK cancel C Inversion Figure 15 30 Acquisition 297 14 Click OK Shape region region Results 2029 5456 Length of longest pulse usec total pulse length 1343 6694 Maximu
134. ctrum f1r 4 Reset F2 and Fl zooming to full spectrum a11 fil Retain horizontal and vertical scaling when modifying dataset or changing to different dataset Effects all data windows keep Alternatively you can enter the corresponding commands as specified between square brackets How to Shift a Spectral Region in the F2 direction left right r Click one of the following buttons Shift to the left half of the displayed region s1 Shift to the right half of the displayed region sr Or r Click hold the button and move the mouse Smoothly shift up down and left right Alternatively you can enter the corresponding commands as specified between square brackets How to Shift a Spectral Region in the F1 direction up down r Click one of the following buttons Shift the spectrum up half of the displayed region su Shift the spectrum down half of the displayed region sd Or r Click hold the button and move the mouse 138 2D Display Smoothly shift up down and left right Alternatively you can enter the corresponding commands as specified between square brackets 9 3 Show Display Properties Regions Files If you right click inside the data window the popup menu shown in Fig 9 3 will appear Display Properti Edit Contour Levels Save Display Region To Restore Display Region From Params Fi File Properties Square Layout Omnia Files
135. d in ZIP format e WINNMR Bruker WINNMR data e A3000 Bruker Aspect 3000 data 1 Note that the TOPSPIN data format is identical to the XWIN NMR data format 66 Dataset Handling e VNMR data acquired on a Varian spectrometer e JNMR data acquired on a Jeol spectrometer e Felix 1D data FID or spectrum which are stored in FELIX format Note that in all cases the data are stored in a single data file which is un packed converted to standard Bruker format 1 e to a data directory tree A Open fromjdx x Options i Open NMR data stored in standard Bruker format ir Open NMR data stored in special formats C Open other file Required parameters File type JEAMP DX OK Cancel Help Figure 4 17 How to Open a ZIP or JCAMP DxX file from the Windows Explorer Data stored in ZIP or JCAMP DX format can also be opened directly from the Windows Explorer You can do that as follows c drag amp drop click hold a file with the extension dx or zip and drag it into the TOPSPIN data area or data window c copy amp paste right click a file with the extension dx or zip and choose copy from the popup menu In TOPSPIN click Edit Paste paste 4 4 Saving Copying Data How to Save or Copy Data You can save the current dataset as follows Dataset Handling 67 1 Click File Save Ctr1 s This will open a dialog box see Fig 4 18 CT x Options Save data
136. data 1 C ts1 3 prog bin sendgui ft executes a 1D Fourier transform Commands are executed on the currently active data window 2 5 Function Keys and Control Keys For several TOPSPIN commands or tasks you can use a control key or function key short cut Focus anywhere in TOPSPIN Put the focus in the command line Display menu bar and toolbars if hidden Put the focus in the browser portfolio F1 Search for string in command help or NMR Guide help Ctrl1 c Copy a text that you selected highlighted in an error box dialog box pulse program title etc to the clipboard Paste text from the clipboard into any editable field The TOPSPIN Interface 37 Focus in the Command Line Ctrl Backspace Kill current input Ctrl1 Delete Kill current input Select previous command if available Select next command if available Focus in the Browser Portfolio Focus anywhere in TOPSPIN Scaling Data Alt PageUp Alt PageDown Scale down the data by a factor 2 7 2 CerI Alt PageUp CerI alt PageDown Alt Enter Performaverticalreset Cer I Al Enter Perform a vertical reset in all data windows Zooming data ale Plus Alt Minus Zoom out Zo Ctr1 Al1t Plus Zoom in in all data windows Ctr1 Alt Minus Zoom out in all data windows Nin Ni nN N hift spectrum up in all data windows hift spectrum to the left in all data windows hift spectrum to the right in all data windows Ni ni N 38 The TOPSP
137. dd User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset 3 In the appearing dialog box see Fig 19 3 a Choose between the options text label or icon The corresponding parameters are enable disabled b Enter the command name the tool tip and the label text or icon file pathname c Fora text label set its font text color and background color 336 User Extensions a Set the separator flag to yes or no and select the data dimension s for which the button must appear Padd tool button eee C Add a button with an icon Required parameters Assign this command to button lit Button tool tip fi D Fourier transform Button label text FT Icon image file name C gif Jpeg png jpg Font of button label text Button label text color Button background color Append separator to button Show button only for data of this dimension JRK Cancel Help Figure 19 3 In the example above a button FT is created with a separator which only appears for 1D datasets and executes the command fe How do I Remove a User Defined Toolbar Button Right click the toolbar button and click Remove this user defined button in the appearing popup menu see Fig 9 5 User Extensions 337 19 7 Wake Button Invisible Wake Button Inactive Reactivate All lnvisible lnactive Buttons Add User Defined Button Remove This
138. dd increment Contour level sign f Positive amp Megative Positive sih Negative Postive Megative Base level 2253560 0 22535600 Level increment fi 00 fi 00 Number of levels fi Ei Fill Clear Aly Cancel Figure 9 13 How to Store interactively set Contour Levels To store contour levels that were set interactively for example by clicking 9 or 2D Display 151 pressing Alt PageUp r Click the following button in the lower toolbar Ef Store contour levels 1s The levels are stored in the file lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt clevels How to Display a 2D spectrum in Image Mode r Click the following button in the upper toolbar Switch to image color display mode im In image mode a spectral region looks like this 50 48 46 F1 ppm 5 4 5 2 5 0 4 8 F2 ppm Note that in image mode the contours are superimposed in black on the image How to Display a 2D Spectrum in Oblique Mode r Click the following button in the upper toolbar x Switch to oblique display mode st In oblique mode a spectral region looks like in Fig 9 14 152 2D Display 5 4 5 2 5 0 F2 ppm Figure 9 14 In this mode you can manipulate the display in various ways Just right click in side the data window and choose one of the options from the appearing popup menu see Fig 9 15 2D Display 153 Larger Smaller Default View
139. e Change the intensity smoothly or r Click one of the following buttons gt Increase the intensity by a factor of 2 2 f Increase the intensity by a factor of 8 8 2 Decrease the intensity by a factor of 2 7 2 8 Decrease the intensity by a factor of 8 8 Reset the intensity vr Alternatively you can enter the corresponding commands as specified between square brackets To manipulate all data windows press the Ctrl key while clicking one of the above buttons How to Change the Horizontal Scaling of the FID or Spectrum r Click hold the button and move the mouse Zoom in out smoothly 1D Display 105 or r Click one of the following buttons Cy Zoom in increase horizontal scaling zi Sl Zoom out decrease horizontal scaling zo El Perform an exact zoom via a dialog box zx a Enter the coordinates of the desired region in the dialog box EJexactzoom ued Please enter the exact coordinates of the desired expansion F1 ppr From b11 0310 To 27 4876 JRK Cancel b Click OK 1 Retrieve previous zoom z1 4M Reset zooming horizontal scaling to full spectrum hr A Reset horizontal zooming and vertical intensity scaling a11 fil Retain horizontal and vertical scaling when modifying dataset or changing to different dataset keep Effects all data windows Alternatively you can enter the corresponding commands as specified bet
140. e Spectrum 0s Click the Spectrum tab spec examid 1H 1 1 Cobo guest el xj Spectrum ProcPars AcquPars Title PulsPrag Peaks Integrals Sample Structure Fid ee ee L 15 10 5 0 ppm This displays the processed data If these do not exist the text No processed data available appears How to Set Processing Parameters us Click the ProcPars tab edp lexamid 1H 1 1 Cobia quest feram 2 01 x Spectrum PracPars AcquPars Title puisProg Peaks Integrals Sampie Structure Fid Reference SF MHz 200 1 SO0000 pectrometel OFFSET pprni fi 6 457 Lowe field limi SR Hz o oo Spectrum ref S 22766 ize of real HZpFT Hz lo 4 sas80 Spectral zm JE E H This opens the processing parameter editor see also chapter 5 1 The following extra buttons are available 1 Undo last value change Can be used to undo multiple changes 108 1D Display amp Status parameter display The button turns green when activated dpp 123 Change processed dataset dimensionality parameter PPARMOD gy Search for specified parameter Changed parameters are automatically saved How to Set Acquisition Parameters r Click the AcquPars tab eda jexam 1d_ 1H 1 1 Ccbio quest l oj x Spectrur ProcPars AcquPars Tite PulsProg Peaks EA Structure Fid olin s Ul SA Experiment Experiment Width PULPROG zg30 7 Current pulse Receiver
141. e Status to disabled 4 Click Apply Clicking the TOPSPIN Options menu will now show the following popup menu Options Window Help Preferences Remote Connection Spectrometer Tools P Administration Tools F The entry Remote connection is greyed and can no longer be used Go back to the Configuration table change the Status of Remote connection to invisible and click Apply Clicking the TOPSPIN Options menu will now show following popup menu Options Window Help Preferences Spectrometer Tools P Administration Tools P The entry Remote connection has disappeared Note that if you disable or remove a menu entry the corresponding command is automatically disabled For example if you disable t Analysis gt Deconvolution dcon entering dcon on the command line will lead to an error message How to Re enable a disabled Command Menu 1 Open the Menu Configuration table as described above 2 Set the Status of a disabled or removed invisible entry to enabled 3 Click OK to close the Configuration table User Preferences 327 How to Re enable All Commands Menus 1 Open the Menu Configuration table as described above 2 Click the Reset button to enable all menus and commands 3 Click OK to confirm the appearing message 4 Click the OK button to close the Configuration table 18 6 Resizing Shifting Toolbar Icons How to Change the Toolbar Icon Size 1 Right click of the t
142. e intensity by a factor of 8 7 8 32 The TOPSPIN Interface Increase decrease the intensity smoothly Reset the intensity vr Buttons for horizontal scaling zooming mW AAA QA EQ o ah HH Reset zooming horizontal scaling to full spectrum hr 41 Reset zooming horizontal scaling and intensity vert scaling a11 Cy Zoom in increase horizontal scaling zi Zoom in out smoothly Zoom out decrease horizontal scaling zo IE Exact zoom via dialog box zx x Retrieve previous zoom z1 fil Retain horizontal and vertical scaling when modifying dataset or changing to different dataset Global button for all data windows keep Buttons for horizontal shifting e 7 He So Shift to the left half of the displayed region s1 Smoothly shift to the left or to the right 4 Shift to the right half of the displayed region sr Shift to the extreme left showing the last data point s10 Shift to the extreme right showing the first data point sr0 The TOPSPIN Interface 33 Buttons for vertical shifting t F 4 Shift the spectrum baseline to the middle of the data field su Smoothly shift the spectrum baseline up or down 4 Shift the spectrum baseline to the bottom of the data field sd 2 2 Command Line Usage How to Put the Focus in the Command Line In order to enter a command on the command line the focus must be there Note that for example
143. e transforms Shortcuts Just like single commands composite commands can be used in Macros AU pro grams and Python programs 6 2 Semi automatic Processing How to Use the Processing Guide in Automatic mode The Processing Guide in automatic mode guides you through the entire process ing sequence of data selection processing printing and archiving with minimum user interaction 1 Click Processing Processing Guide The Processing Guide window will appear as an integral part of the current data window see Fig 6 1 Data Processing 89 MMF Data Processing Guide 7 Open Data Set a Advanced Window Function e Peak U icking Fourier Transtorrn e Integration Phase Correction Plot Print I O ppm Axis Calibration pE E mail Archive S Baseline Corr Figure 6 1 2 In the Processing Guide window a Check Automatic mode b Click Open data set and click OK to open a dataset manually e g from the browser or click Browse to open the File Chooser 90 Data Processing c Click Window function Fourier Transform ete Each processing step will be executed without user interaction How to Use the Processing Guide in Interactive mode The Processing Guide in interactive mode guides you through the entire process ing sequence of data selection processing printing and archiving requiring some user interaction 1 Click
144. ear the Log panel click the Clear button During the simulation process you can freely switch to other panels to view the parameter being optimized After the simulation has finished the Nucleus panel will show the optimized values see Fig 14 7 Ghycine 29 1 Chio guest E e x E Lk leh Blt ob ee oe Boy eje a o Wain Spectrum Nucleus Dip interaction Log Nuc Parameters ly 25109454 3 Mu fish 187 472 pom DeltaitSAj 140 17 ppm Etat SA 0 922 0 1 LE 140 Hz aala Add Delete ppm Figure 14 7 Abort the Simulation To abort a running simulation us Click the r toolbar button After a few seconds the iteration stops and the best spectrum will be shown in the data window Save the Simulation After the simulation process is finished for all spectral regions of interest 1 Switch to the Main panel 232 Analysis 2 Click Save to save all parameters Exit Solids Lineshape Analysis To leave the solids analysis mode 0m Click the toolbar button Simulation details Basic parameters The Main panel shows you a list of basic parameters NUCLEUS the observe nucleus By default this parameter is set to the value of the acquisition parameter NUCI SPIN spin of the observe nucleus It is automatically set according to the selected NUCLEUS EXPs number of experimental spectra NUCs number of nuclei sites of the observe nucleus DIP
145. earing dialog box see Fig 4 15 3 Click OK To open a new procno of the current dataset 1 Enter rep 2 Specify a procno in the appearing dialog box 3 Click OK To open a dataset in a new window 1 Enter rew 2 Specify a dataset in the appearing dialog box 3 Click OK To open a new procno of the current dataset in a new window 1 Enter repw Dataset Handling 65 2 Specify a procno in the appearing dialog box 3 Click OK To open a data browser and read a dataset from there 1 Enter reb 2 Select a dataset from the appearing dialog box 3 Click Display Note that re rep and reb e Replace the data in the currently selected data window e Open the data in a new window when they are used after typing Alt w n e Add the data in the currently selected window if this is in multiple display mode whereas rew and repw e Always open the dataset in a new window How to Open Special Format Data Apart from the standard Bruker data format TOPSPIN is able to read and display various other formats To do this us Click File gt Open open Ctr1 o select the option Open NMR data stored in special formats select the desired file type see Fig 4 17 and click OK A dialog will appear which depends on the chosen file type Just follow the in structions on the screen The following file types are supported e JCAMP DX Bruker Topspin data stored in JCAMP DX format e Zipped TOPSPIN Bruker TOPSPIN data store
146. easily be pasted in any other application such as Excel e Export Export selected integrals Check the box in the lower left corner to export the selected integrals only or uncheck it to export the entire list Then click Export TOPSPIN 1 3 supports exporting 1D integrals in csv format Future version will also 1D exporting integrals in txt format and importing 1D integrals These features are already supported for 2D and 3D integrals Calibrate Integrals to Compare Spectra Integrals from the current and other spectra can be calibrated with respect to a reference integral To do that 1 Right click the reference integral and choose Define as reference from the popup menu This will determine the calibration constant 118 1D Display 2 Right click any integral and choose Calibrate by reference This will divide all integrals by the calibration constant setting the refer ence integral to 1 0 Now you can read any other spectrum and calibrate its integrals with respect to the reference integral defined above To do that 1 Read the spectrum 2 Enter int to define the integral ranges if this has not been done yet 3 Click the Integrals tab 4 Right click any integral in the list and choose Calibrate by reference from the popup menu Note that the calibration constant is lost when TOPSPIN is restarted Display the integral list with peaks The integral list in Fig 8 6 shows only integrals However if peak pick
147. ecked Name of the Frequency List Clicking Apply or OK will open a new dialog box where the selected parameters are shown If no reference frequency is used the values entered as frequencies have to be difference frequencies How to Calculate a Shape from an Excitation Region A shape can be modulated according to specific regions in a spectrum To do that take the following steps 1 Switch to the associated dataset 2 Determine the integral regions interactively 3 Switch back to the Shape Tool interface 4 Click Manipulate Calc Shape from excitation Region region 286 Acquisition EA Manipulate command region x Dataset examid 1H 1 1 Cclbio guest wv Use same Shape for all Regions Carrier Frequency 01 1853 80 Hz Lett Limit Right Limit Shape Flip Angle Initial Phase 2669 58 2066 48 Gauss 190 0 foo 1962 49 1392 44 Gauss 190 0 loo 1330 35 133 04 Gauss 190 0 loo Alignment with respect to Type of 160 Degree Pulse C Beginning of Shape thee Inversion f Center of Shape ily ly gt i End of Shape flz gt Iz Refocussing OK cancel Figure 15 25 If the intrng file does not exist you will be prompted for the number of re gions and the carrier frequency O1 In that case the fields Left Limit and Right Limit are empty Note that overlapping regions are not allowed In Fig 15 25 the default values for Flip Angle Initial Phase Alignment and Type of 180 Degree
148. ectrum ProcPars AcquPars Title gt Figure 13 6 Note that you can instruct TOPSPIN to open new data windows cascaded rather than maximized as well configure cascaded windows command set Window set tings see also chapter 4 3 How to Iconify minimize a Data Window r Click the Z button in the windows title bar Data Window Handling 217 Or r Click Window Iconify all to iconify all windows How to De iconify a Data Window us Click the button or double click the title bar How to Maximize a Data Window t Click the Oj button or double click the title bar The window will cover the entire data area Note that a maximized window can not be moved of resized but can be restored in size and position iconified or closed How to Restore the Size and Position of a Data Window r Click the button or double click the title bar Note that this is only possible if the title bar contains the button This is only the case after the window has been maximized or iconified How to Close a Data Window To close the active data window r Click File gt Close Crt1 w or r Click the x button in the windows title bar To close any data window n Click the x button in the data windows title bar or t Click the title bar and then click File gt Close Crt1 w To close all data windows r Click File Closeall closeal11 218 Data Window Handling How to Iconify all Data
149. ed if only one observe nucleus is defined To set dipolar coupling parameters 1 Click the Dip Interaction panel 2 Click Add if the nucleus is not shown yet 3 Set the nuclei parameters as follows r Enter the values in the parameter field 230 Analysis Or r Click the radio button to the right of the parameter click hold the cor responding toolbar button colored green and move the mouse hori zontally 4 Check the parameters to be optimized during the simulation Start the Simulation Now you can start the iterative simulation To do that t Click the toolbar button The simulated spectrum is displayed in the data window and continuously up dated see Fig 14 6 01 x El eOe Bit eb CMM oo B y is cele Do Main Spectrum Nucleus Dip interaction Log Iteration Status Cycle fizs Best overlap JSR 835069465912 Iteration Log Iteration Started at 1299103 10 31 24 AM SPECTRUM Mame Glycine save Clear Figure 14 6 The parameter window will switch to the Log panel showing Iteration Status including the iteration Cycle and the Best Overlap per centage so far e Iteration Log with the starting parameters and the results of the fit Parameters which are marked with an asterisk have been optimized dur Analysis 231 ing the simulation They are automatically updated in the respective pan els To save the Log panel information click the Save button To cl
