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Topspin3 User Manual

1. Figure 13 14 Fig 13 14 shows row 619 with the 1D baseline at the center of the data window How to Show the Next Previous Row or Column To show the next row column click the following button Show next row column To show the previous row column click the following button Show previous row column 256 2D Interactive Manipulation Alternatively you can turn the mouse wheel while pressing the Shift key to show the next previous rows columns How to Move the Selected Dataset Up Down in the Dataset List To move the selected dataset up click the following button t Move the selected dataset up To move the selected dataset down click the following button 4 Move the selected dataset down 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 13 13 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 PROCNO and displayed in a new data window In the upper left part of this the row number and source 2D dataset is specified see Fig 13 15 257 2D Interactive Manipulation Pxam d HC 1 999 Chio
2. 0 2 20 eee eee 178 10 5 2D Display Options 2 2 6 64 224s bk See a 178 How to Switch between Hertz and ppm Axis Units in F2 and F1 How to Switch on off the Spectrum Overview display 178 How to Switch on off the Projection display 179 How to Switch on off the Grid display 181 How to Display a 2D Spectrum in Contour Mode 182 How to Set the 2D Contour Levels 183 How to Store interactively set Contour Levels 184 How to Display a 2D spectrum in Pseudo Color Mode 185 How to Display a 2D Spectrum in Oblique Mode 185 How to Rotate a 2D Spectrum in Oblique Mode 187 How to Switch between Displaying Positive and Negative levels Chapter 11 nD Display 0 0 0 ccc es 188 11 1 Display Planes of 3D Data 0 0 0 0 000005 188 How to Switch to 2D Plane Display 189 How to Display various Plane Orientations 189 How to Display various Plane Positions numbers 190 11 2 3D Cube Display Mode 0 0 cc eee 191 How to Display the 3D Cube 2 0 2 0 0006 191 How to Rotate the 3D Cube 00 0000 0008 191 How to Scale Up Down the 3D Cube 192 How to Reset the Cube Size and Orientation 192 How to Switch Depth Cueing on off 00 192 How to Display a Cube Front or Sid
3. This allows you to edit the current pulse program The following extra but tons are available here g Toggle status pulse program T Start the graphical pulse program display edcpu1 E Show the pulse program in an external editor nmrsin i Search for more info in the knowledge base How to Display the Peak list Click the Peaks tab 134 1D Display Pxamid 1H 1 1 Chio guest Spectrum FrocPars AcquPars Tithe PuleeProg Integrala Sample Structur Index FT wiF1i ppm Intensity abs Intensity rel Half width ppm 1 19569 9 38319 11472303 78 11 04 0 0044 2 20929 95 3 3332 12495443 09 11 95 0 0037 3 21320 4 3 1900 13371661 03 12 67 0 0037 4 21603 7 3 0861 12663022 38 12 03 0 0040 5 217071 3 0482 13159654 59 12 36 0 0037 6 21947 3 2 9601 13733719 44 12 93 0 0033 7 22658 2 26994 1325189575 12 48 0 0040 B 256579 7 1 2614 15909845 58 15 00 0 0054 5 256615 4 12483 13804594 47 12 98 0 0077 Figure 9 3 This displays the peak list By default the peak list shows the following en tries Peak the peak number v F1 ppm the chemical shift Intensity abs the absolute peak intensity Intensity rel the relative peak intensity Half width ppm the peak width at half height Display the spectral region around a peak Right click the desired peak this will open the popup menu shown in Fig 9 4 135 1D Display Show spectrum p Expand spectrum d In current window Delet
4. 0 00000 52 3 8 User Defined Functions Keys 0 0 0 0 00 e eee 53 3 9 How to Open Multiple TOPSPIN Interfaces 53 Trouble Shooting 0 00 0 cee es 56 4 1 General Tips and Tricks 0 0 0 0 c eee eee eee 56 4 2 History Log Files Spooler Reports Stack Trace 56 4 3 Howto Show or Kill TOPSPIN processes 200005 60 4 4 What to do if TOPSPINhangs 0 000 cece ene 61 4 5 How to Restart User Interface during Acquisition 62 Dataset Handling sri 6 00 te ce bawaare eee Si es 64 5 1 The Topspin Browser 0 000 aaaea ee eee 64 How to Open the Browser in a separate window 68 How to Put the Focus in the Browser 005 68 How to Select Folders inthe Browser 04 5 69 How to Expand Collapse a Folder in the Browser 69 How to Show Hide Pulse program and Title in the browser 69 How to Show Dataset Dates in the Browser 70 How to change the default Top Level Data Directory 71 83 93 Chapter 6 How to Add Remove or Interpret Alias Names 71 952 Creating Data irisak nren eane a A age eee 72 How to Create a New Dataset 0 0 00 eee eee 72 Oo Opening Datla 23 ie ob dee ee es Be ee ee Se ee 73 How to Open Data Windows Cascaded 4 74 How to Open Data from the Browser 000 75 How to Automatical
5. DownArrow Select next command if available 45 The TOPSPIN Interface Focus in the striped tables e b edsolv ednuc peaks ints cortab etc Ctrl C copy the currently selectedtable rows to the system s clipboard as a CS V formatted table The table package assumes that data will always be represented by complete rows rather than individual cells This makes a re binding of Home necessary to enforce the behaviour of jumping to the first row The table package assumes that data will always be represented by complete rows rather than individual cells This makes a re binding of End necessary to enforce the behaviour of jumping to the last row Shift Home The table package assumes that data will always be represented by complete rows rather than individual cells This makes a re binding of Shift Home necessary to enforce the behaviour of selecting all rows starting from the current anchor to the first row Shift End The table package assumes that data will always be represented by complete rows rather than individual cells This makes a re binding of Shift End necessary to enforce the behaviour of selecting all rows starting form the current anchor to the last row Ctrl Numpad Auto resizes all colums such that the data fits optimally 46 The TOPSPIN Interface 47 Focus in the peak table Deletes the current selection of peaks Enter Zooms the spectrum pane in
6. Figure 20 4 Set the desired colours and spacings 4 Click OK Note that table colours and spacings can also be changed from a table To do that right click any table entry and choose Table properties 358 User Preferences 20 1 4 Changing Lines How to Create Thick Lines on the Screen To create thick double width lines for high resolution display or screen dumps 1 Click Options gt Preferences set 2 Click Spectrum in the left part of the dialog box 3 Enable the entry Use thick lines 4 Click OK How to Create Thick Lines on the Printer To create thick double width lines for high resolution display or screen dumps 1 Click Options gt Preferences set 2 Click Printer in the left part of the dialog box 3 Enable the entry Use thick lines 4 Click OK 20 1 5 Changing Fonts How to Change All Fonts of the Topspin Interface 1 Click Options gt 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 359 User Preferences Fig 20 5 shows an example of increasing the font sizes by 4 points Fonts Dialogs Icons Menu font Dialog plain Plain s 18 Change Dialog window font Dialog plain lt Plain 14 Change Command line fant Dialog plain Plain 18 Change status line font Dialog plain Plain 14 Change
7. 244 2D Interactive Manipulation are selected only the first one is increased To show the previous row column click the following button Show previous row column Note that only the selected row column is decreased If all rows columns are selected 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 13 6 Arrange rows columns vertically in a split window How to Return from Multi 1D Phase to 2D Phase Display Click the following 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 a to return to the 2D phase display without save How to Return from 2D Phase Mode Click the following button d Return 13 2 2D Interactive Integration TOPSPIN 2 1 and newer supports interactive 2D integration 245 2D Interactive Manipulation 13 2 1 How to Switch to 2D Interactive Integration Click the corresponding button in the upper toolbar as indicated below Id 30 4 4 jim or enter int on the command line The Tab bar of the active data window will be replaced by a toolbar Fig 13 7 shows an example of a 2D inverse spectrum exam d HC 1 1 Cobio guest Iie xan u col 0 21 ppm 105 67 Hz Index row