150. ee ote eh eee oes 319 How to Change All Fonts of the Topspin Interface 319 How to Change the Font of the TOPSPIN menu 4 320 How to Change the Font of the Tab bar 320 How to Change the Font of Dialog Boxes 040 321 How to Change the Font of the Browser 00005 321 How to Change the Font of the Command Line 322 Chapter 19 How to Change the Font of the Status Line 322 184 Command Line Preferences o 06 cs cava wadecead shea ba eee Pied 322 How to Resize the Command Line 0 0 0000005 322 How to Set the Minimum and Maximum Command Line Size 323 18 5 Disabling Enabling Toolbar Buttons Menus and Commands 323 How to Hide the Upper and Lower Toolbars 323 How to Hide the Menubat jicci0 5 4 e00 2aNiak iama aea 324 How to Disable Remove Toolbar Buttons 324 How to Disable Remove Menus or Commands 324 How to Re enable a disabled Command Menu 326 How to Re enable All Commands Menus 0 327 18 6 Resizing Shifting Toolbar Icons 0 0 0 eee 327 How to Change the Toolbar Icon Size 0 000000 327 How to Shift Toolbar Icons to the Right 327 User Extensions 46 scucicieeicachont auc ieee ses aad obse te 329 LO ASCE NOteDOOK sarsii e E
151. el Dn or Spectrum must be extracted From the 2d relaxation data Figure 14 9 FID or spectrum number which was measured with the longest delay It can be found in the vdlist file in the EXPNO data directory A new data window will appear showing the extracted 1D FID Trans form Phase Processes the extracted 1D FID performing exponential multiplication Fourier transform and automatic phase correction Define Ranges Switches to interactive integration mode Here you can define the ranges for the peaks to be included in the relaxation analysis 1 Click the button in the data window toolbar 2 Put the red cursor line at one edge of a peak or multiplet 3 Left click hold and drag the cursor line to the other edge of the peak or multiplet 4 Do step 2 and 3 for all regions to be defined 5 Click the button and choose Export Regions to Relaxation Module 6 Click toreturn ret Relaxation Window Switches the 1D data window to relaxation analysis mode see Fig 14 10 238 Analysis Relaxation titest 1 1 Crbiol jos 4 Fitting type E G A Ef itis NO P axpt Ti Peak fat 7 229 ppm A Current Peak p We 45s 1of1 ie Intensity Ares Brief Report Peak at 7 221 ppr P 2 211e 000 0 1 215e 000 Ti 194452 SO 3 685e 007 0 5 10 15 20 25 5 Figure 14 10 and performs a default fitting By default this is one component T1 intensity fitting Function type ux
152. erent existing connection 14 5 8 Define Multiplet Connections Once the multiplets of a spectrum are defined you can define the connections between them To define all connections 1 Click the button to see the Report dialog see Fig 14 17 250 Analysis PN Report Multiplets ID shift p J Hz Connection hal 26744 48532 3 J 2 0 4 r Di hi 3 6656 6 9646 Jt 0 4 8332 M3 0 a Find Connections Figure 14 17 2 The multiplets appear in the order in which they have been defined Newly defined multiplets appear with numbers as D s and no multiplet con nections x 0 defined 3 Click the button Find Connections to make the multiplet connections a Set the maximum difference between related couplings or accept the default b Set the lower limit for couplings or accept the default c Check the box Change already defined Connections if applicable d Click OK to define the connections Note that the Report Dialog also offer buttons for Printing the multiplet informa tion copying it to the clipboard and saving it to a text file To define individual connections 1 Select the first multiplet In case of a multi level multiplet click the f or button to select the required level Analysis 251 2 Right click and select Designate Multiplet from popup menu 3 Select the second multiplet In case of a multi level multiplet click the f or J button to select t
153. ermore it allows you to define and list alias names for data The browser appears at the left of the TOPSPIN window and can be controlled from the View menu The browser is similar to the Windows Explorer It shows data directory trees and allows you to expand collapse their elements Figure 4 1 shows a TOPSPIN browser with one top level data directory and one dataset fully expanded 50 Dataset Handling Browser FF olig Alias b ga c me C ibio mN quest m exam d_13C vam 1 M E j3 4 a5 za G __ examid_1H __ examed_CH examed_ He __ xarmed_HH exarmsd EHH HSH Figure 4 1 The TOPSPIN portfolio shows the list of datasets that has been opened so far by the current user Each dataset that you open is automatically added to the current port folio A portfolio with five datasets look like this Browser PFolio Alias b examid 130 1 1 Cibio guest examid 130 2 1 Cobio guest examid 130 3 1 Cobia guest examid 130 4 1 Cobia guest examid 130 5 1 Cobio guest Figure 4 2 Each line displays one dataset showing its name expno procno top level directory and user The TOPSPIN Alias list show a list of alias names for datasets Just right click any Dataset Handling 51 entry to define remove or interpret alias names Browser PF olig Alias Cramicidine toxy Menthal 1H Menthol inadequat Stryichninie C1 3 strychnine C1 Sdeptgo
154. et analysis result is saved in the file mult txt in the procno data Chapter 15 Acquisition This chapter describes TOPSPIN acquisition as far as the interface 1s concerned Individual acquisition command are described in the Acquisition Reference man ual 15 1 Acquisition Guide If you are a new or occasional user we recommend you to acquire your data with the TOPSPIN Acquisition Guide This will guide you through the typical sequence of acquisition steps To start the Acquisition Guide click Spectrometer Acquist tion Guide 256 Acquisition MMF Data Acquisition Guide Close C Automatic mode Mew Experiment Frequency Routing tH Prosol Pars w Temperature Receiver Gain Probe Match Tune Start Acquisition lt En Sample Rotation To Processing Figure 15 1 In Automatic mode the Acquisition Guide will simply execute each command when you click the respective button This requires the acquisition parameters to be set correctly In interactive mode Automatic mode unchecked the Acquisition Guide will at each step open a dialog box offering you the available options and Acquisition 231 required parameters Note that the last button To processing will open the process ing equivalent of the Acquisition Guide the Processing Guide 15 2 Acquisition Toolbar Acquisition can be prepared started and controlled from Spectrometer menu Clicking this menu opens the
155. eter section enter Size of shape 1000 Truncation level 1 Click Options Define Parameter Table e Set Length of shaped pulse to P12 e Set Power level of shaped pulse to SP2 e Set Name of shaped pulse to SPNAM2 and click OK 10 Click Analysis gt Calculate Bandwidth for Refocusing My Acquisition 295 e Enter Total Rotation 180 this calculates the bandwidth factor which is the product of the width of excitation DeltaOmega and the pulse length DeltaT e Enter Delta Omega 40 the bandwidth determined in step 2 this calculates the shaped pulse length DeltaT e Click update parameters to store this pulse length as P12 11 Click Analyses Integrate Shape e Click update parameters to store the name of the shaped pulse to SPNAM2 12 On the associated dataset enter the command ased and check the values of P12 and SP2 If the steps above were performed correctly they should have the values of DeltaT and Change of power level hard power level respectively Note that if the peak is off resonance you need to determine the chemical shift difference between the peak and O1 and set the parameter SPOFFS2 according ly To determine the proper value click put the cursor on the desired peak and subtract the value of SFO1 from the MHz value displayed in the upper left of the data field Example 3 Create a Shaped Pulse for Sel Excitation from Integral Regions 1 Read acquire a 1D reference spe
156. from multiple display mode ret How to Set the Colors of the 15 2 Dataset The colors of the different datasets in the multiple display mode can be set in the User preferences dialog box To set for example the color of the second spec trum 0s Click Options Preferences and click the Change button for the item Color of 2nd ID spectrum 11 5 1D Interactive Baseline Correction Baseline correction can be performed with commands like abs or absd or inter actively as described below How to Switch to Baseline Correction Mode r Click the indicated button in the upper toolbar 4A Sue il aAN or enter basl1 on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 11 12 1D Interactive Manipulation 183 examid_1H 2 1 Cbio guest O x AJ Mie ela B coo ejojas njajagi a EEDE Mouse Sensitivity 1 0 3 16 ppm 954 20 Hz Figure 11 12 Data window in baseline correction mode A The yellow button indicates that the data window is in baseline correc tion mode W Some buttons will turn green when they are clicked As long as a button is green it is active How to Perform Polynomial Baseline Correction 1 Click the following button button turns green Fy Perform polynomial baseline correction In the data window a red horizontal line will appear as well as the equation that describes the polynomial function f x A B x C x D x
157. g button TL Show pulse program parameters ased The button will change to To make this the default setting Click Options Preferences click Miscellaneous check the entry Show reduced parameter set ased and click OK How to Display Acquisition Status Parameters r Click the following button S Show acquisition status parameters Note that the command dpa opens the acquisition parameter editor and automat ically shows the status parameters How to Get Probehead Solvent dependent Parameters r Click the following button lg Set probehead solvent dependant parameters getprosol1 Probehead and solvent dependant parameters can be set up with the command edprosol How to Change Acquisition Data Dimensionality r Click the following button 123 Change data dimensionality This changes the number of parameter columns and value of the acquisition pa rameter PARMODE Parameter Handling 85 How to Set Lock Parameters Enter the command edlock and set the lock parameters in the appearing dialog box For a detailed description of edlock please refer to the Acquisition Refer ence manual or enter edlock on the command line How to Set Routing Parameters Enter the command edasp and set the routing parameters in the appearing dialog box For a detailed description of edasp please refer to the Acquisition Refer ence manual or enter edasp on the command line Chapter 6 Data Processing 6 1 Interactive Process
158. g ihe a Sem wok Die 71 How to Display one of the Found Datasets 73 How to Select Data from the Found Datasets 0 73 How to Add Selected Datasets to the Portfolio 74 How to Save Selected Datasets toa List 0 00 eee 74 Aa Mandine Data Piles is d sos 04 weaken SEA 5 Rae Rsaes Peas Tay 74 How to List Open the Current Dataset Files 74 How to List Open the current Dataset Files in the Windows Explorer 75 4S Data Consistency Check sid sin deh weeded eed Oe eae Hs Ga 76 Parameter Hangin 4 5 5s cnsnw but owe dew enwsee eae a 79 SA Processing Parameters s0 07 lt s 00044 ome wean thane ee hho eee 79 How to Set a Processing Parameter from the Command Line 79 How to Set Processing Parameters from the Parameter Editor 80 How to Undo the Last Processing Parameter Change 81 How to Display Processing Status Parameters 81 How to Change Processed Data Dimensionality 81 5 20 ANCQUISIION Parameters eses uta d paa PA hae he deka oes 82 How to Set Acquisition Parameters 0 00 cece ee eee eee 82 How to Set an Acquisition Parameter from the Command Line 82 How to Set Acquisition Parameters from the Parameter Editor 83 How to Undo the Last Acquisition Parameter Change 84 How to Set Pulse Program Parameters 0 0 00 eee eee 84 How to Display Acqu
159. g on the position of the double headed arrow you can change the win dow height width or both see Fig 13 2 Data Window Handling 213 Filexamid_13C 1 1 C hio guest f3C 4H DRX 300 Cholac 106 7 ppm 8049 1 Hz Index 46 850 Value 4 24947 520E 1 5 1e10 0 5 C O 50 0 0 0 50 0 ppm Figure 13 2 How to Select activate a Data Window The active data window is the window of which the title bar is highlighted The TOPSPIN menu tool bars and command line commands correspond to and act on that window Only one data window is active at a time To activate a different data window n Click in the desired data window or click its title bar Or r Click one of the colored radio buttons above the data area The pressed ra dio button the green one in the example below corresponds to the current dataset M2 examid TH 2 1 Clbio guest If you hold the cursor over one of the buttons without clicking it and wait a few seconds the corresponding dataset specification will be shown Or us Click Window x dataname expno procno dir user 214 Data Window Handling where x is the number of the desired window and dataname expno proc no dir and user refer to the dataset displayed in that window Or 0s Hit the F6 key to activate the next window Repeat that until the desired window is the active window How to Open a New empty Data Window mS Click Window New window Al t w n
160. ght of the object Enable Disable remote access 4 Enter the Administration password as requested 5 In the appearing dialog box click Enable see Fig 17 3 A configure remote access Enable or disable remote access to Topspin Press Enable to allow remote access to this Topspin installation press Disable to prevent remote access default You must restart this TopSpin installation to activate the modification Caution Any previous modifications in the file omniorb cont will be lost Disable Cancel Figure 17 3 312 Remote Control 6 Click OK Now a running TOPSPIN on this PC can be accessed from any computer in the net work 17 7 Note to Windows XP Service pack 2 If the remote PC is running under Windows XP with Service Pack 2 the Windows Firewall is enabled by default In this case the Firewall must be configured for TOPSPIN operations This can be done either during TOPSPIN installation TOPSPIN gt 1 3 only or with the script setfirewall cmd Note that the firewall must to be configured for TOPSPIN e spectrometer control e remote access TOPSPIN can be used for processing analysis on a local datastation even 1f it is not registered on the firewall However you will get a few Security Alert messages during startup 17 8 How to Access ICON NMR from a Remote Web Browser In TOPSPIN 1 3 and newer ICON NMR is web enabled The standard Bruker Auto mation Software now provides a
161. gral and choose Delete from the popup menu To delete multiple integrals 1 Select the integrals while pressing the Ctrl or Shift key 2 Right click one of the integrals and choose Delete from the popup menu Shortcuts Enter key zoom into spectrum i e show region around selected inte gral s Delete key delete the selected integral s from the integral list Ctrl c copy selected integrals to the Clipboard Ctrl a select all peaks Home select the first peak End select the last peak Shift Home select current and first peak and all in between Shift End select current and last peak and all in between Double clicking an integral will show the peaks within the integral region if they exist It they do not exist it will zoom into spectrum showing the inte gral region Note that these keys only work when the cursor focus is in the data window More features 1D Display 121 The right click popup menu has the following extra entry Table properties to set the shown columns and specify their decimal places How to view Sample Information t Click the Sample tab examid_ 1H 1 1 Cobio guest Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample St aj Halott t 4 Sample Information Sample ID Origin Concentration Date Prepared Butter Contact Comment Figure 8 9 This table can be used to fill out any sample information you want to store with
162. grals Sample Structure Fid Figure 18 4 Tab bar with font size 10 Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Struct Figure 18 5 Tab bar with font size 14 How to Change the Font of Dialog Boxes Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Dialog window font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font 6 Click Apply nan amp WwW N e Fig 18 6 shows an example of a dialog box with the font Time New Roman Italic x Please specity data set MAME EXP NO PROCHO DIR LISER guest OK Cancel Browse Find Help Figure 18 6 How to Change the Font of the Browser To change the font of the browser 322 User Preferences Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Dialog window font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font 6 Click Apply nA Ae WwW N m TOPSPIN must be restarted for this change to become effective Note that this change will affect all dialog boxes How to Change the Font of the Command Line Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box
163. h were previ ously entered on the command line To open a command history control win dow click View gt Command Line History or right click in the command line and choose Command Line History or enter the command cmdhist see Fig 2 2 It shows all commands that have been entered on the command line since TOP SPIN was started You can select one or more commands and apply one of the fol lowing functions Execute Execute the selected command s Append Append the first selected command to the command line The appended command can be edited and executed Useful for commands with many arguments such as re Save as The selected command s are stored as a macro You will be prompted for the macro name To edit this macro enter edmac lt macro name gt To ex ecute it just enter its name on the command line The TOPSPIN Interface 35 Command History Execute Append SAVE AS Cancel Figure 2 2 2 4 Starting TOPSPIN commands from a Command Prompt TOPSPIN commands can be executed from a Windows Command Prompt or Linux Shell To do that 1 Open a Windows Command Prompt or Linux Shell 2 Enter a Topspin command in the following format lt tshome gt prog bin sendgui lt topspincommand gt where lt tshome gt is the TOPSPIN installation directory 36 The TOPSPIN Interface Examples C ts1 3 prog bin sendgui re examld 1H 1 1 C bio joe reads the dataset C bio joe nmr exam1d_13C 1 p
164. he asso ciated dataset Note that the latter 1s the sum of the shown Change of power level and the current hard pulse power level e g PL1 How to Integrate Adiabatic Shapes To calculate the power level required for an adiabatic shaped pulse us Click Analysis Integrate Adiabatic Shape integradia The change of power level is calculated from the length of the corresponding 90 pulse and the length of the hard pulse Clicking the Update Parameters button saves the length of the shaped pulse and the required power level to the corresponding parameters of the associated data set How to Start Simulation To evaluate the shape behaviour you can start the TOPSPIN NMRSIM routine 0s Click Analysis Simulation simulate This allows you for example to view the excitation profile or for adiabatic pulses check the adiabaticity 15 9 8 How to Manipulate Shapes Shapes can be manipulated in various ways Most of these functions are only meaningful for RF shapes Frequency Encoding To perform a phase and amplitude modulation encoding one or more offset fre quencies us Click Manipulate Phase modulation acc to Offset Freq offs 284 Acquisition EA Manipulate command offs Alignment Fhase 0 at Middle of Shape h ly Iz I Ending at Phase 0 z gt l Reference Frequency Mo Reference Frequency specified Reference 01 from current Data Set Reference First Frequency in
165. he com mand line If for some reason history is switched off you can switch it on as follows 1 Click Options gt Preferences click Miscellaneous 2 Check the entry Record commands in protocol file 3 Click OK 3 2 2 All log files A full protocol including not only TOPSPIN commands but also dataserver and net work traffic is show by the command ptrace This opens the following dialog Trouble Shooting 45 window 2 ptrace TopSpin Log File Tracer File Time Message a 2 13 15 356 16 135 TOPSPINVersion 1 3 a MDA S4SS616 145 history registration started Egh 2 13 15 36 16 145 2256 Corserver js running ai 213 15 5616 145 2320 java virtual machine started i 2 13 155616 145 current data examad 1 1 Cubio guest nmr i 2 1 3 15 36 16 155 jbrowseDataTree ltl abi soontinste FILE 6 terms wei 2 13 1556 20 671 jbrowseDataTree lbioldata DIRECTORY 2 terms wi 2 13 15 356 26 500 jbrov seDatalres C bio datafgquestnnr DIRECTORY 12 tems crid brow se_dispdata_newy oi 2 13 15 36 29 173 brovseDatalres C bio datafquesthimrexaml d_13C DIRECTORS 9 tems mi 2 13 15 36 29 173 browseDataTree C bioidataiguestnrmnnexami d 13C pdata DIRECTORY of 2 13 15 356 29 1535 browseDataTree C bioidataiguestnrmnuexami d 1 a3Ciapdata DIRECTORY fea 2 13 15 36 29 1935 browseDataTree bio datatquestnmriexam d_13C Sindata DIRECTORY ai 2 13 15 36 29 224 9
166. he leftmost of rightmost multiplet using one of the methods described above Click the button button turns green Right click in the data window and if necessary set the multiplicity to the number of multiplets in the multi level multiplet Move the mouse to the left or right until the grid lines coincide with the mul tiplet peaks and click the left mouse button The multiplet is defined now Analysis 247 6 Click the ill button to leave this mode examid ethanol 1 1 Cobia guest Figure 14 15 In Fig 14 15 the multi level multiplet of the ethanol CH2 group is being defined The left most doublet is already defined The red lines of the coupled grid are positioned on the remaining six peaks of the multiplet 14 5 6 Handling Defined Multiplets Selecting a Multiplet You can select a particular multiplet simply by clicking it in the data field The currently selected multiplet is displayed in the color of the second spectrum de fault red Alternatively you can select a multiplet from the toolbar as follows Select the previous multiplet Th Select the next multiplet Selecting a Level in a Multi Level Multiplet Multi level multiplets can be assigned for a group which couples with multiple other groups for example the ethanol CH2 group Each level can be selected and designated i Select the next level up of a multi level multiplet 248 Analysis J Select the previous level d
167. he required level 4 Right click and choose the Connect Multiplets from popup menu To define individual connections To disconnect multiplets 1 Select on of the multiplets to be disconnected 2 Right click and select Disconnect Multiplets from popup menu Shifting a Multiplet Line Alternatively you can open disconnect a multiplet from the Identifier dialog see Fig 14 16 14 5 9 Further Multiplet Functions The Multiplet Analysis window offers several other function such as 1 Shift multiplet line Click this button and move the vertical cursor line into the capture area of the desired line which 1s then marked by a faint line The left click hold and move the moos to the desired position I gt Shift multiplet vertically Click this button and move the mouse to put the horizontal line cursor above or below the multiplet tree Then left click to shift the multiplet to that position x Remove the currently selected multiplet Clicking this button several times allows you to remove all multiplets d Show Daisy multiplets 1 Undo the last multiplet action Ca Redo the last multiplet action 14 5 10 How to Set Multiplet Options The T button opens a dialog box where you can set various multiplet options as 252 Analysis shown in Fig 14 18 EA Multiplet Options x Distance Lines k Capture Range l T E Points Drift Range 5 E Foints Min Intensity z000 Min Detar f O Labels vertical E
168. hs Rom oS eRe een cs oe eee 99 How to Copy data to Other Applications 00000 99 How to Store Export a Data Window as Graphics File 99 ID DIS AYy S54b3G sie i e rA E Seana heen 101 8 1 The 1D Data Window 0 0 eee teens 101 8 2 Displaying one Dataset in Multiple windows 102 How to Reopen a Dataset in a Second Third etc Window 102 How to Rescale or Shift one Dataset in Multiple windows 103 8 3 Changing the Display of a 1D Spectrum or FID 104 How to Change the Vertical Scaling of the FID or Spectrum 104 How to Change the Horizontal Scaling of the FID or Spectrum 104 How to Shift a Spectral Region to the Left or to the Right 105 How to Shift the Spectrum Up or Down 20 0000 106 S44 Usinethe Tab Dat 2 2icacritare ded eobeeets oF ees oes eat ee S 106 How to Display the Spectrum 00 0 cece ees 107 How to Set Processing Parameters 0000s 107 How to Set Acquisition Parameters 0 000 cece eens 108 Howto Edit the Title 2 2 0 gadaciceeheae aha etn dae eneserd 109 How to Edit the Pulse Program 00 cece eee eens 109 How to Display the Peak list 2 2 0 ene 110 How to Display the Integral list 0 0 0 0 0000 115 How to view Sample Information 0 0 0000 cee ee eee 121 How to Open the Jmol Molecule Structure Viewer
169. i rectory 4 8 Data Consistency Check TOPSPIN maintains audit trail files for compliance with GLP GMP and FDA requirements The processing command that creates processed data from the raw data e g em creates the processing audit trail file auditp txt and inserts the first entry Any processing command that modifies updates the processed data e g ft makes an additional entry Furthermore any command that changes one or more processing status parameters makes an additional entry The audit trail can be checked with the command audit This command opens a dialog box see Fig 4 24 FA Audit trail audit check a x Options C view audit trail of processed data View audit trail of acquisition data f verify audit trails Add a comment to audit trail Cancel Help Figure 4 24 The first two entries allow you to view the audit trail files The third entry per forms an audit trail check 1 e a data consistency check If both raw and processed Dataset Handling 71 data are consistent you will get the message shown in Fig 4 25 Ea auditcheck audit tile for acquisition OK S processing OK raw data checksum OK proc data checksum Ok Figure 4 25 If the data have been manipulated outside of TOPSPIN e g with third party soft ware the checksum will be inconsistent Fig 4 26 shows the message for incon sistent processed data E audit file tor acquisition OK process
170. ial script The flag Show data sets during script execution allows you to either display the currently processed dataset or remain on the current dataset Browse for a dataset list Browse for an existing dataset list starting in the users home directory Browse for a serial script Data Processing 93 Browse for existing serial script Depending on the parameter Script type the browser opens the exp stan nmr py for Script type Python or exp stan nmr lists mac Script type macro TOPSPIN by default searches for for files named ser Edit specified data set list View or edit the list specified in the field Data Set List Edit specified serial script View or edit the script specified in the field Serial script name Create new data set list Opens a dialog box for finding datasets Proceed as follows 1 Specify all search criteria and click OK 2 In the appearing Search result box a Select the desired datasets b Click Save selection 3 In the appearing browser a Navigate to the desired list directory b Enter or select the list filename c Click OK Alternatively you can create a dataset list manually The format of a list entry 1S lt name gt lt expno gt lt procno gt lt dir gt lt user gt An example of a dataset list is examld 13C 11 C bio guest examld 13C 2 1 C bio guest examld 13C 3 1 C bio guest Create new Serial script Opens the appropriate editor to create a new script For Script type Py
171. ide definition If the file does not exist it must be created Here is an example of a user modified T1 T2 guide MyT1T2Toolbar NM t1fid 40 gif NM2 Extract fid TIP SsDo ser CMD t1 fid END NM t1spec 40 gif NM2 STransform TIP SDo ef apk CMD tl spec END NM tlranges 40 gif NM2 SRanges TIP SEnter integ mode CMD tl ranges END NM tliscreen 40 g1if NM2 SRelax Window TIP SEnter Relax mode CMD t1 relax END NM END NM myicon gif NM2 SFit Methods TIP Select fit funcs CMD t1 func END NM c myicons myiconl gif NM2 Start TIP ctl ct2 sim fit CMD tl start END NM c myicons myicon2 gif NM2 Show Report TIP report CMD tl report END NM tlprant 40 gq7f NM2 Print it TIP print CMD tl export END Notes to this guide definition 340 User Extensions e The original Bruker guides are defined in the file toolbar prop in the directory lt tshome gt classes prop The corresponding commands are defined in cmdtab main prop in the same directory e The bold lines in the example above are user modified lines e NM t1fid 40 gif a Bruker defined icon with a size of 40x40 pixels e NM myicon gif a user defined icon which must be located in the user properties directory Caution not in its subdirectory userdefined e NM C myicons myiconl gif a user defined icon located C myicons Using the absolute pathname allows you to store icons in an arbitrary direc
172. ied must be defined 1 Zoom in on the region to be simulated 2 Right click in the data window choosing Define Fitting Region Using Display Region or click DefReg in the panel window This will set the parameters F1P and F2P in the Spectrum panel Alternatively you can enter the values in the respective parameter fields Define Nuclei parameters For each observable nucleus site a set of parameters see below must be set To do that 1 Click the Nucleus panel or the 4 button 2 Click Add if the nucleus is not shown yet 3 Adjust the nuclei parameters until the calculated spectrum approximately fits the experimental spectrum You can do that as follows Analysis 229 r Enter the values in the parameter field Or r Click the radio button to the right of the parameter click hold the cor responding toolbar button colored green and move the mouse hori zontally Note that the calculated spectrum in the data field 1s automatically updat ed as you adjust a parameter see Fig 14 5 4 Check the parameters which must be optimized during the simulation Ghycine 29 1 Cobio quest E O x Wain Spectrum Nucleus Dip Interaction Log Parameters Mo ly 24624167 4 MM Nu tiso 187 472 pom MM Deltafcsa 135 17 ppm MO EtaiCSA 0 962 0 1 Tr LB 140 Hz Add Delete ppm Figure 14 5 Define Dipolar coupling nuclei if they exist Dipolar coupling nuclei can be defin
173. il the grid lines coincide with the remaining multiplet peaks and click the left mouse button The multiplet will be displayed Click the ill button to leave this mode examid ethanol 1 1 Cobia quest SHIFT 2 8141 ppm Li Wee J 0 1756 Hz Figure 14 14 In Fig 14 14 the triplet of the ethanol OH group is being defined The central peak is defined and the black grid lines are in the capture range of the other peaks as shown by the faint lines on the peak maxima 14 5 4 Couple existing Multiplets into a Multi level Multiplet In this mode you can defined a multi level multiplet by coupling already defined multiplets To do that 246 Analysis 1 Click the ra button it turns green 2 Select all multiplets to be coupled by left clicking them Move the mouse to the left or right until the grid lines coincide with the mul tiplet peaks and click the left mouse button Right click in the data window and select Define Multiplet in the popup menu The multi level multiplet will be displayed Click the ie button to leave this mode 14 5 5 Define Multi level Multiplet by Coupled Grid In this mode you can define a multi level multiplet by defining part of the multi plet with one of the methods above and using coupled grid analysis to define the complete multi level multiplet To define a multi level multiplet 1 2 Zoom in on the region around the desired multi level multiplet Define t
174. ing Interactive processing allows full control over the processing sequence However it requires detailed knowledge about the required parameters see chapter 5 1 and commands Therefore it is only suitable for the advanced user New or intermedi ate users are recommended to use the Processing Guide for semi automatic processing see chapter 6 2 How to Process Data with Single Commands Data can be processed by entering single commands on the command line A typ ical 1D processing sequence would be em exponential window multiplication ft Fourier transform apk automatic phase correction sref automatic calibration referencing abs automatic baseline correction This allows you full control over each individual processing step 88 Data Processing How to Process data with Composite Commands Data can also be processed with so called composite commands These are com binations of single processing commands The following composite commands are available e ef Exponential multiplication Fourier transform e efp Exponential multiplication Fourier transform phase correction e fmc Fourier transform magnitude calculation e fp Fourier transform phase correction e gf Gaussian multiplication Fourier transform e gfp Gaussian multiplication Fourier transform phase correction They can be entered on the command line or clicked from the menu For the latter option 0s Click Processing Mor
175. ing OK raw data checksum OK proc data Invalid data checksum Figure 4 26 The fourth entry in Fig 4 24 allows you to add a comment to one of the audit trail files raw or processed Chapter 5 Parameter Handling 5 1 Processing Parameters Processing parameters can be set changed in three different ways e from the parameter editor click the ProcPars tab or enter edp e from the command line e g enter si e from acommand dialog box e g wm How to Set a Processing Parameter from the Command Line Enter the parameter name on the command line For example to set the size 1 Enter si for 1D data the following dialog box will appear CT x Size of real spectrum SI 276s OK cancel 80 Parameter Handling for 2D data the following dialog box will appear joz OK cancel 2 Specify the desired value s e g 32768 or 32k 3 Click OK How to Set Processing Parameters from the Parameter Editor To open the processing parameter editor r Click the ProcPars tab in the Tab bar of the data window or rs Enter edp on the command line examid 1H 1 1 Csbio guest A ProcPars AcquPars Title pulsProg Peaks Integrals Sample Structure Fid ojs A Reference gt Reference Window SF MHz 200 1 900000 Spectrometer Phase OFFSET ppm fi 6 457 Lowy field lirat Baseline _ SR Hz o oo Spectrum ref pone se 22768 Size of reals HZpFT Hz
176. ing has been done the integral list also shows the peaks within each integral range see Fig 8 8 1D Display 119 examid 1H 1 1 Cbig guest 1 Object Integral abs HHntegral 1 21807940 16 1 6664 4 For 8 603 EHintegral 2 20864697 25 1 5943 4 7410 r or0 Peak 5 Peak 6 L Peaks EHntegral 4 examid 1H 1 1 Chio guest 2 4A5009S21 70 3 5003 1 F056 7 408 xl 8 5 8 0 75 7 0 ppm Figure 8 8 Note that the integral entries can be collapsed hiding the peaks or expanded showing the peaks As soon as one or more integrals entries are expanded two extra columns appear showing v F1 ppm the chemical shift of the peak Intensity the peak intensity Depending on whether or not integrals are expanded the right click popup menu contains the following extra items e Expand Expand the current integral showing all peaks within it 120 1D Display e Expand all Expand all integrals showing all peaks within them e Collapse all Collapse all integrals hiding all peaks within them In addition to the integral entry an individual peak within an integral can be activated by placing the cursor on it or selected by clicking it In Fig 8 8 peak 7 is selected and the correlated spectrum is displayed Peak 5 is active which is also shown by the vertical line in the correlated spectrum Delete an Integral from the Integral List To delete one integral r Right click the inte
177. ing the KE button resets individual scaling and shifting Jexam2d_HC 1 1 Cibio guest Ol x Ele R xA Eles te de luf Alt a le gt Fil ppm 56 54 52 5 0 F2 ppm Figure 12 10 How to Scan Rows Columns Click the following button it turns green and move the mouse in the data field LT to scan rows in the 2D spectrum Click the following button it turns green and move the mouse in the data field 24 to scan columns in the 2D spectrum To scale up the displayed row column r Click the left mouse button or turn the mouse wheel up To scale down the displayed row column 204 2D Interactive Manipulation r Click the middle mouse button or turn the mouse wheel down How to Grab a Row Column You can grab a row or column 1 e keep it displayed in the data window as fol lows 1 Scan rows or columns as described above and hold at the desired posi tion 2 Right click in the data window 3 Choose Grab Row Column from the popup menu see Fig 12 11 Note that a grabbed row column appears in the lower apart of the browser It can be selected there and individually scaled or shifted Toggle Rows Columns Extract RowlColumn Grab Row sCoalumn Baseline At Center Baseline At Bottom Figure 12 11 H examzd_HC 1 1 Cobia guest R xA E ts ts de lat a l a e F1 ppm 140 100 669 of l z4 12 10 g 6 4 2 F2 ppm Figure 12 12 2D Interactive Manipulation 205 Fig 1
178. ious regions or various objects spectrum fid parameters etc of the same dataset How to Reopen a Dataset in a Second Third etc Window 1 Select activate the desired dataset 2 Click File Reopen reopen Multiple data windows with the same dataset are indicated with a number in square brackets e g 1 in the title bar see Fig 8 2 103 1D Display O x examid_1H 1 1 Crlbio quest 1 opecirum ProcPars AcquPars Title PulsProg Peaks integ T Ml exam1d_1H 1 1 Cibio guest 3 o A Spectrum ProcPars AcquPars Title PulsProg Peaks integ i EJ o s 23 24 iIndow function Reference LE Hz Figure 8 2 How to Rescale or Shift one Dataset in Multiple windows Display manipulation buttons like and only work on the active data win dow The same counts for the keys Alt PageUP and Alt PageDown How ever when used with the control key they work on all windows for example o gt Hit Ctrl 7 Ctrl Alt PageUp or Ctr1 Alt PageDown 104 1D Display 8 3 Changing the Display of a 1D Spectrum or FID TOPSPIN offers buttons to scale or shift the spectrum vertically and horizontally How to Change the Vertical Scaling of the FID or Spectrum r Hit one of the following the keys e Alt PageUp Increase the intensity by a factor of 2 e Alt PageDown Decrease the intensity by a factor of 2 e Alt Enter Reset the intensity or r Click hold the button and move the mous
179. isition Status Parameters 4 84 How to Get Probehead Solvent dependent Parameters 84 How to Change Acquisition Data Dimensionality 84 Chapter 6 Chapter 7 Chapter 8 How to Set Lock Parameters 200 ccc eeececceeees 85 How to Set Routing Parameters 0 0 0 ee eee 85 Data Processine lt 6 0c 5sitieese 0is 6h t dre Barts Old how Se OARS A AS 87 Gl Interactive PrOCESSIN paee sda o en e Sey Ao ATE ESNE ESA 87 How to Process Data with Single Commands 87 How to Process data with Composite Commands 88 62 lt Semicautoniatic Processing 4 058 edatenedeweudew newt ae US was Sa 88 How to Use the Processing Guide in Automatic mode 88 How to Use the Processing Guide in Interactive mode 90 6 3 Processing Data with AU programs 0 ccc eee 90 6 4 Serial Processing using Python programs 0 000 eee 91 Printing Exporting Data ssssssscsosseccososcesooooee 95 7 1 Printing plotting Data 20 0 0 000 nee 95 How to Print Plot from the Menu 0 0 cee ees 95 How to Plot Data from the Processing guide 0000 97 How to Plot Data with the Plot Editor 0 000 000 97 How to Print the Integral list 0 0 0 0 0 cee eee 97 Howto Print the Peak list i o2bncGart Ader aw atsciarsnt EE Shee reat 98 T2 Export Dala eese eee a
180. ith the FID display buttons as described in chapter 15 8 At the bottom of the window you find the following buttons e Save Save the value of the current parameter 268 Acquisition e Save all Save the values of all changed parameters Restore Restore the value of the current parameter e Restore all Restore the value of all changed parameters e Stop Stop the acquisition and quit the GS window 15 8 Running an Acquisition A typical acquisition is performed as follows 1 Create a new dataset a Click File New new Ctrl1 n SSS hh hCl Prepare for a new experiment by creating a new data set and initializing ts WR parameters according to the selected experiment type MAME EX PNG PROCMO DIR USER solvent koc E Experiment Lise current parame ai TITLE Proton 44 300 Automation Cyclosporin OK Cancel Help Figure 15 11 b Specify the datapath variables name expno procno dir and user select the desired Solvent and Experiment enter the Title and click OK Acquisition 269 The dataset will appear in the data field with no raw and no processed data available 2 Click the AcquPars tab to display the acquisition parameters protona 1 r 5 periment V ictth Receiver Nucleus Durations Power Prograrn Probe Lists Wobble Lock Automation Miscellaneous User Routing 1 Cobio1 guest O x Spectrum ProcPars AcquPars Title
181. ithin a certain layout you can easily swap two TOPSPIN windows with the com mand swin If the data area contains exactly two windows swin simple swaps their position and geometry If it contains more than two data windows swin opens a list from which you can select any window to be swapped with the cur rently selected active window Swapping windows can also be executed from the Window menu Chapter 14 Analysis This chapter describes various TOPSPIN analysis methods including chemical shift measurement signal to noise calculation solids line shape analysis T1 T2 relaxa tion analysis and multiplet analysis 14 1 1D Chemical Shift Distance Measurement How to Measure a Chemical Shift Distance 1 Click the following button button turns green qg Chemical shift distance measurement 2 Left click hold at one peak position and drag the mouse to another peak position The distance in ppm will be displayed 3 Right click in the data window or move the cursor out of the data window to leave distance measurement mode button turns grey 222 Analysis 14 2 1D Signal to Noise Calculation How to Perform Interactive S N Calculation 1 Click Analysis gt Signal Noise Calculation sino The current signal region parameters SIGF1 SIGF2 and noise region pa rameters NOISF1 NOISEF2 are displayed NOISEREG 1 94 ppm 581 90 Hz SIGREG 7 70 ppm 2311 67 Hz 10 0 5 0 0 0 Figure 14 1 Data window in S
182. ividual scaling on off How to Toggle between Superimposed and Stacked Display r Click the following button itt Toggle between superimposed and stacked display How to Shift and Scale Individual Spectra To compare the intensity and chemical shift of corresponding peaks you can shift and scale individual spectra To do this 1 Display the spectra in multiple display mode as described above 2 Expand the spectra to display the desired region or peak 3 Select one of the spectra e g by clicking it in the lower part of the browser 4 Click hold the c button and move the mouse to align the intensities 5 Click hold the amp button and move the mouse to align the peak positions The alignment can be facilitated by showing the difference spectrum 4 button and minimize that Clicking the E button resets individual scaling and shifting The performed scaling and shifting are displayed in the data window see Fig 11 10 and 11 11 1D Interactive Manipulation 181 examid 13C 1 1 Cobio1 guest examld 13C 1 1 Ci bia examld 13C 4 1 C bio Figure 11 10 examid 13 C 1 1 Cobio1 guest 123 3 123 2 123 1 123 0 ppm Figure 11 11 How to Switch on off the Display of Datapaths and Scaling Factors m Click the following button 1 Switch on off display of datapaths and scaling factors 182 1D Interactive Manipulation How to Return from Multiple Display mode r Click the following button Return