8. Edit button properties Add User Detin d Button Remove This User Defined Button Shift lett Shift right Make Button Invisible Make Button Inactive Reactivate All Invisiblednactive Buttons Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset Print Seso0ciated Command Figure 21 4 The button definitions are stored in the file toolbar user prop which resides in the subdirectory userdefined 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 21 7 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 User Extensions 2 Right click at an empty area of the menubar 3 In the appearing popup menu click User_defined Menus User Defined Menus
9. Spectrum TABS font Dialog plain Plain 14 Change Printer font Dialoginput plain s Plain s 10 Change Change size of fonts listed above by points 0 Figure 20 5 4 Click OK to store the new value Fonts Dialogs Icons Menu font Dialog plain Plain 24 Change Dialog window font Dialog plain Plain 20 Change Command line font Dialog plain Plain 24 Change Status line font Dialog plain Plain 20 Change Spectrum TABS font Dialog plain Plain 20 Change Printer font Dialaginput plain Plain 10 Change Change size of fonts listed above by points 0 Figure 20 6 Fig 20 6 shows the same part of the Preferences dialog box after the change of fonts Note that e The value of all 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 gt Preferences set 360 User Preferences 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 Plains 18 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 18 and looks like this File Edit View Spectrometer Processing After changing the font to for instance to
10. Stores the user properties in lt mydir gt lt login id gt prop where lt login id gt is the id under which the user is logged into the operating system Example DPROPDIR x y z USER 1 DPROPDIR CURDIR Stores the user properties in lt tshome gt prog curdir lt login id gt prop where lt login id gt is the id under which the user logged into the operat ing system Please note that the specified directory must writable for all TOPSPIN users 1 The double quotes are only required if the directory contains white spaces 2 Specify exactly 1 space between the pathname and the string USER 350 User Preferences 20 1 2 TOPSPIN Startup Actions How to Open the Last Used Dataset on Startup 1 Click Options gt Preferences set 2 Check under Administration items the option Auto open last used data set when restarting TopSpin How to Define the Startup Actions TOPSPIN allows you to define any commands to be executed automatically after startup To do that 1 Click Options gt Administration gt Edit Startup File 2 Enter the desired startup command s in the appearing editor for example re exam1d_13C 1 1 c bio guest efp apk abs The above lines would cause TOPSPIN to display the dataset C bio data guest nmr examId_13C 1 pdata 1 and execute the command efp apk and abs on it Note that you can use a single forward slash or a double backslash as path separator Note that in TOPS
11. button of the data window toolbar Enter part of a parameter name in the search field and click Click a parameter section e g Phase 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 Click in a parameter field e g PHCO to set the parameter value Click the button to the right of parameters like AUNMP to open a list of the corresponding programs lists 98 Right click the e button to the right of parameters like AUN MP to open the current program list with an editor Hit the Tab key to jump to the next parameter field Hit Shift Tab to jump to the previous parameter field Use the scroll bar at the right of the dialog box to move to parame ters further up or down in the dialog box How to Undo the Last Processing Parameter Change Click the following button 1 Undo last parameter change How to Display Processing Status Parameters Click the following button 5 Show processing status parameters Note that the command dpp opens the parameter editor and automatically shows the status parameters How to Switch to Maxent parameters Click the following button M Switch to Maxent parameters How to Change Processed Data Dimensionality Click the following button 42 Change data dimensionality This changes the number of parameter columns and value of the process ing parameter PPARMOD TO
12. 2 Select the desired Remote system from the appearing dialog box and click OK Ea Connect Please select the system you want to connect to This requires a properly configured TOPSPIM be running on that system Remote systems can be set Up in the Preferences panel see Options menu under the Miscellaneous terri Remote system eteley Figure 19 3 Now you are prompted for a user and password both case sensi tive on the remote computer 342 Remote Control E Please enter the name and password forthe TOPSPIN session on the remote computer This connection is secure User guest Password rere OK cancel Figure 19 4 The TOPSPIN browser will show the exported data directory trees of the remote system You are now ready to acquire process or analyse remote data 19 2 3 Setup the firewall A remote system in a network can be protected by a firewall Any firewall between the local and remote TOPSPIN must be configured for TOPSPIN remote access If the remote PC is running under Windows XP with Service Pack 2 or higher the Windows Firewall is by default installed and running Consider the following possibilities Firewall on PC with Windows XP SP2 or higher Topspin installed If TOPSPIN is installed the firewall is probably configured for TOPSPIN remote access 1 If it is not or you are not sure you can configure it as follows 1 Click Start gt Programs gt
13. 322 title file 133 title of a dataset 25 69 72 133 158 305 356 Title tab 133 toccpn command 85 tojdx command 30 85 toolbar 1D 198 2D 238 configuration 366 extension 378 for acquisition 290 icons 379 381 of the data window 26 154 of the FID display window 307 tips 51 usage 38 tooltips 50 51 top level directory 23 64 71 Topspin color schemes 357 data area 80 83 fonts 360 help 50 installation 318 installation directory 318 startup 18 20 tailoring 348 window 35 topspin command 20 Topspin icon 20 totxt command 85 tozip command 29 85 tshome directory 20 51 318 tuning the probehead 298 U undo last parameter change 99 103 last region operation 213 unzip utility 30 Up Arrow key 42 45 upper toolbar 1D 38 198 2D 238 user defined AU programs 319 buttons 378 381 383 commands 27 31 functions keys 53 plot layouts 118 User Interface functions 374 user preferences 348 user properties directory 53 V Varian spectrometer 82 vertical scaling 127 168 View menu 37 157 virtual spectrometer 31 VNMR data 82 W walk up 32 wbst command 299 wbsw command 299 wildcards 88 window layout 269 l 28 Window menu 37 270 WINNMR data 82 wm command 27 96 wmisc command 85 wobb command 293 298 wobble display 295 frequency 299 procedure 298 steps 299 sweep width 299 window 298 wpar command 85 wra command 85 wrp command 85 wrpa command 29 84 85 X xau command 322 x axis rotation in
14. Pxam d HC 1 1 Chio guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Accu o Frequency axis Y Reference Sl Size of real spe SF MHz Spectrometer ft OFFSET ppm Low field limit o SR Hz oo 000 Spectrum refer U Reneo HZpPT Hz Spectral resolu User F Window function SINE GSIME Window functie gt Figure 10 7 How to Set Acquisition Parameters Click the AcquPars tab eda The 2D acquisition parameter editor contains a column for each of the two dimensions F2 and F1 see Fig 10 8 Note that not all parameters 174 2D Display exist in both dimensions Pxam d HC 1 1 Cobio quest Spectrum ProcPars ACGUPars Title PulseProg Peaks Integrals Sample Structure Fid ACU 175 on S Hive P Fi Fi Frequency axis Y Experiment PULPROt himigcgpcgt Le Current pulse p Atl mod AcQGuistion mo FnokiiDeE Acguistion mac TD 1024 Size of fid Number of Scar Number of durri Loop count for wt Figure 10 8 How to Display the Peak list Click the Peaks tab exam2d HC 1 1 Cobio guest spectrum ProcPars AcquPars Title PulsProg Peaks Integral OF2 ppr WOLF ppr Intensity Annotation P2405 128 2961 32061 761 6 pk 4 2092 44625 903934424 pki 5 7985 59 4354