183. k under cursor from the popup menu see Fig 11 17 Delete All Peaks Delete Peak Under Cursor Delete All Regions Delete Region Under Cursor Pick Peaks On Ranges show Peak List Set hill Set MAKI Figure 11 17 To delete all peaks t Click the t amp button in the data window toolbar Or t Right click in the data field and click Delete All Peaks in the popup menu How to Return from Peak Picking Mode with without Save To return while saving the peak list and peak ranges r Click the following button Hj Save the Peak Region and Peak List and Return sret This will e Save the peak list to the file peak txt and the peak ranges to the file peakrng e Leave the peak picking mode To return while discarding any changes r Click the following button a Return discarding any changes ret 12 1 12 1 1 Chapter 12 2D Interactive Manipulation The upper toolbar of the 2D menu offers various buttons for interactive manipula tion If you click such a button the active data window will switch to the corre sponding mode An interactive manipulation mode is data window specific 1 e it only applies to the active window 2D Interactive Phase Correction 2D spectra can be phase corrected interactively in both the F2 and F1 direction by selecting certain rows and or columns and phase correct them 2D Interactive Phase Correction Procedure How to Switch to 2D Interactive Phase Correction Cli
184. key while the folder is highlighted How to Expand a Folder showing Pulse program and Title c Right click the data name folder button and choose Expand fully amp show PULPROG Title from the popup menu Fig 4 4 shows an example of an expanded dataset showing the pulse program and title exami d_1H 1d z430 Proton examed CH 2d hxcogf examed HO 2dinviggph 2D THASC HSac AY 300 Cyclospor exam2d HH 2d cosygpqf 20 HA COSY gradient AY 300 Autor examad Sd hechdiggsd A S00 Automation Cyclospor Figure 4 4 Dataset Handling 53 Note that collapsing the data name folder will deselect the display of the pulse program and title How to Add Remove a Top Level Data Directory To add a new top level data directory local or remote to the browser 1 Right click any position in the browser 2 Choose Add new data dir from the popup menu see Fig 4 5 3 Enter the top level directory in the dialog box and click OK To remove an existing top level directory from the browser 1 Right click the folder button of the top level directory 2 Choose Remove selected data dir from the popup menu see Fig 4 5 Display Display in Mew vvindovwy Expand Fully Expand amp Show PULPROG Title Copy File Properties Delete Files Add Mew Data Dir Remove Selected Data Dir Figure 4 5 3 Click OK to confirm the appearing message By default the browser shows the TOPS
185. ks from the peak list To delete one peak r Right click the peak and choose Delete from the popup menu To delete multiple peaks 1 Select the peaks while pressing the Ctrl or Shift key 2 Right click one of the peaks and choose Delete from the popup menu To remove possible duplicate peaks c Right click any entry and choose Remove Duplicate peaks To remove possible peaks outside of the spectrum cs Right click any entry and choose Remove Peaks positioned outside of the spectrum Shortcuts Double click a peak zoom into spectrum 1 e show region around that peak Enter key zoom into spectrum 1 e show region around selected peak s Delete key delete the selected peak s from the peak list 1D Display 113 Ctrl c copy selected peaks to the Clipboard Ctrl a select all peaks Home select the first peak End select the last peak Shift Home select current and first peak and all in between Shift End select current and last peak and all in between Note that these keys only work when the cursor focus is in the data window More features The right click popup menu has the following entries see Fig 8 4 Table properties Set the shown columns and specify their decimal places Show detailed information Show peak information dataset information and peak picking parameters When you move the cursor over the peak list the active peak will be highlighted in blue see peak 3 in Fig 8 5 If the c
186. lay Properties Save Display Region To Restore Display Region From Params F112 File Properties If the spectrum is displayed the files in the procno subdirectory are shown If the Fid is displayed the files in the expno subdirectory are shown r Select a file and click Open to view its contents Note that this only makes sense for ascii files How to List Open the current Dataset Files in the Windows Explorer To list the current dataset files in the Windows Explorer 1 Click Files gt Run 2 Select Open file explorer exp1 in the appearing dialog box 3 Click OK Alternatively you can enter the command exp on the command line The Win Geo Options te Open File Explorer Serial Processing Execute AU Prograrn Execute Python Prograrn Execute Macro Cancel Help dows Explorer will be opened showing the processed data files the files in the procno directory of the current dataset Under Linux a Web browser like KDE 76 Dataset Handling Konqueror or Gnome Mozilla will be opened To open a file t Double click the file or right click the folder icon and choose Open If TOPSPIN data area contains no datasets the exp1 command opens the Explorer showing the users home directory When entered on the command line exp1 can also be used with the argument top to open the TOPSPIN installation directory home to open user home directory or with an absolute pathname to open that d
187. m gammab Hz fon resonance 186 0544 Corresp 40 deg square pulse usecisgtici update parameters Figure 15 31 15 Click Options Select associated dataset and select the selgpse dataset 16 Click update parameters specify a name for the shaped pulse and click OK 17 Now switch to the selgpse dataset and start the experiment Chapter 16 Configuration Automation 16 1 NMR Superuser and NMR Administration password During TOPSPIN installation you are prompted to define the username for the so called NMR Superuser Under Windows this must be the name of an existing user Under Linux it can also be a non existing user which is then automatically created by the installation program After the installation the NMR Superuser is the owner of all TOPSPIN program files Logging in as this user allows you to remove these files change file permissions etc The name of the NURSUPERUSER will be stored in the file lt tshome gt conf nmrsuperuser the NMR Administration password to be used for TOPSPIN configuration commands This password can be freely chosen and is not connected to any user It is asked for by TOPSPIN commands like cf expinstal11 etc The encrypted NMR Administration password is stored in the file lt tshome gt conf nmradminpassword Note that the NMR Superuser login password and the NMR Administration password have different purposes and are totally independent Changing one of them does not affect the other
188. m on the display to show the peak or peak group of interest Then type deon or click Analysis Deconvolution 1 15 How to Compute Fids by Simulating Experiments TOPSPIN includes a virtual spectrometer that computes fids of any dimension A real spectrometer excites a sample with high frequency pulses defined by a pulse program and measures the resulting fid The virtual spectrometer performs this Getting Started 25 1 16 task mathematically by solving the quantum mechanical Liouville equation The sample must be entered in form of a spin system description For the computa tion the same pulse program and acquisition parameters are taken as for the real experiment The result is a time domain signal which can be processed with TOP SPIN in the same way a measured fid is processed Techniques such a selective excitation gradient enhanced spectroscopy and the handling of mixtures are sup ported To start the virtual spectrometer tS Enter nmrsimon the command line or click Analysis gt Simulate Fid How to Add Your Own Functionalities The TOPSPIN functionality can be extended with various user defined commands programs etc How to Create Macros Writing a macro is the simplest way to create a user defined command Just enter the command edmac select a file and enter a sequence of regular TOPSPIN com mands and or Python commands Save the file under a name of your preference You have created a ne
189. mber expno and click OK How to Save Processed Data as Pseudo Raw Data Click File gt Save Ctr1 s Select the option Save other file Select File type Ir li as fid genfid or 2rr 2ii as ser genser Click OK Enter a destination expno nan Aa Ww N m optionally you can specify further data path specifications 6 Click OK 4 5 Deleting Data How to Delete a Specific Dataset c Right click the data name expno or procno in the browser then click Delete In each case a delete dialog will appear The dialog box for a data expno for an is shown in Fig 4 19 Dataset Handling 69 x Options Delete the raw data files of the selected EXPNOs Show more delete options JRK Cancel Help Figure 4 19 You can choose to delete just the raw data delete the entire expno with all procnos or open further delete options In the later case the dialog box shown in Fig 4 20 will appear How to Delete Types of Datasets To delete certain types of data like 1D raw data 2D processed data etc us Click File gt Delete Or rs Enter delete on the command line The dialog window shown in Fig 4 20 will appear Here you can select the data type and selection criteria 70 Dataset Handling TT x Delete Options C Acquisition data Processed data Data acquired at certain dates 1Draw data tid 4D processed data Cri 2080 raw data ser 2D processed data 2rri
190. multiple display 179 superimpose 1D spectra 175 cursor information 127 integral trails labels 127 main status parameters 127 I 15 peak labels 127 spectra 21 title of a dataset 127 SW parameter 259 swap data windows 219 sweep width 259 swin command 219 switch to the last 2D data 30 to the last 3D data 30 synchronized experiments 228 T T1 calculation 16 T1 T2 Relaxation 235 tl guide command 235 T2 calculation 16 Tab bar 1D 102 106 2D 134 139 3D 159 configuration 106 316 font 320 usage 106 Tab key 81 83 tabbed pane 139 159 316 TCP IP port 308 temperature unit window 218 Terminal Window 18 time domain signal 25 title bar 29 101 102 133 212 213 216 217 218 304 title file 109 title of a dataset 20 52 57 109 127 268 318 Title tab 109 tojdx command 24 67 toolbar 1D 161 2D 193 configuration 324 extension 334 for acquisition 257 icons 337 of the data window 21 124 of the FID display window 270 tips 39 usage 30 tooltips 39 top level directory 20 49 53 Topspin color schemes 318 communication 309 data area 64 66 fonts 320 help 39 installation 301 installation directory 301 portfolio 50 startup 17 18 tailoring 313 window 27 topspin command 18 Topspin icon 18 totxt command 67 tozip command 23 67 tshome directory 18 39 301 309 tuning the probehead 261 U undo last parameter change 81 84 last region operation 173 unzip utility 24 Up Arrow key 33 37 upper toolbar 1D
191. ne Correction Line 4 185 How to Change the Mouse Sensitivity 0 0 0 185 How to Save the Baseline Correction and or Return 185 How to Perform Cubic Spline Baseline correction 185 How to Delete Spline Baseline Points from the screen 186 How to Return from Cubic Spline Baseline mode with without Save 187 ID Interactive Peak Piekna aise auton Ms been teen dea SS x 187 How to Switch to Peak Picking Mode 0 0000 eee 188 How to Define New Peak Picking Ranges 040 188 How to Change Peak Picking Ranges 0 000 ce eeee 189 How to Pick Peaks in Peak Picking Ranges only 189 How to Delete all Peak Picking Ranges 0040 189 How to Define Peaks Manually 0 0 0 0 cee eee eens 190 How to Pick Peaks Semi Automatically 0040 190 How to Delete Peaks from the Peak List 190 10 How to Return from Peak Picking Mode with without Save 191 Chapter 12 2D Interactive Manipulation cceccccccccees 193 12 1 2D Interactive Phase Correction snes 0 00 00 eee 193 How to Switch to 2D Interactive Phase Correction 193 How to Perform a Typical 2D Interactive Phase Correction 194 How to Scale or Shift Individual Rows Columns 197 How to Perform Smooth Phase Correction 0
192. ne Positions numbers Click one of the following buttons Show the next plane Show the previous plane t Scan planes smoothly E Enter the exact plane number 10 2 Cube Display Mode How to Display the 3D Cube Click the following button fq Show 3d cube see Fig 10 2 158 3D Display Jexam3d 1 1 Cobio guest l olx Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Molecule Fid Figure 10 2 How to Rotate the 3D Cube Click hold one the following buttons and move the mouse up down a Rotate cube around x axis Rotate cube around y axis z Rotate cube around z axis How to Scale Up Down the 3D Cube 1 Right click inside the data window 2 Choose Larger or Smaller from the popup menu see Fig 10 3 How to Reset the Cube Size and Orientation Click the following button R Reset to default size and orientation 3D Display 159 How to Switch Depth Cueing on off 1 Right click inside the data window 2 Choose Depth Cueing On off see Fig 10 3 Depth cueing makes data points which are closer to the viewer appear brighter and those that are further away appear dimmer This increases the depth effect of the 3D image Larger smaller Default View Depth Cueing On Off Spectrum Components Properties Files Figure 10 3 How to Display a Cube Front or Side view Click one the following buttons 12 Show F1 F2 plane 23 Show F2 F3 plane
193. ne points 185 integral regions 166 NMR ADMINISTRATOR password 299 NMR SUPERUSER 299 peak ranges 188 peaks 190 de iconify data window 217 delete AU program 304 data 68 integrals from display 170 noise region S N 223 peaks from a peak list 190 signal region S N 223 spline baseline points 186 Delete key 33 depth cueing in 3D 159 deselect data in multiple display 178 integral regions 166 dialog box font 321 difference spectrum in baseline correction 184 in multiple display 179 dimensionality of a dataset 28 81 82 84 108 dipolar coupling 229 dir command 20 disable commands 324 menus 324 toolbar buttons 324 Display button 19 65 73 menu item 59 176 display 1D acquisition status parameters 108 1D data 101 1D FID 124 1D integral list 115 1D peak list 110 1D processed data 107 1D raw data 124 1D spectrum 107 1D spectrum overview 124 2D contours 148 2D data 133 2D FID 143 2D grid 147 2D integral list 142 2D peak list 141 2D projections 145 2D spectrum in contour mode 148 2D spectrum in image mode 151 2D spectrum in oblique mode 151 3D cube 157 3D data 155 columns in 2D phase correction 194 contours in 2D phase 194 data from the browser 20 60 data from the portfolio 60 data in multiple windows 102 dataset file list 128 dataset properties 128 expno procno list 60 found dataset 73 full spectrum in 2D phase correction 195 integrals 20 JCAMP data 24 manipulation 103 mani
194. nerate Shapes Gradients The Shape Tool allows you to generate RF and gradients shapes Various Basic Classical or Adiabatic shapes can be created from the Shapes menu Additionally Solids Imaging and Decoupling shapes are available How to Generate a Gauss shape To generate a Gauss shape us Click Shapes Classical Shapes Gauss A Gaussian shaped curve will appear in the data section The parameter section shows the two parameters that can be set for a Gauss 276 Acquisition Size of Shape the number of shape data points Truncation level the minimum amplitude at the edge of the shape If you change these parameters the displayed shape will automatically be updat ed To save the shape click E enter a Name e g mygauss Title Flip Angle and the Type of Rotation see chapter 15 9 5 and click OK How to Generate a ShapFour shape To generate an RF shape that is defined by Fourier coefficients w Click Shapes Classical Shapes Shap Four The following dialog box will appear SSS hh Parameters for ShapFour 1000 Size of Shape fa Mumber of coefficients Mame of coefficients file E Fourier coefficients taken from file OK Apply cancel Figure 15 17 Here you can enter the Size of Shape and the Number of coefficients Clicking OK or Apply will open a further dialog box see Fig 15 18 where you can enter the required coefficients A ShapFour shape is defined by two coefficients arrays a O 1
195. ng Display Region or click DefReg in the panel win dow The displayed parameters SI O1P SF SW SWH LB GB and SR are used by the fitting calculations They are defined by the corresponding processing parameters command edp Nucleus Parameters The section Model shows the spectrum model type which was selected in the Spectrum panel The section Parameters contains the nucleus dependent model parameters The available parameters and the corresponding toolbar buttons are J Ty Signal intensity Nu iso isotrope chemical shift given in ppm Delta CSA Chemical shift anisotropy parameter in ppm can be pos itive negative or zero K Eta CSA Asymmetry parameter 0 lt Eta lt 1 234 Analysis kH CQ Quad Quadrupolar coupling constant in kHz a Eta Quad Asymmetry parameter of the quadrupolar coupling tensor LE LE 6 gt O lt Eta lt 1 Alpha Euler angle of the CSA amp Quad tensor Beta Euler angle of the CSA amp Quad tensor Gamma Euler angle of the CSA amp Quad tensor Line broadening parameter half width if GB 0 Gauss broadening parameter If GB gt 0 then LB must be negative Gauss component of the Gauss Lorentz ratio 0 0 lt GL lt 1 0 Lorentz curve GL 0 Gauss curve GL 1 Used only by the Gauss Lorentz model Dipolar coupling Theta dipolar Phi dipolar Dipolar nucleus parameters TOPSPIN 1 3 supports a maximum of ten dipolar cou
196. nmrt for peak 1 If the dataset was already fitted the previous type of fitting is performed The fitting curve is displayed in the data section and a Brief Report is shown in the parameter section If this default fit ting is appropriate you can view interpret and print the results as described be low If not you can perform the desired fitting as described below Perform Fitting and Calculate the Relaxation Time Depending on the experiment you can perform the appropriate fitting as fol lows 1 Select a Fitting type Intensity or Area Either every point reflects the intensity of the biggest peak in the defined integral range or the integral itself Both of them can be used but depending on the experiment one of them usually give a better fitting curve 2 Click the button to open the parameter dialog box Select a Func tion Type and set the required parameters see below Click OK Analysis 239 3 Perform fitting and calculate the relaxation time gt Fit the relaxation curve for the current peak gt Fit the relaxation curve for all peaks View and interpret the results as described below Function Types and Parameters The TOPSPIN relaxation routine offers functions for various relaxation experi ments with up to 6 components uxnmrtl for one component T1 experiments Set the parameter List file name to the list type used during the acquisition The T1 fitting function is defined by the function
197. normal display mode How to Delete all Peak Picking Ranges r Click the button in the data window toolbar Or n Right click in the data field and click Delete All Ranges in the popup menu 190 1D Interactive Manipulation How to Define Peaks Manually 1 Click the following button button turns green ii Define peaks manually A red vertical line will appear in the data window 2 Put the red cursor line at the desired peak and click the left mouse button The peak label will appear at the top of the data window 3 Repeat step 2 for each peak to be defined 4 Click the green button to leave the Define peaks mode How to Pick Peaks Semi Automatically 1 Click the following button button turns green il Define peaks semi automatically 2 Move the cursor into the data window 3 Put the cursor line near the desired peak 4 Left click to pick forward or Right click to pick backward see Fig 11 16 A red cursor line will appear at the nearest peak whose intensity is between MI and MAXI 5 Right click to add the selected peak to the peak list see Fig 11 16 Add Peak Ta List Fick Backward Figure 11 16 The peak label will appear at the top of the data window 6 Click the green button to leave the define peaks semi automatically mode How to Delete Peaks from the Peak List To delete a specific peak 1 Right click on a defined peak 1D Interactive Manipulation 191 2 Choose Delete pea
198. nsity 1D 104 intensity in 2D 135 search mask 72 zoom factor 32 105 resize command line 323 data window 212 graphics 99 resolution of a screen dump 22 99 restore adjusted acquisition parameters GS 268 size and position of a data window 217 toolbar 324 uncorrected baseline 185 retrieve previously entered commands 33 rew command 20 64 Right Arrow key 33 37 52 rotate 3D cube 153 158 routing parameters 85 S S N value 224 Sample tab 121 sav command 30 36 save 1D baseline correction 184 185 1D integrals 173 1D phase correction 164 acquisition data 68 adjusted acquisition parameters GS 267 AU program 25 304 I 13 color scheme 318 cubic spline baseline points 187 current window layout 218 data 23 30 36 66 data in analog filtered format 67 data to a JCAMP DX file 24 data to a ZIP file 23 data window to a graphics file 22 99 entire dataset 66 67 integral regions 172 macro 25 parameters 108 peak list and peak ranges 191 phase correction 2D 197 200 portfolio 54 processed data 68 processed data as pseudo raw data 68 pulse program 110 121 sum or difference spectrum 179 title of a dataset 109 scale 1D integrals 171 1D spectrum 104 2D spectrum 134 3D cube 158 individual spectra in multiple display 21 175 180 row column in 2D phase 198 scaling factor of integrals 171 scan planes of 3D data 157 rows columns in 2D 203 screen dump 22 99 screenDump wmf file 99 scroll bar 81 84 search criteria 54
199. ntents of the procno directory 130 1D Display CL x Directory Ccrbioldatafiguestiiimeirexam d_ 1TH pdatast Last modified Size in bytes a 2 be auditp tet intrng meta m meta ext outed parr tet peak fet proc procs title mm E fC O E O A os Open cancel Figure 8 15 The contents of any file in the list can be displayed as follows 1 Select a filename it will be highlighted 2 Click Open Note that this only makes sense for ascii files e g acqu proc or files with the extension txt Dataset files can also be displayed opened with the command exp1 This opens the Windows Explorer or under Linux the Konqueror or Mozilla showing the contents of the procno directory 8 7 Saving Display Region The currently displayed spectral region can be stored as follows n Right click in the data window and choose Save Display Region To This will open the dialog box shown in Fig 8 16 Save display region to x Options f Parameters Fis e g used by restore display 3 dpl C Parameters ABSF1 2 e g used by abst apkt C Parameters STSRISTSI fused by strip fh Cancel Figure 8 16 How to Save the Display Region for Re display r Click Parameters F1 2 dp1 The saved region can be restored as follows cS Right click in the data window and choose Restore Display Region from Params F1 2 How to Save the Display Region for Baseline or Phase
200. nzip utility Zipping can be applied to 1D 2D 3D and 4D data e Saving a dataset in JCAMP DX format This format is a IUPAC standard and is available for 1D and 2D datasets Data and parameters are stored in readable text ASCII format To store data in JCAMP type tojdx click File gt Save or type Ctr1 s To convert and display a JCAMP DxX file type fromj dx 9 e E mailing data to a desired destination Type smail or click File gt Send To The mailing format is either zip or JCAMP DX both of which allow for data compression in order to keep the transferred data size as small as possible 1 13 How to Import NMR Data Stored in Special Formats TOPSPIN allows you to convert various data formats to standard Bruker format for display and processing Click File gt Open and select Open NMR data stored in special formats Then follow the instruction on the screen 1 14 How to Fit Peaks and Deconvolve Overlapping Peaks Peaks of a 1D and 2D NMR spectrum can be approximated by a Lorentzian Gaus sian or a mixture of these line shapes Overlapping peaks may be deconvolved into a sum of such line shapes TOPSPIN shows the deconvolution result 1 e peak positions line widths and inte grals on the screen and stores it in the file dconpeaks txt Furthermore it switches to multiple display mode to show the original spectrum and the sum of the computed line shapes superimposed To start deconvolution expand the spectru
201. o specify or edit an annotation click inside the Annotation field and enter a character string The peak annotations are shown in the correlated spectrum see Fig 9 8 exam d HC 1 1 Cbio guest 1 oO x 30 F1 ppm ad a8 3 4 3 0 F2 ppm Figure 9 8 How to Display the Integral list t Click the Integrals tab 2D Display 143 exam2d_HC 1 1 Cjbio guest O x Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample Struc aj amp Object HHntegral 1 0 00 0 0000 EHntegral 2 0 00 0 0000 EHntegral 3 0 00 0 0000 EHntegral 4 19717450 50 1 0000 EHntegral 5 0 00 0 0000 vF 2 ppm F1 ppm Intensity Hrexs 55751 126 2371 3446703 37 peak 7 5 6386 126 2227 4532891 75 Hntegral 7 0 00 0 0000 1 Figure 9 9 This displays list of integrals if these have been calculated command int The list is basically the same as for 1D spectra The only difference is that when peaks are shown there are two columns for the chemical shift v F2 ppm the chemical shift in the F2 direction v F1 ppm the chemical shift in the F1 direction Furthermore a stored or exported 2D integral list can be imported as follows 1 Right click an entry to open the popup menu 2 Click Import 3 In the appearing dialog box navigate to the directory where the list resides and select the integral list As such you can import an integral list from a different dataset or a
202. o that 1 Click the following button button turns green i Preview corrected spectrum show difference The corrected spectrum will be displayed in red 2 If the baseline is correct click the HI button to save the correction If fur ther correction is needed click the E button to show the original spectrum and the red correction line 1D Interactive Manipulation 185 How to Reset the Baseline Correction Line 1 Click the following button Reset the red correction line to zero If the difference spectrum is displayed the A button is active clicking the reset button will restore the original spectrum How to Change the Mouse Sensitivity r Click one of the following buttons 1 Increase double the Mouse Sensitivity inc t Decrease halve the Mouse Sensitivity dec Reset the Mouse Sensitivity How to Save the Baseline Correction and or Return To return while saving the baseline correction r Click the following button Hj Save baseline correction and Return sret This will perform the following tasks e Execute the baseline correction bem e Save the baseline correction values A B C D and E e Leave the baseline correction mode To return while discarding any changes Click the following button 4a Return Discarding any changes ret How to Perform Cubic Spline Baseline correction r Click the following button fi Define points for cubic spline baseline correction The to
203. ode a 263 150 BSMS Control Panel r ran i a ote eaten eke eee ees 264 15 7 Interactive Parameter Adjustment GS 0 0 0 0 c eee aes 266 15 8 Running an Acquisition 0 0 cece eens 268 P59 ShapetOol 2c45 400 oS cous tenuis veo be ie Sk Se eee Ane 212 Configuration Automation sssssssssosesesesesssooo 299 16 1 NMR Superuser and NMR Administration password 299 How to Change the NMR Administration Password 300 162 COMMCUTAUONs au4 tel ou coat eed eo hw ie Oe eae Near a he ards 300 How to Perform a Default Configuration on a Datastation 301 How to Perform a Customized Configuration on a Datastation 301 LO Paramcter Set CONVErSION gt cy caso anewusaas Raaes Bad as Seay A Keoe 302 IOA AMOMANON WS eichsabeceaced secede heat sea aad a wes 303 How to Install AU Programs 1 0 0 0 0 cc eee ees 303 How to Open the AU Program Dialog Box 303 How to Switch to the List of User defined AU Programs 303 How to Switch to the List of Bruker defined AU Programs 304 How to Create an AU Program 0 0 cee ee eee 304 How to Edit an Existing AU Program 0 000 ee eee 304 How to Execute an AU Program cece ccc eens 304 How to Delete an AU Programi esi idee aay teat ked owed a 304 How to Show Comments short descriptions in the AU Program List 305 Chapter 17 Remote Control cc ccc cc ccc cree
204. ol Example 1 Create a Shaped Pulse for Multiple Solvent Suppr using WET To create a shaped pulse 1 Acquire a reference 1D spectrum 2 Click 2 to switch to frequency list mode e Select the frequency list type and enter the list name freglist If you get a message that this list already exists click Overwrite to overwrite the existing list or click Cancel and specify a new name e Move the vertical cursor line to the desired frequencies e Left click the desired frequencies 292 Acquisition e Click Hj to save the frequency list and return 3 To view the frequency list t Enter edlist f1 freqlist and click OK It should look for example like this O 300 19 3759 74 OT Tasg 6712 96 Click Cancel to close the list 4 Enter stdisp to start the Shape Tool interface 5 Proceed as follows tS Click lt choose Open Shape select Sinc 1000 and click OK Or r Click Shapes Classical Shapes Sinc and enter Size of shape 1000 Number of cycles 1 in the parameter section 6 Click Manipulate Phase modulation acc to Offset Freq offs In the appearing dialog box see Fig 15 28 e Select Ending at Phase 0 e Select Reference O1 from current Data Set e Check the box Frequencies taken from Frequency List e Set Length of Pulse to 10000 e Set Name of Frequency List to freqlist or the name you specified in step 2 e Click OK 7 Check the frequency values in the appearing dialog box see Fig
205. olbar of the data window will change as shown in Fig 11 13 186 1D Interactive Manipulation 3 examid_1H 2 1 Cobo guest 0 41 ppm 124 28 Hg DEFINE LIST OF FOINTS Left click inside data window p 2 760 ppm 1 426 ppm Define Delete Right click on defined peak save Click right mouse button Figure 11 13 Data window in spline baseline correction mode The cursor line in the data window turns red If a list of baseline points already exists you are prompted to overwrite or append to these points If you choose Ap pend the labels of the existing points are displayed on the screen If you choose Overwrite no labels are displayed Nevertheless the existing points are only overwritten when you define and save new points To define new baseline points 1 Move the cursor line to a baseline point and left click at that position 2 Do this for at least five baseline points Fig 11 13 shows a spectrum with five defined baseline points Note that here the points have been chosen at the right part of the spectrum for display reasons on ly How to Delete Spline Baseline Points from the screen To delete one baseline point 1 Right click the baseline point position in the data window 2 Choose Delete Current from the popup menu see Fig 11 14 1D Interactive Manipulation 187 Quit save amp UIt List baslonts Delete All Delete Current Enter zoom Figure 11 14 To delete all baseline points 1
206. one by system administrators who want to disable certain functions for standard users User Preferences 325 Open the Menu Configuration table as follows 1 Click Options Preferences set 2 Click Fonts Dialogs Icons in the left part of the dialog box 3 Click the Change button of the entry Disable Enable menus and commands The table consists of the following columns Command Satu You can disable remove e Menus e g Options to be found in the column Menu e Sub menus e g Options gt Administration tools to be found in the column Menu e Menu entries e g Options Preferences to be found in the column Description e Commands e g set to be found in the column Command Note that in this configuration table each menu entry corresponds to a certain command In the TOPSPIN menu most commands are indicated in square brackets behind the corresponding menu entries e g us Processing Fourier transform ftf Menu entries which are not used very often appear without the corresponding command indicated e g rs Options Preferences However if you want you can look up the corresponding command in this case set in the configuration table and use it As an example we will describe how you can disable remove the menu entry Re mote connection in the Options menu 1 Open the configuration table as described above 2 Scroll to the Description Remote connection 326 User Preferences 3 Set th
207. onsist of a series of 1D FIDs measured with varying delays and stored as pseudo 2D data To analyze these data Topspin offers an easy to use T1 T2 Relaxation Guide Relaxation curves of various experiment types with up to six components can be fitted To start the Relaxation Guide 0s Click Analysis T1 T2 Relaxation t1lguide This will open the dialog box as shown in Fig 14 8 236 Analysis MMF Relaxation Guide bk Extract Slice 4 h Start Calculation L e Close Define Ranges a Relaxation Window PrintvExport Figure 14 8 Just click the successive icons and follow the instructions on the screen Note that holding the cursor over an icon shows the command line command that is executed when the icon is clicked If you prefer to execute these commands from the com mand line just click the Close button to close the Relaxation Guide Extract Slice Prompts you for the FID or spectrum to be extracted for peak determination see Fig 14 9 Click FID to extract an FID or Spectrum to extract a spectrum Note that the latter only works if the pseudo 2D data have been processed If you click Analysis 231 FID the extracted FID is automatically processed We recommend to enter the EA Extract a row from 2d data 5 x his row should correspond to an experiment vith the maximurn or minimum delay tire All further data preparation will be done in respect to this rove pectrurri Canc
208. oolbar 2 In the appearing popup menu see Fig 18 8 click t Change Icon Size Reactivate All InvisibleInactive Buttons Add User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars wpe SHIFT ESC to reset Figure 18 8 3 Enter the icon size in the appearing dialog and click OK How to Shift Toolbar Icons to the Right 1 Right click at an empty area of the toolbar 2 In the appearing popup menu see Fig 18 8 click t Change Toolbar Offset 3 Enter the toolbar offset in the appearing dialog and click OK Chapter 19 User Extensions TOPSPIN offers various ways to extend the standard commands buttons programs etc 19 1 User Notebook You can create your own user specific notebook with the command r View Notebook nbook SSS Lt iC Save Clear cancel Figure 19 1 This can be used to store and retrieve any personal notes information etc 330 User Extensions 19 2 19 3 Macros A macro contains a sequence of TOPSPIN commands It can be created with the command edmac A simple macro for processing and plotting the current dataset 1S em EG apk sref autoplot All entries in a macro file must be written in lower case letters In TOPSPIN 1 3 and newer a macro may contain Python commands Any line in a macro that starts with py gt executes a Python command An example of such a macro is re examld 13C 1 1 C bio gues
209. orrelated spectrum is also displayed a vertical line moves along showing corresponding position in the spectrum see Fig 8 5 114 1D Display Jexamid_1H 1 1 Cibio guest f i loj x spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample stru 1j vWF ppm Intensity Automatic Automatic Automatic Automatic Automatic 8 6 8 4 8 2 8 0 7 8 ppm Figure 8 5 As soon as you click a peak it is selected and displayed in red see peak 1 in Fig 8 5 Note that this peak remains selected 1 e is used by Enter and Delete until a different peak is selected To extend the peak list with Regions Type and Index entries right click any part of the header bar To sort the peaks according to peak number ppm value or intensity click the header of the respective entry Note that when you delete peaks from the peak list they are automatically re moved from the corresponding file You cannot undo a delete action Peaks are only available if peak picking has been done command pp The peak list can be printed with print Ctr1 p List items can be selected with the mouse copied with Ctr1 c and pasted to other applications e g a text editor 1D Display 115 How to Display the Integral list 0s Click the Integrals tab 1i lipp lippf exam1d_1H 1 1 Cobo guest 1 Spectrum ProcPars AcquPars Title PulsProg Peaks lritegrals Sample qj jral rel Peaks
210. osite commands 88 processing parameters 79 80 parameters 1D 107 parameters 2D 140 Processing Guide 23 88 Processing menu 23 29 Processing Reference Manual 20 39 procno 60 64 68 75 129 ProcPars tab 23 79 80 107 140 projections of a 2D spectrum 21 145 properties I 12 of a dataset 73 128 of a printer 96 prosol parameters 269 pseudo raw data 68 pulse program 19 24 52 109 display 110 parameters 84 108 269 PulsProg tab 109 Python programs 26 331 334 337 Q QUIT AU macro 91 QUITMSG AU macro 91 R re command 20 64 176 read color scheme 318 data formats 65 integrals from disk 167 the prosol parameters 269 window layout 218 reb command 19 65 re enable disabled commands 326 reference peak in 1D calibration 174 in 1D phase correction 162 163 in 2D calibration 207 in 2D phase correction 197 referencing 87 reg file 173 relaxation curve 235 remote connections 313 remote control 307 remove commands 324 data from multiple display 178 datasets from the portfolio 54 menus 324 toolbar buttons 324 top level directory from the browser 53 reopen a dataset 102 reopen command 58 102 rep command 20 64 replace the current portfolio 74 repw command 64 rescale 2D projection 146 data in multiple windows 103 reset 1D baseline correction 185 1D phase values 163 3D cube size and orientation 158 default find criteria 72 F1 zoom factor in 2D 137 F2 and F1 zoom factor 137 F2 zoom factor in 2D 137 inte
211. ow to Create a New Dataset 1 Click File New new Ctrl1 n or Click the button in the upper toolbar 2 Specify the dataset name expno procno dir and user in the appearing dia log box If one or more datasets are open the fields are initialized with the current dataset see Fig 4 8 Dataset Handling 57 3 Click the down arrow of the Solvent box and choose a solvent from the list or type a solvent name 4 Click the down arrow of the Experiment box and choose a parameter set from the list or type a parameter set name 5 Type the dataset title in the TITLE box 6 Click OK Prepare for a new experiment by creating a new data set and initializing ts WR parameters according to the selected experiment type exam d_i H EXPNO PROCNO l DIR USER solver koci Experiment Lise current params bat TITLE Proton AV 300 Automation Cyclosporin CK Cancel Help Figure 4 8 A dataset will be created and initialized with the parameters of the chosen exper iment No fid or spectrum are available yet They can be created by data acquisi tion and data processing respectively 4 3 Opening Data TOPSPIN allows you to open data in several ways from the browser the menu the 58 Dataset Handling Explorer or the command line Furthermore data can be opened e in an existing data window replacing the current dataset e inadata window which is in multiple di
212. owing button Hj to save execute and return This will perform the following tasks e Execute phase correction e Save the current phase correction values e Leave the multi 1D phase mode Click the following button to return to the 2D phase display without save How to Return from 2D Phase Mode Click the following button aA Return 12 2 2D Multiple Display and Row Column Handling 2D multiple display shows a 2D spectrum with an arbitrary number of 1D and or 2D spectra superimposed Spectra are ppm aligned or Hz aligned according to the selected axis unit A superimposed 1D spectrum is automatically displayed in the direction of the matching nucleus for a hetero nuclear 2D or in the F2 direction for a homo 2D Interactive Manipulation 201 nuclear 2D Although multiple display is normally used for spectra with matching nuclei it allows you to superimposed spectra with non matching nuclei You will get a warning that the nuclei do not match Just just click OK to continue How Switch to Multiple Display mode and Read Multiple Spectra Switching to multiple display and reading multiple spectra can be done in two different ways e Read a 2D dataset and click to switch to multiple display mode Then add 1D and or 2D spectra e g from the browser or with re Or e Select multiple spectra in the browser right click one of them and click Display For a more detailed description of reading multiple data in m
213. own of a multi level multiplet Designating a Level in Multi Level Multiplets A level of a multi level multiplet can be designated to connect with another mul tiplet To do that ns Right click in the multiplet and choose Designate Multiplet The designated level is displayed in the color of the fourth spectrum default pur ple Note that the selected level can be different from the designated level 14 5 7 Define Multiplet Identifiers To define multiplet identifiers 1 Left click the multiplet 2 Right click the multiple and select Define Multiplet Identifier in the popup menu 3 Specify the multiplet identifier in the appearing dialog and click OK Alternatively multiplet identifiers can be defined by clicking the P button and double clicking the respective multiplet lines in the appearing Report dialog This will open the Identifier dialog see Fig 14 16 Just fill out the field Identifier and click OK Analysis 249 A Define Multiplet Identifier And Connection Number 1 Identifier CHS Cancel J Hz T 0801 Disconnect Displ homo nuclear hetero nuclear Connection 465270 OH 6 9987 amp CH 46210 CH J Hz ID Hetero List Figure 14 16 Note that the dialog also offers a button to Disconnect the current multiplet and a field Connection that shows all possible connections using the follow ing flags amp the current connection a non existing connection a diff
214. p Print the current dataset Ctr1 p print Copy the data path of the active data window to the clipboard copy Paste the data path on the clipboard to the active data window paste d Switch to the last 2D dataset 2d 3d Switch to the last 3D dataset 3d For more information on dataset handling please refer to chapter 4 3 Buttons for interactive manipulation A AMO Tj The functions of the individual buttons are A Switch to phase correction mode J Switch to calibration mode wI Switch to baseline correction mode The TOPSPIN Interface 31 iL Switch to peak picking mode T Switch to integration mode itt Switch to multiple display mode q Switch to distance measurement mode For more information on interactive manipulation refer to chapter 11 and 12 Buttons for display options bp EL The functions of the individual buttons are ha Toggle between Hz and ppm axis units Ei Switch the y axis display between abs rel off ult Switch the overview spectrum on off HH Toggle grid between fixed axis off For more information on display options please refer to chapter 8 5 and 9 5 How to Use the Lower Toolbar The lower toolbar contains buttons for display manipulations Buttons for vertical scaling intensity manipulation f2 4 fh gt Increase the intensity by a factor of 2 2 2 Decrease the intensity by a factor of 2 7 2 Increase the intensity by a factor of 8 8 8 Decrease th
215. pecification consists of the five variable parts of the data directory tree in this case C bio data guest nmr exam1d_1H 1 pdata 1 The text boxes are initialized with the dataset in the current data window How to Open Data from the Explorer Konqueror or Nautilus You can open a dataset from the Windows Explorer as follows 1 Open the Windows Explorer You can do that in two different ways rc from the Windows Start button Navigate to the data name expno or procno or r by entering the command exp1 in TOPSPIN The Explorer shows the con tents of the current dataset procno directory Navigate to the desired data name expno or procno exp1 can also be used with the argument top to open the TOPSPIN installation directory home to open user home di rectory or with an absolute pathname to open that directory 2 Now you can open a dataset with 64 Dataset Handling o gt drag amp drop click hold a dataset name or any of its sub folders or files and drag it into the TOPSPIN data area or data window or c copy amp paste right click a dataset and choose copy from the popup menu In TOPSPIN click Edit gt Paste paste see Fig 4 16 Edit View Spectromete Copy Find data Ctrl F Figure 4 16 Likewise a dataset can be opened from the Windows Search window or Internet Browser How to Open Data from the Command Line To open a dataset from the command line 1 Enter re 2 Specify a dataset in the app