15. e Click View gt 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 respective ly To do that Click Options gt Preferences set Click Fonts Dialogs Icons in the left part of the dialog box Specify the Minimum visible command lines gt 0 Specify the Maximum visible command lines Minimum visible Click Apply ah O N 20 3 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 365 User Preferences from the appearing popup menu see Fig 20 12 To restore the toolbars press the keys SHIFT ESC Wake Button Invisible Wake Button Inactive Reactivate All lnvisibletnactive Buttons Add User Defined Button Remove This User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ES to reset Print Associated Command Figure 20 12 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 menubar press the keys SHIFT ESC How to Disable Remove Toolbar Buttons Buttons of the upper or lower toolbar can be disabled
16. gt T1 T2 Relaxation t1lguide This will open the dialog box as shown in Fig 15 8 280 Analysis MMF Relaxation Guide Vane Fitting Function Extract Slice Se tha Start Calculation Lo ot Define Ranges Display Report a Relaxation window PrintvExport Figure 15 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 com mand that is executed when the icon is clicked If you prefer to execute these commands from the command 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 determina tion see Fig 15 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 FID the extracted FID is automatically processed 281 We recommend to enter the FID or spectrum number which was meas EA Extract a row from d data 2 Fid or Spectrum must be extracted From the 2d relaxation data This rowe should correspond to an experiment vith the maximum or minimum delay time All further data preparation will be done in respect to this row Figure 15 9 ured with the longest delay It can be found in the vdlist file in the EXPNO data directory Then you can choose between e Manual Integration This will switch to Inter
17. home to open user home directory or with an absolute pathname to open that directory The command expl spect opens the Explorer in lt tshome gt conf instr current instrument gt The command expl prop opens the Explorer in the user s prop erties directory User HOME topspin lt name_ of PC gt prop By entering expl lt illegal argument gt all available options are shown 2 Now you can open a dataset with 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 copy amp paste right click a dataset and choose copy from the pop up menu In TOPSPIN click Edit gt Paste paste see Fig 5 17 Edit View Spectromete Copy Find data Ctrl F Figure 5 17 Likewise a dataset can be opened from the Windows 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 appearing dialog box see Fig 5 16 80 Dataset Handling 81 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 2 Specify a procno in the appearing dialog box 3 Click OK To open a data browser and re
18. 1 Click Options gt Preferences set 2 Click Administration Items in the left part of the dialog box 3 Click the Change button to the right of the object Automatic locking of TopSpin when idle time exceeded 4 Enter the maximum allowed idle time in minutes in the dialog and click OK 336 Regulatory Compliance 337 Remote Control 19 1 19 2 Chapter 19 Remote Control Remote control TOPSPIN supports remote control This means for example that you can control your spectrometer from any PC in the laboratory network or over the internet 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 ena bled which means it can be controlled from any web browser which is net worked to the spectrometer Note that remote access is operating system independent How to Establish a Remote Connection from your PC In order to establish a remote connection you have to perform a few steps both on the local and on the remote system Note that the local system is the computer you are sitting at and the remote system is the computer you are connecting to Up to 5 local systems can connect to TOPSPIN on a remote system 338 19 2 1 Setup the remote system The remote system must be enabled for remote access and furthermore individual data directories must be exported En
19. 1D Display How to Set Processing Parameters Click the ProcPars tab edp examid 1H 1 1 Cobio guest Spectrum ProcPars AcquPars Title PulseProq Peaks Integrals Sample structure Fid Accu 4 he A SF KHz Spectrometer fre 2i OFFSET ppm Low field limit of SR Hz ooo Spectrum revere HZpPT Hz Spectral resolutic Y Window function window tunctior L wt 4 This opens the processing parameter editor see also chapter 6 1 The following extra buttons are available 1 Undo last value change Can be used to undo multiple changes MI Switch to Maxent parameters 5 Status parameter display The button turns green when activated dpp 123 Change processed dataset dimensionality parameter PPARMOD Y Collapse expand all parameter sections Search for specified parameter Changed parameters are automatically saved 131 1D Display How to Set Acquisition Parameters Click the AcquPars tab eda examid 1H 1 1 Chio guest spectrum ProcPars AcguPars Title PulseFrog Peaks Integrals Sample Structure Fid Acgu 2 T Y Experiment PULPROG At mod a modi Size of fid Number of Scar Number of durrirr Loop count for t Spectral width a gt This opens the acquisition parameter editor see also chapter 6 1 The following extra buttons are available 1 Undo last value change Can be used to undo multiple changes
20. 2 Select Open file explorer exp in the appearing dialog box see Fig 5 25 3 Click OK Alternatively you can enter the command exp1 on the command line The Windows 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 Konqueror or Gnome Mozilla will be opened To open a file Double click the file or right click the folder icon and choose Open 93 Dataset Handling Options O Open File Explorer OQ Open Command Prompt Shell Serial Processing Execute AU Program OQ Execute Python Program Execute Macro Start Top Spin Text Editor Figure 5 25 If TOPSPIN data area contains no datasets the exp1 command opens the Explorer showing the users home directory When entered on the com mand line exp1 can also be used with the argument top to open the TOP SPIN installation directory home to open user home directory or with an absolute pathname to open that directory 94 Dataset Handling 95 Parameter Handling Chapter 6 Parameter Handling 6 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 a command 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 t
21. 256 JRK Cancel 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 acquisition parameter editor Click the AcquPars tab in the Tab bar of the data window or Enter eda on the command line Fig 6 2 shows an example of the acquisition parameter editor with the Ex periment parameters displayed 101 Parameter Handling examid 13C 1 1 CiBio guest Spectrum PracPars ScquPars Title PuleeProg Peaks Integrals Sample structure Fid Acqu OnS Hv ae YF Experiment PULPROcs zapo o LE Current pulse pr Atl mod Acquisition mace TD Size of fid 3 MS Number of Scar DS Number of durrirr TOO Loop count for t Width J Receiver Fits darog Receiver gain Figure 6 2 The processing parameter editor supports the following functions Collapse expand a parameter section by clicking the button Note that the section Width in Fig 6 2 is collapsed Collapse expand all parameter sections by clicking the large button of the data window toolbar Enter part of a parameter name in the search field and click amp Click a parameter section e g Experiment at the left of the dialog box The section becomes highlighted and the corresponding pa rameters will appear in the right part of the dialog box Click in a parameter field e g TD to set the parameter value
22. 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 re trieving previously entered commands After that you can go forward to more recently entered commands as follows Hit the 4 Down Arrow key on the keyboard How to Change Previously Entered Commands 1 Hit the lt Left Arrow or gt Right Arrow key to move the cur sor 2 Add characters or hit the Backspace key to remove characters 3 Mark characters and use Backspace or Delete to delete them Ctrl c to copy them or Ctrl v to paste them In combination with the arrow up down keys you can edit previously en tered commands How to Enter a Series of Commands lf you want to execute a series of commands on a dataset you can enter the commands 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 fol lows right click in the command line and choose Save as macro 3 4 Command Line History TOPSPIN allows you to easily view and reuse all commands which were previously entered on the command line To open a command history con trol window click View gt Command Line History or right click in the 42 The TOPSPIN Interface command line and choose Command Line History or enter the
23. 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 Click Window gt Arrange as a Grid Depending on the number of windows they will be arranged vertically and or horizontally see Fig 14 3 265 Data Window Handling Pojexam1d_13C 2 1 Cjhbio guest l oO x Spectrum ProcPars AcquPars Title PulsFrog Peaks Figure 14 3 To arrange data windows in stack see Fig 14 4 Click Window gt Arrange in Stack Pojexam2d_HC 1 1 Cibio que Figure 14 4 266 Data Window Handling To arrange data windows side by side see Fig 14 5 Click Window gt Arrange Side by Side Fa exa M ee EA E feces el ead Figure 14 5 To cascade data windows see Fig 14 6 Click Window gt Cascade IH 1 Ol x C Ol x exam2d_HC 1 1 Chia guest M f Figure 14 6 Note that you can instruct TOPSPIN to open new data windows cascaded rather than maximized as well configure cascaded windows command set gt Window settings see also chapter 5 3 How to Iconify minimize a Data Window Click the button in the windows title bar 267 Data Window Handling Or Click Window gt Iconify all to iconify all windows How to De iconify a Data Window
24. Change Menu Font Define Right Click Action Hide Menubar type SHIFT ES to reset 4 In the appearing dialog box see Fig 21 5 a Click Add Menu and specify the Menu Name in the appearing dia log b Click Add Menu Item and specify the Menu Item menu entry name and the corresponding Command in the appearing dialog c Click Apply EA User Defined Menus Menu tem t Cormmangd Figure 21 5 The new menu will appear in the menubar Furthermore the dialog box in Fig 21 5 contains the following buttons e Remove Remove menu names and or menu items 382 User Extensions 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 userdefined of the user properties direc tory To locate this directory enter the TOPSPIN command hist 21 8 Adding User Defined Guides 383 TOPSPIN offers several guides like the Acquisition Guide command aqguide the Processing Guide command prguide and the T1 T2 Guide command t1guide 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 l
25. Click OK A dialog box will appear showing the matching datasets For example if you select the option An entire dataset 1 Select dataset entries for deletion selected entries are highlighted To select multiple entries click them holding the Shift or Ctrl key 2 Click OK to delete the entire data directory If you select the option Acquisition data or Processed data you can choose between deleting the data files only and deleting the entire exono or procno directory respectively see Fig 5 21 Data directory Cupio User quest Mame 13 Options G Delete the selected EXPMOs with all their PROCMOs O Delete the raw data files of the selected EXPNOs FXPHO 4COU DATA Figure 5 21 88 5 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 find to open the Find data window see Fig 5 22 EN Find data Searching will be performed in all data directories marked inthe data directories list below The checkboxes at the right will enforce exact matching if enabled MAMIE EXPNO PROCNG USER Title Pulse Frog Dimension Data type Date fram riria Date till rirfdddsyy Data directories Figure 5 22 2 Enter the search items in the upper part of the dialog Note that e There will be searched for items containing the specified string e Exact matchi
26. Click the button to the right of parameters like PULPROG to open a list of the corresponding programs lists 102 Parameter Handling 103 Right click the e button to the right of parameters like PUL PROG to open the current program list with an editor Hit the Tab key to jump to the next parameter field Hit Shift Tab to jump to the previous parameter field Use the scroll bar at the right of the dialog box to move to parame ters further up or down in the dialog box How to Undo the Last Acquisition Parameter Change Click the following button 1 Undo last acquisition parameter change How to Set Pulse Program Parameters Click the following button TL Show pulse program parameters ased The button will change to a To make this the default setting Click Options gt Preferences click Miscellaneous check the entry Show ased parameter selection with eda and click OK How to Display Acquisition Status Parameters Click the following button g Show acquisition status parameters Note that the command dpa opens the acquisition parameter editor and automatically shows the status parameters How to Get Probehead Solvent dependent Parameters Click the following button g Set probehead solvent dependant parameters getprosol Probehead and solvent dependant parameters can be set up with the command edprosol Parameter Handling How to Change Acquisition Data Dimensionality Click th
27. Click the indicated button in the upper toolbar 2d 3d A A A SD a or enter int on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 12 3 The first button define integrals is automatically activated is green Pxamid 1H 1 1 Cobio guest Mouse Sensitivity 1 0 0 99 ppm 493 4a Hz DEFINE REGION MODE Define Drag using left mouse button Return Lett click highlighted icon Figure 12 3 Data window in integration mode I The yellow button indicates that the data window is in integration mode B 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 204 1D Interactive Manipulation data window along with the integral values You can remove them change them or add to them as described below How to Define Integral Regions To define integral regions interactively 1 Click the following button button turns green Define integral region interactively Note that the define integrals button is automatically activated on en tering the integrals mode 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 g
28. Delete the selected entries elect the first entry a elect 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 DownArrow Select next entry UpArrow Select previous entry Focus in a Plot Editor rRe OO Ctrl tab Display next layout Displaynextlayout elect all objects Ctrl n Open a new layout Open an existing layout Ctrl p Print the current layout Print the current tayout oe lose the Plot Editor window Linux only Ctrl r Raise the selected object Ctrl t Reset X and Y scaling of all marked objects Oo 2 ss Ctr1 v Paste the object from the Clipboard Ctr1 w Open the attributes dialog window Ctr w Open the attributes dialog window Ctr1 x Cut the selected object and place it on the Clip board Undo the last action Note that the function of function keys can be changed as described in chapter 3 8 3 Help in Topspin TOPSPIN offers help in various ways like online manuals command help and tooltips How to get a Panorama Tour For a quick overview over TOPSPIN Interface Acquisition Processing Analysis and Documentation The TOPSPIN Interface Click Help gt Panorama Tour How to Open Online Help documents The online help manuals can be opened from the Help gt Manuals sub menu For example to open the manual that you are reading now Click Help gt Manu