216. play 1 Select the dataset s you want to remove 2 Click the following button 1D Interactive Manipulation 179 it Remove selected data from the screen Note that the data on disk are not affected Furthermore the first spectrum cannot be removed from the screen How to Display the Sum or Difference Spectra r Click one of the following button button turns green A Show the difference between the first and the sum of the other datasets Show the sum of all datasets in the multiple display window How to Save the Sum or Difference Spectra 1 Click the following button F Save the displayed sum or difference spectrum 2 In the appearing dialog box specify the destination procno How to Display the Next Previous Name Expno To compare a series of spectra you can interactively increment or decrement the dataset name or expno A dataset name is incremented according to the ICON NMR naming convention of increasing extensions e g name 001 name 002 etc r Click one of the following button button turns green E Show the previous name expno E Show the previous name expno Ei Set the increment options Clicking this button will open the following dialog 180 1D Interactive Manipulation 0 x Data set increment options Increment O Expno Name Expno increment fi Preserve individual scaling we Here you can choose to increment the expno or name set the expno incre ment and switch ind
217. pling partners Note how ever that you can only simulate one observable nucleus site at a time if you define dipolar coupling nuclei NUCLEUS Coupling nucleus partner Spin Nucleus dependent Spin Read only D dip Dipolar coupling constant Angle2 Euler angle of dipolar coupling vector Angle3 Euler angle of dipolar coupling vector Note that Dipolar couplings are invariant to the first Euler angle rotation around the Z axis so this angle value cannot be set Analysis 235 The Simplex algorithm The Simplex iteration minimizes the least square difference of the experimental spectrum and the superimposed simulated spectra between FIP and F2P The Best overlap value is determined as described below Calculate the area between the curves of the experimental and the calculated spectra A dif Sum Abs Yexp i Ycalc i Calculate the area of the experimental spectrum A exp Sum Abs Yexp i Compare these to area values Overlap 100 1 A dif A exp Overlap 100 if A dif 0 This is the theoretical maximum of the signal overlap Overlap 0 if the calculated spectrum is similar to the experimental one with same area but they do not overlap Overlap gt 0 but lt 100 Partial overlap Overlap gt 70 90 good agreement Overlap lt 0 No agreement Change the initial parameters and start a new sim ulation 14 4 Relaxation Analysis Typically relaxation data c
218. pulations 31 mode of the lock window 263 molecule structure 122 options 31 options 1D 124 peaks 20 planes of 3D data 155 156 positive negative 2D levels 153 processing status parameters 1D 108 projections 21 rows in 2D phase correction 194 settings 30 special data formats 65 spectra 19 spectrum overview in 2D 144 status parameters 81 84 sum difference spectrum 179 superimposed 1D spectra 175 superimposed 2D spectra 200 y axis 31 125 zipped data 23 display properties 21 distance measurement 1D 221 2D 208 mode 31 DORR parameter 228 double rotation experiments 228 double headed arrow 212 222 Down Arrow key 33 37 dpa command 108 dpp command 81 84 108 drag amp drop data 64 66 E eda command 82 83 108 140 edasp command 85 edau command 25 91 303 304 330 edcpul command 109 edit AU program 304 commands 34 contour levels 149 integral ranges 168 pulse program 109 signal noise regions 223 title of a dataset 109 Edit menu 29 edlev command 134 149 edlock command 85 edmac command 25 330 edp command 23 79 80 107 140 edprosol command 84 edpy command 26 331 edti command 109 ef command 88 90 efp command 88 271 em command 23 87 email data 24 empty data window 59 enable disabled commands 326 menus commands 323 Enter key 37 60 equidistant sequence of levels 149 Esc key 33 Euler angle 234 execute AU program 303 304 macro 25 330 Python program 26 exit command 36 42 expand a data directory
219. pulldown menu shown in Fig 15 2 Spectrometer Processing Analy Data Acquisition Guide Basichselective Experiments ICOR NMR Adjustments Acquisition Setup sample Shim control Tr Y F F F F F F Accessories Shape Tool stdisp Acquisition Status Bar Onlott Figure 15 2 Here you find several cathegories of acquisition related commands Each entry give access to a submenu with various commands Fig 15 3 for example shows the Setup submenu 258 Acquisition Hardware Configuration ct Experiment Installation expinstall Parameter set conversion paracon Probe table setup edhead Solvent dependent parameter setup edprosol Lock parameter setup edlock Nuclei table setup ednuc Solvent table setup edsoaly Amplifier linearization setup cortab Convert gradient field maps convfieldmaps Figure 15 3 For most entries the command line command for example expinstal1l1 is specified in square brackets Furthermore Topspin can be configured command set such that right clicking any menu entry will display the corresponding com mand line command For convenience common acquisition commands can also be started from the TOP SPIN toolbar The right part of the upper toolbar shows the following buttons Pe Oly Tl e Start the acquisition Acquires NS scans in the current dataset overwriting possibly existing data Equivalent to the command zg mg Halt the acquisition This stops
220. rage Power Level calcpav The result is the percentage of the average power of a square pulse of the same length How to Integrate Classical Shapes To calculate the power level required for a classical shaped pulse tS Click Analysis Integrate Shape integr3 Gauss integra f10610 0 Length of pulse usec fi o0 0 Total rotation degree z s g0 deg hard pulse usec Results 0 4116 integ Ratio comp to square on res 7 7110 Corresponding difference dB 49 2615 Change of power level dB Update parameters Figure 15 23 Fig 15 23 shows the parameter section where you can enter the length of the soft pulse the flip angle and the length of the 90 hard pulse Soft pulse and hard pulse length are initialized with the values of the corresponding parameters of the associated dataset If these values are zero or if no dataset is associated de fault values are taken a 10000 us soft pulse and 50 us hard pulse The result for a Gaussian shape with 1000 points and 1 truncation 1s shown The Integral ratio and the Corresponding difference in dB are calculated from shape amplitude and phase assuming equal pulse length and flip angle for soft Acquisition 283 and hard pulse The Change in power level however is calculated from the specified pulse lengths and rotation Clicking the Update Parameters button saves the length of the shaped pulse and the change in required power level to the corresponding parameters of t
221. rs Title PulsProg Peaks Integrals Sample ad 4 Object 7 Integral integral 2 Hintegral 3 integral 4 integral 5 integral abs 21786348 44 20849330 75 45796921 97 131363188 00 204r 3381 47 tHntegral 6 1068216295 19 integral rel 1 6650 1 5934 3 5000 10 0393 1 5647 61 6376 J2 D D O Figure 7 2 How to Print the Peak list 1 Click the Peaks tab of the data window see Fig 7 3 2 Enter print or Ctrl p examid_ 1H 1 1 Chio guest D n Se WwW he F260 3 016 3 321 3 178 3 0649 3 035 P26 6 03 6 36 BPS 5 96 6 41 Figure 7 3 Range F1 from Range F1 to TOF r 4100 r056 4 491 3 979 0 304 0 603 Ford r405 6 158 4 464 3 977 Printing Exporting Data 99 7 2 Exporting Data How to Copy data to Other Applications Under MS Windows you can easily copy the data window contents to other ap plications To do that us Click Edit Copy copy This will copy the data window contents to e the clipboard After that you can paste the clipboard contents to any Win dows application e the Windows Metafile file screenDump wmf in the user properties directory enter hist to locate this directory The Windows Metafile can be imported by other applications or send to a different computer Please note Some programs when importing spectra from the clipboard or metafile do not display the contained information correctly Particularly when you resi
222. s gt Increase the intensity decrease the levels by 2 2 f Increase the intensity decrease the levels by 8 8 2 Decrease the intensity increase the levels by 2 7 2 8 Decrease the intensity increase the levels by 8 78 Reset the intensity to the last saved intensity contour levels vr Alternatively you can enter the corresponding commands as specified between square brackets To manipulate all data windows press the Ctrl key while clicking one of the above buttons How to Switch on off Square 2D layout Right click inside the data field and click Square Layout On Off 136 2D Display exam2d_HC 1 1 C ibio guest l ojx Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid ch ch qm LL o co o a qm 8 6 F2 ppm Figure 9 2 The F2 scaling will be adjusted to reach a square display How to Zoom a 2D spectrum in out r Click one of the following buttons i Zoom in zi Zoom out zo El Perform an exact zoom via a dialog box zx EJexactzoom ed Please enter the exact coordinates of the desired expansion F1 ppm f af ioe E 2169 CK Cancel a Enter the coordinates of the desired region in the dialog box 2D Display 137 b Click OK 1 Retrieve previous zoom z1 HH Reset F2 direction zooming to full spectrum 2r Reset F1 direction zooming to full spe
223. s To give system administrators control over this traffic e g for firewall configuration default port numbers can be configured by entries in the file lt tshome gt prog server corba conf This file contains one line for each object and looks like this ConfigurationServer 5500 CPR 5500 CPRCallback 5501 NMRDataServer 5505 310 Remote Control FidDataServer 5510 GSServer 5511 BsmsServer 5512 EdacbServer 5513 EdteServer 5514 LockDataServer 5515 For the component NMRDataServer several instances could be active which then automatically use increasing port numbers 5505 5506 5507 The ports used for remote connection are derived by adding 100 to these numbers That means to enable remote control over a firewall secured connection the ports 5600 5615 must be opened on the firewall for the local system 17 4 How to Make a Remote Connection without a Local License TOPSPIN requires a license to operate on your local computer However you can make a remote connection without a local license To do this you have to start TOPSPIN as follows 1 Open a Windows Command Prompt or Linux Shell 2 Go to the TOPSPIN installation directory 3 Enter topspin client 4 TOPSPIN will start up and show an empty data field but no browser Before startup you will get the error message The program failed to com municate with local Just click OK to continue 5 Click Options Remote connection and establish
224. s number of dipolar coupling nuclei TRIANG number of triangles involved in powder spectrum simulation with several random oriented crystallites The default value of 32 gener ally results in a good quality spectrum MAXITER maximum number of iterations SSIZE initial step size for the iterated parameters The value represents the fraction of the initial parameter value It ranges from 0 0 to 1 0 with a default of 0 1 The values of NUCs and DIPs will automatically be updated when you add or delete nuclei from the Nucleus and Dip Interaction panels Spectrum parameters Spel TOPSPIN 1 3 supports only one experimental spectrum to be fitted Models Available fitting models are Gauss Lorentz CSA QUAD central QUAD all Analysis 233 and QUAD amp CSA Experimental Spectrum Shows the datapath variables of the experimental spectrum Parameters The following parameters are available MASR rotation speed of the single axis MAS VAS experiments or DOR outer axis speed DORR inner rotation speed in DOR experiment Angle and AngleInt the outer and inner rotation angles SBands and DORBands number of calculated side bands F1 and F2 the left and right edge of the experimental spectrum F1P and F2P the limits of the region to be fitted These must be within the F1 F2 range To define FIP and F2P interactively expand the spectrum and right click in the data window choosing Define Fit ting Region Usi
225. s are only shown if peak picking and integration have been performed respectively see also chapter 11 1 8 How to Display Projections 1D Spectra with 2D Spectra To display projections or 1D spectra in tandem with a 2D spectrum 1 Open a 2D spectrum 2 If no projections are shown click the 3 button in the upper toolbar or enter pr on the command line 3 Move the cursor into the F1 or F2 projection area 4 Right click and choose one of the options With External Projection an existing 1D spectrum can be read This can be a regular 1D spectrum or a 2D projection that was stored as a 1D spectrum With Internal Projection the positive projection can be calculated and displayed An alternate way to calculate projections is the following 0s Click Processing Display Projections projd 1 9 How to Superimpose Spectra in Multiple Display TOPSPIN allows you to compare multiple spectra in Multiple Display mode To enter this mode click the i button in the upper toolbar or enter md on the com mand line When you open a dataset now for example drag one from the browser it will be superimposed on the current spectrum rather than replacing it Several multiple display functions are available now in the data window toolbar Most importantly you can scale and shift each spectrum individually This allows exact alignment of corresponding peaks of different spectra Multiple display mode is supported for 1D and 2D spectra In 2D
226. s piu qo 2 phol 30m mc 0 to FOled exit 110 1D Display This allows you to edit the current pulse program The following extra buttons are available here F Save the pulse program under its current name E Save the pulse program under a new name 7 Reload the pulse program Undo modifications since the last save amp Switch to status pulse program E Show the pulse program in an external editor Tl Start the graphical pulse program display nmrs im How to Display the Peak list Click the Peaks tab examid_1H 1 1 Cobia guest O x Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample Structure Fid wo F1 pp Intensity 6 706 0 64 Figure 8 3 This displays the peak list By default the peak list shows the following entries Peak the peak number v F1 ppm the chemical shift Intensity the peak intensity Display the spectral region around a peak r Right click the desired peak this will open the popup menu shown in Fig 8 4 1D Display 111 Show spectrum Delete In correlated window Remove Show detailed information Copy Export impart Table properties Figure 8 4 Here you can choose from the following options tS Show spectrum In correlated window to open a new data window showing the full correlated spectrum us Expand spectrum In current window to change the current data window to spectrum display showing the
227. s such as JCAMP DX and ZIP E mailing data Processing 1D 3D fids and spectra window multiplication various trans forms Fourier Hilbert DOSY phase correction baseline correction inte gration peak picking linear prediction smoothing adding spectra etc Displaying multiple superimposed spectra 1D and 2D Simulating 1D and multi dimensional fids given a pulse program and a spin system virtual spectrometer nmr sim Calculating T1 T2 relaxation times Fitting peaks with Lorentzian and Gaussian line shape models deconvolve overlapping peaks Multiplet analysis Automatic 1D 2D and 3D peak picking Automatic 1D 2D and 3D integration Line shape analysis of solids spectra Data acquisition with Bruker Avance type spectrometers Supporting automated and walk up spectrometers ICON NMR Remote spectrometer control including web enabled ICON NMR Adding user defined functionalities to TOPSPIN AU programs Macros and Python programs Getting Started 17 Available Documentation Under the TOPSPIN Help menu you will find the following documentation e Avance Beginners Guide Step by step 1D HR experiments e Users guide User Interface Display Interactive functions e Control and Function keys Control and Function keys in TOPSPIN and Plot Editor e Pulse Program Catalog graphics representation of Bruker pulse programs e Command Index alphabetical list of commands with execute search help and macro options
228. scale the amplitude of a shape to a specified percentage 0s Click Manipulate Scale Amplitude scale and enter the desired scaling factor percentage How to Add Constant Phase To add a constant phase to the shape us Click Manipulate Add constant Phase addphase and enter the phase to be added How to Perform Time Reversal To time reverse a shape us Click Manipulate Time Reversal trev How to Expand Shape To expand a shape according to a specified phase list supercycle t Click Manipulate Expand Shape expand Acquisition 289 and selected a phase cycle The following standard phase cycles are offered mlev4 mlev16 p5 150 deg p5 330 deg p5m4 p5m16 p9 p9m16 p5p9 For example mlev4 has the following supercycle 0 0 180 180 In addition the entry YourOwn appears which allows you to define your own phase cycles These can be saved for later usage The specified file must have the extension expand It is stored in the directory lt user home gt topspin hostname shapetool 15 9 9 How to Set Shape Tool Options When the Shape Tool window is selected the upper three entries in the TOPSPIN Options menu concern the Shape Tool How to Change the Relation between Shape Tool and TOPSPIN parameters To define the relation between Shape Tool parameters and TOPSPIN acquisition parameters r Click Options Define Parameter Table 290 Acquisition A dialog box will appear with
229. servable nuclei 1 e 25 sites of a nucleus Ten other nuclei can be defined as dipolar coupling partners of the observed nucleus Topspin 1 3 allows only one observed nucleus site 1f you define heteronuclear dipolar cou plings Spectrum Preparation Before starting Solids Line Shape Analysis the 1D spectrum must be properly phase corrected and baseline corrected Switch to Line Shape Analysis Mode To switch to Solids Line Shape Analysis mode tS click Analysis Solids Lineshape Analysis solaguide This opens the workflow as shown in Fig 14 3 226 Analysis Solids Line Shape Analysis Guide e Define Model E Setup Sidebands he Define Fit Range Define Muctei Frint Export Setup Parameters Terminate Figure 14 3 Clicking Enter here will split the data window in two Experienced users can en ter this mode directly and skip the workflow with the command sola Analysis 221 lolx ae Le ke Ola IE ob E RAMa B y me gt Main Spectrum Nucleus Dip Interaction Log Parameters NUCLEUS jac oP Ih 0 PLP 972 EAPS i a HUTS E a DIFs O00 TRIANG eye MAAITER 500 0 500 ppm Figure 14 4 The right part of this window is the data window showing the 1D experimental and calculated spectrum The left part is the parameter window with five panels where the second one the Main panel is selected by default The simulation pro
230. sing Panel Close To 20 Tips Figure 19 2 To write this button panel take the following steps 1 Open the Windows Explorer and navigate to the subdirectory userdefined User Extensions 333 5 of the users properties directory 5 Create a text file with the name cmdpanel lt name gt prop where lt name gt is the name of the button panel Enter the button definitions including Panel title Colors Toggle buttons Top buttons Panel layout Panel buttons and Tooltips Save the file under a name cmdpanel_ lt xxx gt prop where lt xxx gt is the actual name of your command panel Make sure the extension of the file is prop and not txt prop txt or anything else Enter bpan lt xxx gt on the command line to open the button panel Here is an example for a small button panel for 1D processing Color definitions used in this file RGB BLUEI 515 2048 255 YELDOWL 255S 2555 0 GREEN1 84S 1965S 20 Title definition TITLE 1D Processing Panel TITLE COLOR 05 05 255 Toggle button definition TOGGLE BUTTON To 2D TOGGLE CMD bpan bproc2d TOGGLE TIP Switch to 2D processing Top row button definition TOP BUTTONS EMS SFTS SPKS TOP COLORS YELLOW1 YELLOW1LS YELLOW1 TOP CMDS emsS f t pk TOP TIPS Exponential multiplication Fourier transforms Phase correction 1 To locate this enter hist and look for the entry User properties directory 334 User Extensions
231. splay mode being superimposed on the current spectra e in anew data window which becomes the active window Note that if a dataset is already displayed in one window and it 1s opened in a sec ond existing window it still replaces the dataset in the latter one As a result the same dataset will be displayed in two windows see also command reopen How to Open Data Windows Cascaded By default a new data window appears maximized filling the entire data field and covering possibly existing window You can however configure TOPSPIN to open new windows cascaded This is convenient if you want to open several data win dows and then select one To open new windows cascaded 1 Click Options Preferences set 2 Click Window Setting in the left part of the dialog box The right part of the dialog box shows the window settings see Fig 4 9 a Oy new internal windows cascaded rather than maximized configure cascaded window m Figure 4 9 3 Check Open new internal windows cascaded rather than max 4 Optionally you can configure the cascaded windows by clicking the respec tive Change button This will open the dialog box shown in Fig 4 10 Dataset Handling 59 e E Define the properties of cascaded windows All numbers must be in the range 0 1 They are the fractions of the maximum windows sizes In the respective dimension Width of window Height of window offset to previous window