29. Display Display In New Window Display As 2D Projection Sort This Column Sort Reverse Show Details save selection in file Add selection to dataset group File Properties Files Process Selected Datasets Figure 5 24 Display Display the selected dataset s in the current data window If multiple da tasets are selected they are displayed in the same data window in multi ple display mode Equivalent to clicking the Display button or pressing Enter Display In New Window Display the selected dataset s in a new window If multiple datasets are selected they are displayed in the one new data window in multiple dis play mode Display As 2D Projection Display the selected dataset as a projection of the current 2D dataset A dialog will appear allowing you to choose F1 projection F2 projection or both If multiple datasets are selected only the first one is considered If the current dataset is not a 2D dataset nothing happens Sort This Column Dataset Handling Sort the selected column in ascending order Sort Reverse Sort the selected column in descending order Save Selection in file Save the list of selected datasets in a text file First opens a file dialog where you can select or specify a filename The saved dataset list can for example be used for serial processing command serial see also Process Selected Datasets below Add selection to dataset group Selected datasets can b
30. Equivalent to the command stop Ww Open the online FID display window Shows the currently acquired Acquisition Fil lt FID Only works during acquisition Equivalent to the command acqu Open the Lock display window Shows the lock signal Equivalent to the command lockdisp Open the BSMS contrrol suite Calculate the experiment time Shows the total experiment time and file size of the raw data Equivalent to the command expt Set SFO1 O1 O2 and O3 interactively Puts a red cursor line in the data window A left click at the desired frequency opens a dialog box where you can set 01 O2 and or O3 Set the sweep width to the current region and the spectrometer fre quency to the center of the current region Update the parameters SW and SFO1 respectively Setup a frequency list interactively 16 3 Data window Toolbar TOPSPIN 2 0 and newer support dataset specific acquisition display Figure 16 5 It is activated by clicking the Acgu tab of the data window toolbar Alternatively to open the Acgu tab you can right click in the staturs bar under the TopSpin command line Figure 16 4 show acquisition display 3 Start rga Start acquisition Amplifier Control Acquis Start wobble WTU start gs Kelvin Stop acquisition UE 297 0 no acquisitic Figure 16 4 292 amp Bruker TOPSPIN 2 1 on HEBE as nmrsu i a ses Acquisition File Edit View Spectro
31. PASSWORD A password for this user required for using TOPSPIN and for applying an electronic signature 18 3 2 How to set up internal users 333 In order to define or modify the list of internal users enter the command uadmin Or Click Options gt Preferences gt Administration items Click the Change button to the right of the object Setup users for Top Spin internal login logoff and esign You will be prompted for the NMR administrator password A dialog will appear Regulatory Compliance EA User Administration uadmin F Enforce login for working with Topspin User ID User Mame Allowed Signature Meanings Carol Smith Diane Lopez all James Evans review Larry Hill approval Add User Change Meanings Passwd Length Figure 18 5 where you can add remove and or modify users 18 3 3 How to change the internal user password To change the password of the internal user enter chpwd on the command line or Click Options gt Administration gt Change internal user password and enter the new password twice as requested 18 3 4 Login Logoff The uadmin command allows the administrator to make a TOPSPIN internal user mandatory To do that enable Enforce login for working with Top Spin at the top of the dialog click Save Close and restart TOPSPIN After the restart a login prompt will be displayed and TOPSPIN cannot be used with 334 Regulatory Compliance 18 3 5 335 out entering
32. 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 2 Click hold the following button it turns green and move the mouse b Integral bias correction 208 1D Interactive Manipulation until the integral bias is correct 3 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 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 o Integral slope correction until the integral slope is correct 3 Release the mouse button turns grey How to Set the Limit for Bias Determination Click the following button Limit for bias determination 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 IIl Reset the mouse sensitivity How to Calibrate Normalize Integrals Calibrating integrals means setting 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 12 6 3 Enter the desired value for the reference integral and click OK Normalizing integrals means setting the
33. by default off see Options gt Preferences gt Acquisition The processed data audit trail Each procno sub directory contains a text file auditp txt the audit trail of the processed data It reflects the processing state of the processed data and contains a checksum for the file itself auditp txt and a checksum for the real processed data files 1r 2rr 3rrr The latter checksum links the audit file with the processed data By means of the checksums any illegal manipulation of the audit file or the processed data file can be detected using the TOPSPIN commands audit or auditcheck Whenever a processing command is performed the current audit file is updated with this command and its associated parameters When processing starts from scratch from a raw data file the existing audit file is overwritten As such the processed data can always be regenerated from raw data by applying the commands and parameters listed in the audit trail If the laboratory management does not allow data files or audit trails to be deleted a respective saving procedure must be established For this pur pose TOPSPIN provides data copying commands which may be called ina user defined macro or AU program before a new acquisition or processing Starts Viewing audit trails Since audit trails are regular ASCII text files they can be viewed or printed with any text editor outside of TOPSPIN Within TOPSPIN you can use the command audit for t
34. by the tag user comment You may also add a comment to the raw data or processed data audit trail from an AU program using the macros AUDITCOMMENTA comment or AUDITCOMMENTP comment respectively Alternatively you can store the comment ina file auditc txt in the expno or procno directory and use the macros GDCHECK_RAW or GDCHECK Auditing user defined data manipulations When manipulating a data file with a user defined algorithm e g by means of an AU program or external program the data file and the respective audit trail become inconsistent detectable with the command auditch eck and the data set is no longer compatible with regulations In order to 328 solve this problem TOPSPIN provides a function CheckSumFile which adds the correct data checksum to the audit trails and a function AuditAppend for additional text an alternative to the comment function described above These functions are described in the AU manual which can be opened by clicking Help gt Manuals gt Programming Manuals AU pro gramming 18 1 7 Audit Trails in JCAMP DX and ZIP archives The TOPSPIN commands tojdx and tozip allow you to store a data set into a single file in the internationally standardized ASCIl type JCAMP DX format or in the well known ZIP format respectively Both storage formats retain the audit trails When unpacking such files with fromjdx or fromzip respectively the original data set in standard Bruker format is res
35. data from the Explorer 72 data from the menu 21 IconNmr interfaces 30 Linux Shell 19 new data window 252 new procno 74 online help documents 45 special format data 75 Topspin command index 46 open command 34 41 70 75 Options menu 33 overview spectrum 1D 145 2D 169 P paper format 300 paracon command 300 parameter adjustment window 93 284 change 92 96 97 display 23 editor 89 90 93 94 field 91 92 95 96 files 85 handling 89 name 89 93 search 122 123 value 91 95 parameter set 65 78 PARMODE parameter 123 paste command 34 73 76 peak alignment 24 212 display 23 fitting 28 group 28 labels 149 150 222 list 223 224 l 10 list 1D 125 222 list 2D 166 picking mode 220 position 260 position alignment 212 ranges 224 peak picking 1D automatic 220 1D interactive 220 mode 35 mode 1D 220 ranges in 1D 221 222 peak txt file 224 peakrng file 224 Peaks tab 112 125 166 phase correction 1D automatic 99 100 1D interactive 191 2D interactive 225 first order 1D 193 mode 34 mode 1D 192 mode 2D 226 pivot point in 1D 192 values 1D 194 zero order 1D 193 PHCO parameter 91 193 230 PHC1 parameter 193 231 pivot point in 1D phase correction 192 in 2D phase correction 229 pk command 194 plane display in 3D 180 plot data from the menu 109 data from the Plot Editor 112 data from the Processing Guide 111 layouts 25 plot command 110 112 Plot Editor 25 110 Plus key 42 polynomial baseline correction