232. ssed data and are used for further processing display or plotting Changing them can make the dataset inconsistent In rare cases however it can be useful to change a status parameter and TOPSPIN allows you to do that from the command line If for instance you want to change the F1 status parameter MC2 of a 2D dataset you have to enter 82 Parameter Handling smc2 Note that the command s is used for 1D 2D and 3D dataset TOPSPIN automati cally recognizes the dimensionality of the data and displays the parameter in all relevant dimensions Note that for example the parameter MC2 only exists in F1 5 2 Acquisition Parameters How to Set Acquisition Parameters Acquisition parameters can be set changed as follows e from the parameter editor click the AcquPars tab or enter eda e from the command line e g enter td e from the interactive parameter adjustment window enter gs How to Set an Acquisition Parameter from the Command Line Enter the parameter name on the command line For example to set the time do main size 1 Enter td for 1D data the following dialog box will appear x Size of fid TD e5536 JRK Cancel for 2D data the following dialog box will appear TT x Size of fid F2 F1 TD fi 024 256 JRK Cancel Parameter Handling 83 2 Specify the desired value s e g 65536 or 64k 3 Click OK How to Set Acquisition Parameters from the Parameter Editor To open the
233. ssing Guide 23 88 automation 25 26 303 autoplot command 90 96 autostart prop file 314 Avance spectrometers 16 301 axis units 31 124 144 175 207 B background of a data window 318 Backspace key 33 backward peak picking 190 baseline correction 1D 87 182 mode 30 182 bem command 185 bias correction 168 bio molecular experiments 26 bnmr command 332 bnmrsel command 332 bpan command 333 browser 27 28 36 49 59 font 321 in multiple display mode 177 202 Bruker AU programs 25 303 data format 19 23 24 62 65 66 74 example datasets 20 53 BSMS control panel 264 BSMS display window 218 bsmsdisp command 264 C calibration 87 1D interactive 173 2D interactive 206 mode 30 173 206 cf command 18 43 299 300 301 chemical shift 180 chemical shift distance 1D 221 2D 208 CHEMSTR parameter 122 C language 25 90 330 331 clevels file 151 clipboard 22 36 close active data window 217 lock display window 263 264 the active data window 36 wobble window 262 close button 29 close command 36 cmdhist command 34 cmdindex command 40 cmdtab_user prop file 41 collapse a data directory 49 52 color scheme 318 colors of data objects 317 of the lock display 317 on the printer 317 command audit 76 definition 41 dialog box 79 help 39 index 40 interpreter 309 line 33 34 322 command line commands 258 focus 33 36 font 322 history 33 34 preferences 322 resize 323 usage 33 Command Prompt 18
234. t 1 Open the file cmdtab user prop located in the subdirectory userde fined of the user properties directory to locate this directory enter hist and look for the entry User properties directory The file cmdtab user prop is initially empty and can be filled with your own command definitions 2 Insert e g the following lines into the file _f3 sem JE 2CErIL CEE _f3alt Spk ie Soha Le JESCtrl Sreb _f5alt popt 3 Restart TOPSPIN Now when you hit the F3 key the command em will be executed In the same way Ctrl F3 Alt F3 F5 Ctr1 F5 and Alt F5 will execute the com mands ft pk halt reb and popt respectively You can assign any com mand macro AU program or Python program to any function keys Only the keys Alt F4 F6 Ctr1 F6 and Alt F6 are currently fixed Their function cannot be changed 2 8 How to Open Multiple TOPSPIN Interfaces TOPSPIN allows you to open multiple User Interfaces This is for example useful to run an acquisition in one interface and process data in another To open an addi tion interface enter the command newtop on the command line or click Window New Topspin To open yet another interface enter newtop in the first or in the second interface The display in each interface is completely independent from the others As such you can display different datasets or different aspects of the same dataset e g raw processed regions scalings etc When the dataset is re processed in
235. t efp py gt NEWWIN open new window re examld 1H 1 1 C bio guest efp py gt x INPUT DIALOG py gt if x None EXIT py gt y 2 1int x 0 py gt MSG done y str y Note that commands like NEWWIN INPUT_DIALOG MSG and EXIT are Bruker defined whereas x and i are original Python commands Once created a macro can be executed by entering its name on the command line AU Programs An AU program may contain TOPSPIN commands AU macros and C language statements It can be created with the command edau A simple AU program which performs the e fp command on a series of dataset expno s is include lt lib util h gt User Extensions 331 int first max char string 80 first expno GETINT Enter first expno to process first max 10 GETINT Enter number of expnos max WPAR tmpmefp proc expno first TIMES max RPAR tmpmefp proc EFP IEXPNO END DEXPNO DELPAR tmpmefp QUITMSG multiefp finished Note that TOPSPIN commands like EFP and RPAR and AU macros like IEXPNO are written in upper case letters whereas C language statements like are written in lowercase letters Once created an AU program can be executed by entering its name on the command line For more information on writing AU programs t Click Help Programming AU programming 19 4 Python Programs A Python program may contain TOPSPIN commands User Interface fun
236. t data window Note that if the search result consist of only one dataset this is automatically se lected and you can skip step 1 How to Select Data from the Found Datasets In the search result window see Fig 4 23 74 Dataset Handling 0S Hold the Ctr1 key and left click several datasets to select these datasets Or 0S Hold the Shift key and left click two datasets to select these datasets and all datasets in between Or c Click Select all to select all datasets in the search result How to Add Selected Datasets to the Portfolio 1 Select the desired dataset s as described above 2 To add them to the portfolio t Click Add to portfolio to extend the current portfolio Or us Click Replace portfolio to replace the current portfolio How to Save Selected Datasets to a List 1 Select the desired dataset s as described above 2 Click Save selection 3 In the appearing browser a Navigate to the desired list directory b Enter or select the list filename c Click OK Dataset lists can be used by the acquisition or by serial processing command serial 4 7 Handling Data Files How to List Open the Current Dataset Files A Bruker dataset is represented by a directory tree which contains files in the ex pno and procno subdirectories These files contain the actual data parameters lists etc Dataset Handling 75 ns Right click inside the data window and choose Files from the popup menu Disp
237. te arg we 208 Chapter 13 Data Window Handling ccc ccc ccc cccccccccees 211 RonF Data Wind Ow Sina ota sesettes dae rete Bete Sake tte woh a ar ae ae 211 How to Move a Data Window 0 0 0 0 cece ee ees 212 How to Resize a Data Window 0 00 0 ccc eens 212 How to Select activate a Data Window 0005 213 How to Open a New empty Data Window 0005 214 How to Arrange Data Windows 0 0c cece eee eens 214 How to Iconify minimize a Data Window 00000 216 How to De iconify a Data Window 000 cece eens 217 How to Maximize a Data Window 0 00 00 cece eee 217 How to Restore the Size and Position of a Data Window 217 How to Close a Data Window 0 cc eee ee eee eee nas 217 Chapter 14 Chapter 15 Chapter 16 How to Iconify all Data Windows 0 0 0 eee ee eee 218 How to Maximize all Data Windows 00 02 ee eee 218 How to Activate the Next Data Window 00 0c 218 3 2 Window layouts 60 02 due denis ose wae RN eae Le Re ES wae Sok 218 How to Save the Current Window Layout 4 218 How to Read a Window Layout 0 0 0 cece eee es 218 How to Swap Data Windows 00 ccc cee eee eens 219 RMA YSIS aeo tere Sarg era orgnangree aoe Oe fe AASE REA 221 14 1 1D Chemical Shift Distance Measurement 221 How
238. the acquisition after the current scan has fin ished All data acquired so far are saved Equivalent to the command halt Stop the acquisition This stops the acquisition immediately Data acquired after the last disk write if any are lost Equivalent to the command stop Open the online FID display window Shows the currently acquired FID Only works during acquisition Equivalent to the command acqu F Open the Lock display window Shows the lock signal Equivalent to the command lockdisp z Calculate the experiment time Shows the total experiment time and file size of the raw data Equivalent to the command expt Acquisition 259 4 Set SFO1 O1 O2 and O3 interactively Puts a red cursor line in the data win dow A left click at the desired frequency opens a dialog box where you can set O1 O2 and or O3 Set the sweep width to the current region and the spectrometer frequency to the center of the current region Update the parameters SW and SFO1 respectively fl Setup a frequency list interactively 15 3 Acquisition Status Bar The acquisition can be followed and controlled from the acquisition status bar Before you use the acquisition status bar it must be configured from the User Pref erences window To do that 1 Click Options Preferences set 2 Click Acquisition status bar in the left part of the User preferences box This will show the status bar items see Fig 15 4 Acquistion sta
239. the data window you the Display Properties dialog box can also be opened from the View menu 1D Display 127 How to Superimpose the Cursor Information To superimpose the cursor information on the spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Cursor information in the appearing dialog box and click OK How to Superimpose the Title on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Title in the appearing dialog box and click OK How to Superimpose the main Status Parameters on the Spectrum l 1 Right click in the data window and choose Display Properties dopt 2 Check Status parameters in the appearing dialog box and click OK How to Superimpose the Integral Trails Labels on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Integrals and if desired Integral labels in the appearing dialog box 3 Click OK If no integrals appear the integral regions have not been determined yet This can be done with the int command How to Superimpose Peak Labels on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Peak list in the appearing dialog box and click OK If no peak labels appear peak picking has not been done yet This can be done with the pp command How to Show Individual Data Points of the Spectrum 1 Right click in the data window
240. the dataset The table can easily be modified or extended with the following func tions To select an item double click it F Save the sample information table with the dataset E Save the sample information table as default w Reload the original table discarding any changes Add a new item to the table You will be prompted for an identification name and the desired number of lines 122 1D Display Remove the selected item from the table Move the selected item one place up in the table Move the selected item one place down in the table How to Open the Jmol Molecule Structure Viewer n Click the Structure tab jmo1 exam id_13C 11 Cibo quest 41 Cibio guest EEE Spectrum ProcPars AcquPars Title PulsProg Peaks Integrais Sample Structure Fia File Edit Display View Measure Extras alm 8 amp ale a Select Atoms 0 Atoms Selected pO Figure 8 10 opens the Jmol molecule structure viewer TOPSPIN 1 3 contains Jmol version 10 This has the following features The viewer displays the structure file that resides in the expno of the current dataset If this does not exist the structure file defined by the acquisition parameter CHEMSTR is displayed CHEMSTR can define a full pathname or a filename In the latter case the file is searched for in the directory defined in the User Preferences To set this directory click Options Pref erences select
241. the right of the object Change spectral window color scheme and select an element from the appearing list 4 Click OK TOPSPIN is delivered with two colors schemes e light default a white background with black axes e dark a dark blue background with a white axes User Preferences 319 18 3 Changing Fonts How to Change All Fonts of the Topspin Interface 1 Click Options Preferences set 2 Click Fonts Dialogs Icons in the left part of the dialog box 3 Set the entry Change size fonts listed above by points You can enter a positive or negative number Fig 18 2 shows an example of increasing the font sizes by 4 points Fonts Dialogs flcons Menu font Dialog plains Plain 16 Change Dialog window tont Dialog plains Plain 12 Change Command line font Dialog plains Plain 16 Change Status line font Dialog plains Plain 16 Change Printer font Dialoglnputplain ss Plains 100 Change Change size of fonts listed above by points 4 Figure 18 2 4 Click OK to store the new value Fonts Dialogs flcons lenu font Dialog plain Plain 20 Change Dialog window font Dialog plain Plain 16 Change command line font Dialog plain Plain 20 Change Status line fant Dialog plain Plain 20 Change Printer font Dialodlnputplain Plain 10 Change Change size of fonts listed above by points J Figure 18 3 Fig 18 3 shows the same part of the Preferences dialog box dialog bo
242. the selected integral regions from the display r Click the following button amp 4 Delete selected integral regions from the display To delete a single integral region from the display 1 Right click in the integral region 2 Choose Delete from the popup menu see Fig 11 5 To delete all integral regions from the display r Click the following buttons 1D Interactive Manipulation 171 Select all integral regions 4 Delete selected integral regions from the display Note that regions are only deleted from the screen Regions which are saved on disk in the int rng file are not affected How to Scale Selected Integrals Integral scaling only manipulates selected integrals However if no integrals are selected it works on all integrals r Click one of the following buttons gt Scale up selected integrals by a factor of 2 f2 Scale down selected integrals by a factor of 2 Scale selected integrals up down smoothly To scale up down integrals by a factor entered via a dialog 1 Click the following button Scale integrals via a dialog 2 Enter a scaling factor e g 2 5 in the appearing dialog Falscale es Scale selected integrals scaling Factor b s000 CK Cancel 3 Click OK to apply this factor To scale all integrals to the same height r Click the following button Scale unscale all integrals to the same height The individual scaling factor for each region 1s displayed above
243. they also show TOPSPIN system processes Note that killing such processes may kill TOPSPIN 3 4 What to do if TOPSPIN hangs If for some reason TOPSPIN hangs please do the following Under Linux 1 Open a Shell 2 Enter lt tshome gt prog bin script killtopspin where lt tshome gt is the TOPSPIN installation directory Under Windows 1 Click Start Programs gt Bruker TOPSPIN TOPSPIN 1 3 Bruker Utilities 1 3 2 In the appearing window 48 Trouble Shooting Click killtopspin Normally this kill all TOPSPIN processes including cpr cprserver dataserver and Java 3 5 How to Restart User Interface during Acquisition If Topspin hangs up during a data acquisition you can restart the user interface without disturbing the acquisition To do that 1 An amp WW Open the file lt tshome gt prog curdir lt user gt history where lt tshome gt is the TOPSPIN home directory and lt user gt is the user who started TOPSPIN Look for the term Java Virtual Machine and check its PID Open the Task Manager Windows or System Monitor Linux Stop the Java w exe process with the PID found in the history file Open a Windows Command Prompt or Linux Shell Go to the TOPSPIN Installation directory Enter topspin client Chapter 4 Dataset Handling 4 1 The Topspin Browser and Portfolio TOPSPIN offers a data browser portfolio from which you can browse select and open data Furth
244. thon edpy is executed for Script type macro edmac is executed The name of a se rial script macro of Python must start with ser_ Python scripts must have the extension py A standard example is the python script ser _efp py 94 Data Processing An example of a simple processing sequence is exponential window multiplica tion Fourier transform and automatic phase correction of a 1D dataset A TOPSPIN macro performing this task would be ef apk A Python programs performing the same task would be EF APK Note that Python programs are much more versatile than macros Details on Python programming can be found under Help Programming Python programming Note that serial processing can also be started as follows e Click Processing Serial Processing or e Click File gt Run select Execute Serial script on Data set list and click OK Chapter 7 Printing Exporting Data 7 1 Printing plotting Data How to Print Plot from the Menu The current data window can be printed as follows 1 From the TOPSPIN menu t Click the button amp in the upper toolbar or Click File Print or Enter print or Ctrl p All these actions are equivalent they open the Print dialog box see Fig 7 1 96 Printing Exporting Data Print Ctrl P plot f ad Options Print active window prnt Print weith layout start Plot Editor plot Print with layout plot directly autoplot
245. tion halt Close the FID window Clicking the j button to switch to real time FT turns the button green and Acquisition pe opens two extra buttons ki Switch between FID and spectrum m x Real time FT settings i Toggle calculation of peak with at 50 5 5 and 1 1 height Shown as status parameters Clicking the button opens the following dialog window EA Configure realtime ft q x Set options for realtime f Window function Fhase correction mode mE Baseline correction mode guad OK Cancel The acquisition information will appear in the acquisition status bar at the bottom of the TOPSPIN window for example Acquisition information Information Fid Flash Lock POVWWCRR TI residual time 3m30s x ae experiments 1 1 DARA 4 When the acquisition has finished r Enter efp to process the FID The processed spectrum will be displayed in the data window that was opened upon creating the dataset see Fig 15 14 22 Acquisition protona 1 1 Cbio1 guest oj x Spectrum ProcPars AcquPars Title PulsePrag Peaks Integrals Sample Structure Fid r 7 15 10 5 0 ppm Figure 15 14 From here the processed data can be analysed printed and or archived 15 9 Shape tool The Shape tool interface allows you to create manipulate RF shapes and gradients To start the Shape Tool interface us Click Spectrometer Shape Tool or enter stdisp
246. try it is selected and you can execute one of the commands from the popup menu see Fig 8 7 The keys Enter and Delete work on the selected entry active integral the entry on which cursor resides Integral in Fig 8 6 The active integral is also marked in the correlated spectrum by a black vertical line see lower part of Fig 8 6 and description below When you move the cursor over the integral list the vertical line in the correlated spectrum moves along with it and vice versa 1D Display 117 to open a new data window showing the full correlated spectrum t5 Expand spectrum In current window to change the current data window to spectrum display showing the re gion around the selected integral 0s Expand spectrum In correlated window to open a new data window showing the region around the selected inte gral lower part of Fig 8 6 Note that clicking the marked entry in the right click popup menu is equivalent to pressing of the Enter key Export Import Entries of the Integral List Entries of the integral list can easily be exported to Excel or any other program as follows 1 For multiple integrals Select the desired entries while pressing the Ctrl or Shift key 2 Right click an entry to open the popup menu see Fig 8 7 3 Click one of the following menu items e Copy Copy the selected integral s entry to the Clipboard Equivalent to clicking Edit gt Copy or hitting Ctr1 c Copied integrals can
247. try is marked with an X Now you can use the lt gt buttons at the upper right of the window to go to the previous or next entry respectively Add log files By default the procol txt history and dataserver log files are shown To include additional log files to the ptrace list click File Add specify the file and click Open Note that most log files are stored in the directory lt tshome gt prog curdir lt user gt Save the log messages To save log messages in a text file click File gt Save and specify the output text file 3 2 3 Create a Stack Trace If TOPSPIN hangs it can be useful to sent Bruker a stack trace about a possible cause You can create a stack trace as follows 1 Move the cursor into the TOPSPIN startup window 2 Under Windows hit Ctrl Break Ctrl1 Pause Under Linux hit Ctr1 Control backslash 3 Copy the appearing text into a text file Trouble Shooting 47 3 3 How to Show or Kill TOPSPIN processes To show the currently running TOPSPIN processes enter the command show or kill on the command line A list of processes will appear showing the process command dataset etc EA Active commands and processes x Command Details Sort modules Kill Close F Figure 3 2 Fig 3 2 shows a list with one process command xfb To kill a process select it in the list and click the button Kill The command show all or kill all work like show and kill except that