36. myicons myiconl gif a user defined icon located C myi cons Using the absolute pathname allows you to store icons in an arbitrary directory NM indicates the start of the second icon column NM2 the text to appear underneath of the icon The sign is man datory 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 pro gram 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 mytlguide EM J MC N CL tutor TutStarter ME startTuto rial AR MyTlTZToolbar My Tl T2 Tutorial Here e MyT1T2Toolbar Is the toolbar identifier as it is used in the file COOlDar Users prop 384 User Extensions 385 e My T1 T2 Tutorial Is the title as it appears at the top of the guide lf your guide is a Bruker modified guide you can also redefine the original Bruker command i e specify t1 guide instead of myti1guide Note that the original Bruker guide is then no longer acces sible 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 35 42 118 159 8 co
37. 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 TOPSPIN in the same way a measured fid is processed Techniques such a selective excitation gradi ent enhanced spectroscopy and the handling of mixtures are supported To start the virtual spectrometer Enter nmrsim on the command line or click Analysis gt Simulate Fid 2 14 How to Add Your Own Functionalities The TOPSPIN functionality can be extended with various user defined com mands programs etc How to Create Macros Writing a macro is the simplest way to create a user defined command Just enter the command edmac create a file and enter a sequence of reg ular TOPSPIN Commands and or Python commands Save the file under a name of your preference You have created a new TOPSPIN command Just enter its name on the command line to execute it edmac shows a list of all available macros and allows you to execute one How to Create AU automation Programs Writing an AU program is another way of creating a new TOPSPIN com mand AU programs are more complex and more powerful then macros They are C language programs which may contain C statements regular TOPSPIN commands and various predefined AU macros and functions AU programs can perform various tasks such as dataset handling parameter handling acquisition processing analysis and printing Note that AU pro
38. zoom 1D data 36 119 2D data 161 in 2D phase correction 227 zoom 1D 2D data 42 Symbols command help 52 2d command 38 3d command 38 all command 40 128 170 basl command 227 omp files 27 I 15 ozip files 29 83 cal command 217 259 co command 182 dec command 203 209 229 244 dopt command 158 159 168 331 dx files 83 emf files 27 f r command 170 f2r command 170 gif files 379 381 gr command 181 hr command 40 128 hz command 154 178 im command 185 inc command 203 209 229 244 nt command 204 246 jpeg files 27 379 381 jpg files 27 379 381 kKeep command 41 129 170 Is command 185 It command 187 v command 183 md command 26 219 ov command 155 178 ph command 51 200 238 ph180 command 202 ph90 command 202 phr command 202 png files 27 121 379 381 pp command 232 pr command 25 179 prop files 269 et command 203 214 226 230 231 236 retsab command 231 s2d command 203 sd command 41 129 171 sino command 273 sl command 41 129 171 sl0 command 41 129 sr command 41 129 171 srO command 41 129 sret command 203 213 229 236 st command 185 su command 41 129 171 tif files 121 txt files 162 vr command 40 127 168 wmf files 27 121 y command 155 Zi command 40 128 170 z command 40 128 170 zo command 40 128 170 zxX command 40 128 170 2 command 39 48 127 168 8 command 40 127 168 2 comma
39. 107 373 378 381 magnitude calculation 107 matching the probehead 298 MAXI parameter 234 maximize all data windows 269 data window 268 maximum command line size 365 MC2 parameter 100 menu bar 37 commands 37 configuration table 367 369 entries 37 367 font 360 361 settings 348 MI parameter 234 minimize data window 267 minimum command line size 365 Minus key 48 mixtures 31 molecule structure viewer 152 mouse sensitivity in 1D baseline correction 229 in 1D integration 209 in 1D phase correction 203 in 2D phase correction 244 move data window 263 Mozilla 93 162 multiple display 1D 39 218 251 1D 2D 26 76 81 2D 26 251 in deconvolution 30 multiple display mode 76 218 multiple window display 125 multiplet 205 multiply with increment in 2D levels 183 N nbook command 372 negative 2D levels 187 new command 38 45 72 305 newtop command 54 next channel for wobbling 299 command 45 dataset in Browser 47 parameter field 99 103 plane in 3D 190 row column in 2D phase correction 244 256 window in data area 45 265 269 NMR ADMINISTRATION password 316 NMR SUPERUSER 316 nmradminpassword file 316 nmrsim command 31 nmrsuperuser file 316 noise region 273 274 NOISF1 parameter 273 NOISF2 parameter 273 notebook 372 NS parameter 291 O O1 parameter 292 O2 parameter 292 O3 parameter 292 objects of a dataset 26 125 263 348 354 355 356 oblique display of 2D spectra 185 187 of 3D planes 189 online hel
40. 207 read color scheme 338 data formats 75 integrals from disk 198 the prosol parameters 287 window layout 256 reb command 21 74 re enable disabled commands 350 reference peak in 1D calibration 206 in 1D phase correction 192 193 in 2D calibration 247 in 2D phase correction 229 referencing 99 reg file 204 relaxation curve 263 remote connections 329 remove commands 348 data from multiple display 210 menus 348 toolbar buttons 347 reopen a dataset 116 l 11 reopen command 67 116 rep command 22 74 repw command 74 rescale 2D projection 171 data in multiple windows 117 reset 1D baseline correction 217 1D phase values 193 3D cube size and orientation 183 F1 zoom factor in 2D 161 F2 and F1 zoom factor 161 intensity 1D 118 intensity in 2D 159 search mask 83 zoom factor 36 119 resize command line 346 data window 250 graphics 113 resolution of a screen dump 25 114 restore adjusted acquisition parameters GS 286 size and position of a data window 255 toolbar 348 uncorrected baseline 217 retrieve previously entered commands 37 38 rew command 22 74 Right Arrow key 38 42 62 rotate 3D cube 178 182 routing parameters 97 S S N value 262 Sample tab 142 sav command 34 41 save 1D baseline correction 217 1D integrals 204 1D phase correction 194 acquisition data 78 adjusted acquisition parameters GS 285 AU program 30 302 color scheme 337 I 12 cubic spline baseline points 219 current window layout
41. 256 data 27 34 41 77 data in analog filtered format 78 data to a JCAMP DxX file 28 data to a ZIP file 27 data window to a graphics file 25 114 entire dataset 77 78 integral regions 203 macro 29 parameters 122 123 peak list and peak ranges 224 phase correction 2D 229 232 238 processed data 78 processed data as pseudo raw data 78 pulse program 142 sum or difference spectrum 210 title of a dataset 124 scale 1D integrals 202 1D spectrum 118 2D spectrum 158 3D cube 183 individual spectra in multiple display 24 207 212 row column in 2D phase 230 scaling factor of integrals 203 scan planes of 3D data 181 rows columns in 2D 242 screen dump 25 114 scroll bar 92 96 search criteria 82 data 82 field in the parameter editor 91 95 result window 83 select AU program 303 color scheme 338 data 57 data in multiple display 208 209 data window 251 default printer 300 expno procno combination 69 first expno procno 69 folders in the browser 62 font 342 343 344 integral regions 197 199 lock signal color 337 multiple datasets 69 multiple folders 62 peaks in 2D phase correction 226 plot layout 110 printer 110 remote system 323 row column in 2D phase 229 spectra in 2D multiple display 241 spectrum color 336 spectrum print color 337 Topspin window 257 selective excitation 29 semi automatic peak picking 222 processing 100 sensitivity of the GS slider 284 of the mouse 194 200 217 231 serial command 104 serial p
42. 29 graphic functions 355 graphics files 25 114 grid display 35 172 281 window arrangement 252 gs command 93 276 284 GS parameter adjustment window 284 H halt an acquisition 274 275 halt command 274 276 288 Hardware requirements V helium level 282 Help button 46 menu 33 45 help in Topspin 44 on commands 46 help command 46 Hertz axis units 145 169 hist command 47 50 357 362 364 history file 362 hostname of a remote system 323 HTML page 46 I iconify all data windows 256 data window 254 iconnmr command 30 image display of 2D data 176 of 3D planes 180 import data 28 inconsistent dataset 92 initial guess 268 install AU programs 20 300 pulse programs 20 Topspin 297 installation directory 64 298 299 installnmr script 298 int command 149 Integral list 2D 167 integral bias 199 display 23 label 197 list 1D 134 regions 195 196 197 198 203 scaling factor 203 slope 200 trails 149 203 values 196 Integrals tab 134 167 205 integrals txt file 205 integration 1D automatic 194 198 1D interactive 194 195 198 mode 35 195 204 205 intensity alignment in multiple display 212 decrease 1D 118 158 increase 1D 118 158 manipulation 35 reset 1D 36 118 158 scaling 2D 159 interactive 1D baseline correction 214 1D calibration 205 1D data manipulation 189 1D integration 194 1D peak picking 220 1D phase correction 189 191 1D signal to noise calculation 260 2D calibration 246
43. 2D data manipulation 225 2D phase correction 225 data manipulation 25 34 335 modes 34 parameter adjustment 93 284 processing 99 Processing Guide mode 103 interface fonts 340 internal projection 24 Internet Browser 73 intrng file 199 202 204 IP address of a remote system 323 IUPAC standard 28 J JCAMP DX format 28 75 76 78 Jeol spectrometer 75 l 8 Jmol molecule structure viewer 143 JNMR data 75 K KDE konqueror 86 keyboard commands 33 kill command 53 Konqueror 86 153 L Left Arrow key 38 42 62 Levenberg Marquardt algorithm 268 li command 134 195 Liouville equation 29 lipp command 134 lippf command 134 list 167 1D integrals 134 2D integrals 167 2D peaks 166 AU programs 300 baseline points 218 Bruker AU programs 302 color schemes 338 data files 85 151 EXPNOS PROCNOS 69 found data 83 integrals 112 204 macros 29 opened datasets 59 60 61 parameter sets 65 peaks 112 222 peaks 1D 125 plot layouts 110 solvents 65 user defined AU programs 302 local Topspin interface 319 lock parameters 97 signal 281 lock command 282 lock display colors 337 mode 281 window 256 275 277 281 lockdisp command 275 281 lock in procedure 281 Lorentzian deconvolution 28 lower toolbar 35 macros in AU programs 103 355 in Topspin 29 47 100 354 359 362 magnitude calculation 100 matching the probehead 279 MAXI parameter 222 maximize all data windows 256 data window 255 maximum command line size
44. 3D 187 191 xmac command 31 X y axis display 39 155 y axis rotation in 3D 187 191 Z z axis rotation in 3D 191 zero order phase correction 1D 202 2D 242 243 zg command 291 293 306 ZIP data format 29 82 zoom 1D data 40 128 2D data 170 in 2D phase correction 240 zoom 1D 2D data 48 I 29 I 30
45. 81 field 37 115 120 157 object colors 336 data window 21 31 33 68 73 76 2D 157 3D 179 color scheme 337 contents 25 113 creation 68 handling 33 249 in 1D peak picking mode 220 in 1D phase correction 192 in 2D calibration mode 246 in 2D multiple display mode 239 in 2D phase mode 226 233 in baseline correction mode 215 in calibration mode 206 in integration mode 195 in multiple display mode 208 in S N measurement mode 261 in spline baseline correction mode 218 objects 24 popup menu 146 162 printing 109 reopen 116 tab bar 1D 121 tab bar 2D 165 toolbar 24 dataset active 251 colors 214 dir 21 305 directory tree 21 72 expno 21 60 65 305 files 86 153 handling 29 57 last 2D 34 last 3D 34 last used 332 name 21 60 65 73 procno 21 60 65 305 procno directory 73 properties 150 selection in multiple display 209 specification 72 251 title 65 top level directory 60 user 21 60 65 305 variables 78 datastation configuration 299 dcon command 28 350 dconpeaks txt file 28 deconvolution 28 default color scheme 338 command line size 345 configuration 299 find criteria 83 menu font 342 pivot point in 1D phase correction 192 pivot point in 2D phase 229 plane in 3D display 179 printer 111 Tab bar 335 zero order phase correction 193 define cubic spline baseline points 218 integral regions 196 NMR ADMINISTRATOR password 297 NMR SUPERUSER 297 peak ranges 221 peaks 222 de iconify data window 255
46. 9 6 1D Display BB examid_ 1H 1 1 Cibin Busse Figure 9 6 As soon as you click a peak it is selected and by default displayed in red See peak 1 in Fig 9 6 Note that this peak remains selected i e is used by Enter and Delete until a different peak is selected To extend the peak list for example with Regions Type and Index en tries 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 Peaks are only available if peak picking has been done command pp The peak list can be printed with print Ctr1tp List items can be se lected with the mouse copied with Ctrl c and pasted to other applica tions e g a text editor 142 1D Display 143 How to Display the Integral list Click the Integrals tab 1i Lipp lippf examid_1H 1 1 Cobia guest 1 _ O xi KID mintegral 1 21807940 16 Integral l 200564697 26 1 54945 0 ford r 4100 Integral 4 131427635 19 10 0425 0 6 158 4 491 integral 5 20492465 62 1 5658 0 4 404 3 979 Integral 6 1068531r028 12 01 6307 0 3 977 0 304 O x lajo 8 0 75 7 0 65 ppm Figure 9 7 This displays the integral list upper part of Fig 9 7 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 o
47. Bruker TOPSPIN gt 1 During TOPSPIN installation you can choose to automatically configure the firewall or not PC s delivered by Bruker Germany always have the firewall configured for TOP SPIN 343 Remote Control TOPSPIN lt version gt gt Bruker Utilities 2 Click Miscellaneous 3 Double click Command Prompt 4 In the Command Prompt window enter cd prog bin utilities Miscellaneous setfirewall cmd auto Firewall on PC with Windows XP SP2 no Topspin installed Configure the firewall as described in the Installation Guide for Win dows XP On all other systems the firewall must be configured manually by the net work administrator To do that view the file lt tshome gt prog server corba conf and open the ports specified here incremented by 50 For more information please refer to the installation guides for Windows or Linux or inspect the contents of the file corba conf Note that the firewall must be configured for TOPSPIN e spectrometer control e remote access TOPSPIN can be used for processing analysis on a local datastation even if it is not registered on the firewall However you will get a few Security Alert messages during startup 19 3 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 Windo
48. Change the Width of the Signal Region or Noise Region 19 4 DECONVOIUNON situa wn o446 ett daa ibe be Se OER a 2 6 15 5 Relaxation Analysis 0 0 0000 cc ees 280 Chapter 16 Acquisition 000 ccc ees 288 16 1 ACQUISITION GUlGG 2 yop 8 Ve goss Ane tee Scat Sarin ob wee 288 16 2 Acquisition Toolbar 0 0 0 ee 290 16 3 Data window Toolbar 0 0 00 ees 292 16 4 Acquisition Status Bar 0 0 0 0 ce eee 294 16 5 Command Queuing and Scheduling 005 297 16 6 Tuning and Matching the Probehead 298 MGs WSOC ck cha g cca Sgt ches a creak Sogn ster acest oad nn ere adhe Se sa 299 16 8 BSMS Control Panel 0 0 0 0 0 0c cee 301 16 9 Interactive Parameter Adjustment GS 303 16 10 Running an Acquisition 2 0 0 0 ee eee 305 16 11 Shape 100M lt 5 ancanc armed or otc tition ota aaa amp amp bade 4d 309 Easy definition of Shape pulses 0 00000 ee 311 Chapter 17 Configuration Automation 00 0c eee ees 316 17 1 NMR Superuser and NMR Administration password 316 How to Change the NMR Administration Password 317 17 2 Configuration ss mets ged eG eats smo a ja ete oe Oe eee a hte 317 How to Perform a Default Configuration on a Datastation 318 How to Perform a Customized Configuration on a Datastation 318 17 3 Parameter set conversion 00 0c eee eee eee 319 17 4 Automa