248. tting the value of a reference integral and adjusting all other integrals accordingly To do that 1 Right click in the reference integral region 2 Choose Calibrate from the popup menu see Fig 11 5 3 Enter the desired value for the reference integral and click OK Normalizing integrals means setting the sum of all integrals and adjusting indi vidual integral values accordingly To do that 1 Right click in the reference integral region 2 Choose Normalize from the popup menu see Fig 11 5 170 1D Interactive Manipulation 3 Enter the desired sum of all integrals and click OK Select Deselect Calibrate Moarmalize Lastscal Delete Figure 11 5 Calibrating and normalizing only effects the current dataset To scale integrals with respect to a reference dataset choose lastscal from the right click popup menu see below How to Scale Integrals with respect to Different Spectra Integrals can be scaled with respect to the last spectrum that was integrated inter actively To do that 1 Right click in the reference integral region 2 Choose Lastscal from the popup menu see Fig 11 5 As such you can compare integrals of different spectra Note that this only make sense for spectra which have been acquired under the same experimental condi tions The scaling factor is stored in the file lt tshome gt prog curdir lt user gt intscale How to Delete Integral Regions from the Display To delete
249. tus bar Auto open acquisition status bar Include time Include sample temperature Include acquisition status Include acquisition indicator Include lock signal Include MAS spinning rate qA lt 1 lt 1 lt 1 lt 1 41 Include peak power check POYWCHE indicator Figure 15 4 3 Check the desired entries To switch the acquisition status bar on tS Click Spectrometer Acquisition Status Bar On Off Or 260 Acquisition r Right click in the status line at the bottom of the TOPSPIN window and choose the popup menu Acquisition Status Bar On Off With the entries selected above the right part of the status bar will look like this AcCQuisition information Fid Flash Lock POVWWOHR WTU Time X Kelvin 03 57 0 acquisition running 9939 Dec 10 The acquisition status bar not only displays information it also allows you to per form various actions e g e Double click the Time field to view detailed time and date information e Double click the Lock field to open the lock display e Double click the Fid Flash field to open the wobble display e Right click the Fid Flash field to switch on off FID flashing e Right click the Acquisition information field to open the following popup menu show acquisition display Start rga Start acquisition Start wobble Start qs stop acquisition from this menu you can start various acquisition commands e Right click the VTU field to open the following popup menu
250. u Item and specify the Menu Item name and the corre sponding Command in the appearing dialog c Click Apply FA User Defined Menus x Menu Mame Menu tem Commangd Add Menu Add Menu term ii Up Down Apply Apply Close Cancel Figure 19 5 The new menu will appear in the menubar Furthermore the dialog box in Fig 19 5 contains the following buttons e Remove Remove menu names and or menu items e Apply Close Apply any changes and close the dialog box e Up Down Move up down the menu name list e Cancel Close the dialog box discarding any changes User defined menu definitions are stored in the file umbar_menubarld prop umbar menubar2d prop or umbar_menubar3d prop depending on the data dimensionality These files resides in the subdirectory userdef ined of the User Extensions 339 19 8 user properties directory To locate this directory enter the TOPSPIN command hist Adding User Defined Guides TOPSPIN offers several guides like the Acquisition Guide command aqguide the Processing Guide command prguide and the T1 T2 Guide command t1lguide You can set up your own guides which can be adaptations of Bruker guides or new written ones In order to do that you must edit the file toolbar user prop and cmdtab_user prop in the directory lt user properties directory gt userdefined To identify this directory enter the command hist in TOPSPIN The file toolbar user prop contains the gu
251. ultiple display mode see chapter 11 4 In multiple display mode the Tab bar of the active data window is replaced by a toolbar see Fig 12 7 Ol x PM exam2d_HC 1 1 Cobio guest H R wA Ees ts dy lut 24 tl Jiao Fi ppm 62 60 58 56 54 52 50 F2 ppm Figure 12 7 Multiple display with two 2D spectra superimposed 202 2D Interactive Manipulation x exam2d_HC 1 1 Cbio guest l l ol ELY R xA Biles ts d tjut a l a la 70 60 50 F1 ppm 6 5 6 0 5 5 5 0 F2 ppm Figure 12 8 Multiple display with a 1D spectrum superimposed on a 2D spectrum a The yellow button indicates that the data window is in multiple display mode Some buttons will turn green when they are clicked As long as a button is green it is active The browser portfolio in multiple display is split in two parts see Fig 12 9 The additional lower part shows e which datasets are displayed in the active data window e which datasets are selected they are highlighted I exam2d_CH 1 1 Cbio quest WW exam2d_H 1 1 C bio quest Figure 12 9 2D Interactive Manipulation 203 How to Align Multiple 2D Spectra 2D spectra in multiple display can be individually shifted To do that 1 Select one of the spectra in the lower part of the browser 2 Click hold the fs button and move the mouse Fig 12 10 shows a region of two comparable 1H 13C inverse 2D datasets which are shifted relative to each other Click
252. ursor over the interactive phase correction button you will see the following TEANS interactive phase correction ph The corresponding command line command in this case ph is indicated be tween square brackets Note that the tooltip also appears in the status bar at the bottom of the TOPSPIN window 40 The TOPSPIN Interface How to Get Help on Individual Commands To get help on an individual command for example ft cs Enter ft or r Enter help ft In both cases the HTML page with a description of the command will be opened Note that some commands open a dialog box with a Help button Clicking this button will show the same description as using the help command For example entering re and clicking the Help button in the appearing dialog box fejre si Please specify data set MAME examid_ 1H EXPNO PROCNO DIR lc ieg USER guest OK Cancel Browse Find Help opens the same HTML file as entering help re or re How to Use the Command Index To open the TOPSPIN command index rs Enter cmdindex or t Click Help gt Command Index From there you can click any command and jump to the corresponding help page The TOPSPIN Interface 4 2 7 User Defined Functions Keys The default assignment of functions keys is described in chapter 2 5 and in the document us Help Control and function keys You may assign your own commands to functions keys Here is an example of how to do tha
253. ution 24 lower toolbar 31 M macros in AU programs 90 331 in Topspin 25 41 88 330 334 337 magnitude calculation 88 managuide command 241 MASR parameter 228 matching the probehead 261 MAXI parameter 190 maximize all data windows 218 data window 217 the Topspin window 29 maximize button 29 maximum command line size 323 MC2 parameter 81 menu bar 29 commands 29 configuration table 325 326 entries 29 325 font 320 settings 313 MI parameter 190 minimize data window 216 minimize button 29 minimum command line size 323 Minus key 37 mixtures 25 molecule structure viewer 122 mouse sensitivity in 1D baseline correction 185 in 1D integration 169 in 1D phase correction 163 in 2D phase correction 199 move data window 212 Topspin window 29 Mozilla 76 130 multiple display 1D 31 175 201 1D 2D 21 60 65 2D 21 200 in deconvolution 24 multiple display mode 60 175 multiple window display 102 multiplet 166 237 multiplet analysis 241 multiply with increment in 2D levels 149 N nbook command 329 negative 2D levels 153 new command 30 36 56 268 I 10 newtop command 41 next channel for wobbling 262 command 37 dataset in Browser 37 parameter field 81 83 plane in 3D 157 row column in 2D phase correction 199 window in data area 36 214 218 NMR ADMINISTRATION password 299 NMR SUPERUSER 299 nmradminpassword file 299 nmrsim command 25 110 nmrsuperuser file 299 noise region 222 NOISF1 parameter 2
254. ver the internet This means you can control your spectrometer from your office desk or from your PC at home Using your local TOPSPIN interface you have access to the remote data directories and remotely running TOPSPIN commands Furthermore in TOPSPIN 1 3 and newer ICON NMR is web enabled which means it can be controlled from any web browser which is networked to the spectrometer Remote access is operating system independent 17 2 How to Establish a Remote Connection from your PC In order to establish a remote connection please do the following on the local PC 1 Click Options Preferences set 2 Click Miscellaneous in the left part of the dialog box 3 Click the Change button at the entry Setup remote systems e Server ID an arbitrary name which is just a mnemonic to easily identify the remote system 308 Remote Control e Hostname or address the hostname or IP address of the remote host e TCP IP port number the port number of the remote TOPSPIN The Server ID can be freely chosen whereas the hostname and TCP IP port number can be identified using the hist command Run hist on the re mote system and look for the line To connect to this Topspin use host port Before you can establish a remote connection you have to make sure the remote PC is open for remote access see chapter 17 6 Then do the following on the local PC 1 Click Options Remote connection 2 Select a Remote system from the appe
255. w AT t Click Analysis gt Calculate Bandwidth for Inversion bandw2i For the inversion band width the Mz magnetization is used How to Calculate Bandwidth for Refocusing To calculate the refocusing band width factor Aw AT 280 Acquisition w Click Analysis gt Calculate Bandwidth for Refocusing bandw2ry For the refocusing band width the My magnetization is used How to Calculate Special Bandwidths Further routines for the evaluation of various magnetization components are available under the menu item Special Bandwidth Calculations How to Calculate the Maximum RF Field Strength for Classical Pulses To calculate the RF field strength for classical pulses t Click Analysis gt Calculate gammaBlImax calcb1mo Fig 15 21 shows the resulting parameter section for a Gauss shape Gauss calcbima 1000 0 Length of pulse usec fi a0 0 Total rotation degree o o Offset Hz Results 474 45 Gammabl mai pl at 0 Hz fon res Hz 2675 2543 Corresp 90 deg square pulse usec Figure 15 21 The result consists the field strength yB1max 27 and the corresponding 90 square pulse length To obtain this result the integral of the shaped pulse is com pared to that of a square pulse of same length with the latter being normalized to 1 The maximum power is yB1 max 2r YB1 2m square pulse of same length integral ratio where YB 1 27 square pulse of same length 1 pulse length 360
256. w TOPSPIN command Just enter its name on the command line to execute it The command xmac shows a list of all available macros and allows you to exe cute one How to Create AU automation Programs Writing an AU program is another way of creating a new TOPSPIN command AU programs are more complex and more powerful then macros They are C lan guage programs which may contain C statements regular TOPSPIN commands and various predefined AU macros and functions AU programs can perform var ious tasks such as dataset handling parameter handling acquisition processing analysis and printing Note that AU programs do not support graphics related tasks TOPSPIN is delivered with a large set of Bruker AU programs for data processing and acquisition Just enter edau to see them listed in a dialog box The easiest way to create anew AU program is to select a Bruker AU program save it under Getting Started a new name and modify it to your needs The chosen name is now available as a new TOPSPIN command Alternatively you can open a new file from the AU dia log box and write your AU program from scratch For details on Bruker AU programs and writing your own AU programs click Help Programming AU Programming How to Create Python Programs Writing a Python program is yet another way of creating a new TOPSPIN com mand Python is a new generation scripting and object oriented programming lan guage Python programs are even
257. ween square brackets How to Shift a Spectral Region to the Left or to the Right r Click hold the following button and move the mouse Smoothly shift to left or right 106 1D Display or r Click one of the following buttons Shift to the left half of the displayed region s1 Shift to the right half of the displayed region sr W Shift to the extreme left showing the last data point s10 Shift to the extreme right showing the first data point sr 0 Alternatively you can enter the corresponding commands as specified between square brackets How to Shift the Spectrum Up or Down To shift the FID or spectrum display up or down r Click hold the button and move the mouse t Smoothly shift the spectrum baseline up down or r Click one of the following buttons Shift the spectrum baseline to the middle of the data field su 4 Shift the spectrum baseline to the bottom of the data field sd Alternatively you can enter the corresponding commands as specified between square brackets 8 4 Using the Tab bar Tabs of the data window can be activated by clicking them or by entering the cor responding commands as specified between square brackets on the command line Note that command line commands always work on the currently selected active data window The Tab bar can be configured from the User Preference box command set 1D Display 107 How to Display th
258. wever only peaks with the defined minimum intensity are used see Fig 14 18 The three methods are described here for the ethanol CH3 OH and CH2 group respectively You can use one of these methods depending on the type of spectrum and your own preference In this example the chosen methods for each group is arbitrary exam1d_ethanol 1 1 Csbio1 jos _ ex MIB t Hoan alla at Lb t XoalT Bam fe oI 3 5 3 0 25 2 0 15 ppm Figure 14 11 14 5 1 Define multiplet by region In this mode you simply define the region around the multiplet The multiplet is Analysis 243 automatically defined from the peaks within the region At least two peaks must exist in the region to be defined To define the multiplet 1 Click the button it turns green 2 Click hold the left mouse button on one side of the multiplet region drag the mouse and release it at the other side of the region The multiplet will be displayed 3 Click the fj button to leave region mode examid ethanol 1 1 Cobia guest oi Sm all alee a i Figure 14 12 In Fig 14 13 the triplet of the ethanol CH3 group is being defined The marked area shows the defined region 14 5 2 Define multiplet manually In this mode you can define a multiplet by assigning individual peaks No prior 244 Analysis peak picking is required If however peaks have been picked they are used examtd_ethanol 1 1 Cabio guest O x MIF HH aa al nla oat bk
259. x after the change of fonts Note that 320 User Preferences e The value all four font entries has been increased by 4 e The font of the dialog box itself is larger e The change size has been reset to 0 How to Change the Font of the TOPSPIN menu To change the font of the TOPSPIN menu 1 Click Options Preferences set 2 Click Fonts Dialogs Icons in the left part of the dialog box 3 Click the Change button to the right of the Menu font object Menu font dialog Plainf16 Change 4 Select the desired name style and or size in the appearing dialog box 5 Click OK to store the new font 6 Click Apply The default menu font is Dialog Plain 1 and looks like this File Edit View Spectrometer Processing After changing the font to for instance to Serif Italic 18 the menu looks like this File Edit View Spectrometer Processing A change in menu font also affects all sub menus and popup menus How to Change the Font of the Tab bar Click Options Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Click the Change button to the right of the Dialog window font object Select the desired name style and or size in the appearing dialog box Click OK to store the new font Click Apply Non Fk U N m User Preferences 321 Fig 18 4 and Fig 18 5 shows a Tab bar with font size 10 and 14 respectively Spectrum ProcPars AcquPars Title PulseProg Peake Inte
260. y i Toggle cursor information on off Cursor information consists of the point number and amplitude phase value t Wrap unwrap phase actual phase phase modulo 360 P Toggle between polar and cartisian coordinates 15 9 3 How to Save a Shape Gradient as a 1D dataset To save the current shape gradient stored under a procno of the associated dataset click ld Save shape gradient as a 1D dataset 15 9 4 How to Superimpose Multiple Shapes Gradients Several shapes gradient can be displayed superimposed using the following but tons Add the currently displayed shape to multiple display H Switch to multiple display mode This shows all added shapes gradi ents superimposed 15 9 5 How to Save a Shape Gradient To save a shape gradient click the button EL Save a Shape or Gradient or a fraction of it and select Save Shape Save Gradient or Save Fraction A dialog window appears Acquisition 275 where you can enter a File Name Title Flip Angle and the Type of Rotation Pisave Shape as Gauss Marne Citst2a expistaninmillistswave Gauss Title 00 Flip Angle Excitation ss Type of ro OK Cancel Figure 15 16 If you save a fraction of a shape or gradient the above dialog is preceded by the following dialog x start End 1000 OK cancel Enter the Start and End point and click OK 15 9 6 How to Ge
261. you are a new or occasional user we recommend you to process your data with the TOPSPIN Processing Guide This will guide you through the typical sequence of processing steps To start the Processing Guide click Processing Processing Guide In Automatic mode the Processing Guide will simply execute each processing command when you click the corresponding button This requires the processing parameters to be set correctly In interactive mode Automatic mode unchecked the Processing Guide will at each step open a dialog box offering you the available options and required parameters For example the phase correc tion button offers various automatic algorithms as well as an option to switch to interactive phasing mode How to Archive Data TOPSPIN 1 3 provides the following methods for data archiving e Copying a dataset to a desired destination directory which could for instance be located on a server Type wrpa click File Save or type Ctrl1 s e Saving a dataset in a ZIP file A standard Bruker dataset is a directory tree which contains several files Zipping a dataset stores the entire data direc tory tree into a single file with the extension bnmr zip To zip a dataset type tozip click File Save or type Ctr1 s To unpack and display a zipped dataset enter fromzip Note that bnmr zip files are fully com 24 Getting Started patible with the well known PC zip format and can be unpacked with any common u
262. ze title bar button button menu bar Bruker TOPSPIN 1 3 on nmr datastation as Administrator File Edit View Spectrometer Processing Analysis Options Window Help upper E E ee Eee eee ee le eee ee ee eee close a ever 3 S Bea AAt W toolbar 2 42 8 8 Flo AA Ql Ge o gt l Browser PFalio Alias 1 0 x data area examigd_ 130 exam d_1H examed CH examid HC exam2d_HH examsd scroll arrows command line status bar 1D data window 2D data window Figure 2 1 Note that the menus and toolbars depend on the data dimensionality The descrip tions below hold for 1D data For 2D and 3D data the menus and toolbars are sim ilar and will be discussed in the chapters 9 10 and 12 respectively How to Use Multiple Data Windows TOPSPIN allows you to use multiple data windows Data windows can be opened from the browser or from the Window menu They can contain the same of dif ferent datasets Data windows can be arranged from the Window menu One of them is the active current data window The active window The TOPSPIN Interface 29 can be selected by clicking inside the window or hitting F6 repeatedly has a highlighted title bar has the mouse focus is affected by menu toolbar and command line commands A cursor line 1D or crosshair 2D is displayed in all data windows at the same position Moving the mouse affects the cursor in all data windows How to Use the Title bar
263. ze the im ported graphics sections of the text the spectrum or the axis sometimes have dis appeared Usually this is only a display problem When you print the respective page the representation is correct How to Store Export a Data Window as Graphics File The clipboard and metafile formats are resizable vector formats In addition to this TOPSPIN allows you to save the contents of a data window in a graphics file of selectable type e g png tif wmf etc To do that 1 Click File gt Export exportfile 2 Navigate to the storage folder 3 Enter the destination filename and extension 4 Click Export The resolution of such a screen dump equals the resolution of your screen When you import a graphics file into an other program you may loose information when resizing the graphics Chapter 8 1D Display 1 The 1D Data Window The 1D data window consists of a data field a title bar a Tab bar and buttons Fig 8 1 shows a data window with a 1D spectrum 102 1D Display maximize data button field nE O deb minimize close Tab bar button button examid 1H 1 1 Cbio guest X spectrum ProcPars AcquPars Title PulsePrag Peaks ecrals Sample Structure Fid in J t imi in E 10 g 6 4 2 ppm Figure 8 1 8 2 Displaying one Dataset in Multiple windows TOPSPIN allows you to display one dataset in multiple data windows This is for example convenient to view var

Users Guide - UC Davis Nuclear Magnetic Resonance Facility

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