49. Layout Onia Files Figure 10 5 Here you can select various display properties region setting and file prop erties If you choose Display Properties a dialog box see Fig 10 6 will appear 172 2D Display Please select the components to be displayed together with the spectrum if available Cursor information F x Title Status parameters Acquistion parameters H UO oO Integrals x Integral labels x Peak labels b Contour levels bar s Show projections s Electronic Signature b Molecular Structure Visible projections OO FA OF2 F1 F2 Figure 10 6 Here you can set various display options including parameters integrals peaks contours projections and electronic signature The number of dis played digits for the integral and peak labels can be set in the User Pref erences click Options gt Preferences gt Spectrum 173 2D Display 10 4 Using the Tab bar The 2D 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 display see chapter 9 4 There are however some differ ences which are discussed below How to Set Processing Parameters Click the ProcPars tab edp The 2D processing parameter editor contains a column for each of the two dimensions F2 and F1 see Fig 10 7 Note that not all parameters exist in both dimensions
50. Left click hold a data name expno or procno and drag it into a mul tiple display data window The data will be superimposed on the cur rently displayed data or Right click a data name expno or procno and choose Display from the popup menu the data will be displayed in the current data win Dataset Handling dow or Right click a data name expno or procno and choose Display in new window from the popup menu the dataset will be displayed in a new data window 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 between Then right click one of the selected datasets and choose Display from the popup menu A new window will be opened showing the selected datasets in multiple display mode However if the current window was already in multiple display mode the selected spectra will be superimposed on the currently displayed spectra 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 TOP SPIN then opens a dialog box from which you can select the desired exp no procno combination see Fig 5 13 Clicking Open will open the selected dataset whereas clicking Print will print the displayed dataset list You can however configure TOPSPIN to automatically open the first avail able expno p
51. Loop count for t Bo width F Receiver RG Receiver gain DY us i Dwell tire is hisel Caer sardine od 4 4 I gt Figure 16 16 K Optionally click m to show the pulse program parameters only b Click the ig button to read the prosol parameters Or Set the relevant parameters manually As an alternative to step 2 you can set the acquisition parameters in teractively in the GS window see par 16 9 3 To start the acquisition e Click gt in the upper toolbar or enter zg on the command line The data window toolbar will automatically switch to the Acqu tab and 306 Acquisition 307 the FID display window will appear FID protona 1 1 Cubio quest SPE Title PulseProg Peaks Integrals Sample Structure Fid 4cqu ie tele e be g fA Cyelasoern Figure 16 17 The buttons in the toolbar have the following functions Iw Show FID in shuffled mode W Show FID in unshuffled mode horizontally arranged i Show FID in unshuffled mode vertically arranged Ww Show FID in unshuffled mode interleaved ki Switch between FID and spectrum Gy Stop the acquisition stop m Halt the acquisition halt Clicking the fj button to switch to real time FT turns the button green and opens two extra buttons IR Switch between FID and spectrum of Real time FT settings Toggle calculation of peak with at 50 5 5 and 1 1 height Shown as status parameters Clickin
52. NOISEREG 1573 4 Click OK Note that as you change the width the right limit is modified correspond ingly The left limit is kept The S N value is automatically recalculated and displayed Deconvolution The Analysis menu of TopSpin offers the possibility of deconvolution This line shape tool is especially useful to interprete complex spectra in which peaks can not be defined clearly Deconvolution calculates theoretical sig nals with different methods for example Gaussian Lorentzian or a mixture of these line shapes As a result information of peak position line width and integrals of deconvolved signals are available Furthermore it is possible to display them graphically With this auxiliary tool peaks of 1D and 2D NMR spectrum can be interpreted more easily Overlapping peaks may be deconvolved into a sum of such line shapes To start deconvolution expand the spectrum on the display to show the peak or peak group of interest Deconvolution can be activated from the command line by typing decon or from TopSpin toolbar by clicking Analysis gt Line Shape Fitting gt Lorentz Gauss Deconvolution The following 2 6 Analysis 21 1 dialog box will appear Q Deconvolution will operate on the currently displayed spectral region Please press OK if the desired region is visible Otherwise press CANCEL expand the spectrum accordingly and re enter deconvolution Figure 15 3 After clicking OK different a
53. Properties An information box as displayed in Fig 9 15 will appear 159 1D Display EA Properties examid 1H 1 1 CABio quest Dimension Proc Acqu Pulse program Acquisition date Nucl SFO1 MHz Solvent Acquired data available Processed data available Figure 9 15 Note that this is status information which cannot be changed How to Display a List of Files of a Dataset Right click inside the data window choose Files Fig 9 16 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 160 1D Display Directory CBO Wataiguestininrexan d_ 1H audita txt cyclosporina pdb fic format temp prosol_History pulseprograr sample infto prop Scon Uxnitrir par os Figure 9 16 Fig 9 17 shows the file list that appears when the Spectrum tab is active i e when the processed data are displayed It is the contents of the procno directory 161 1D Display PH File list Directory CBO Wataiguestinimnr lexan d 1H pdatar qi T E auditp txt curdat un Vv email xariid 1H_1_1 pdt interny last plot vp layout swp outd parm txt peak txt peaks portt portfolio por proc procs title cn Figure 9 17 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
54. S it turns green 2 Move the mouse into the region to be copied 3 Left click hold and move the mouse to the desired position 4 Release the mouse to copy the region How to Delete all Integral Regions 1 Click the button ag 2 Click OK to confirm deletion How to Read Import Integral Regions 1 Click the button 2 Click Read intrng to read the last stored integral ranges 250 2D Interactive Manipulation 251 or Click Import Integration Regions to import an exported integral region file see below How to Save Export Integral Regions 1 Click the button m 2 Click Save Regions to intrng to save the regions to the current dataset PROCNO file int2drng or Click Export Integration Regions to export the integration region file for general usage i e usage with other datasets How to Return from 2D Integration mode Click the following button Ej to save the current integral regions and return Click the following button a to return to the 2D integration mode without save 13 3 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 nuclear 2D Although multiple display is norma
55. TL Show pulse program parameters ased s Status parameter display The button turns green when activated dpa g Set probehead solvent dependant parameters getproso1 3 Set nuclei and routing edasp 2 Change raw dataset dimensionality parameter PARMODE Y Collapse expand all parameter sections 4 Search for specified parameter Changed parameters are automatically saved Note that the and E button to the right of the PULPROG parameter allow 132 1D Display you to show the pulse program list or edit the current pulse program re spectively How to Edit the Title Click the Title tab edti examid 13C 1 1 CiBio guest spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Scgu 1301H AY 300 Automation Cholesterylacetate 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 E Save the title file under a new name 3 Reload the title file Undo modifications since the last save E Open the title file with the external editor defined in User Prefer ences 133 1D Display How to Edit the Pulse Program Click the PulsProg tab examid 13C 1 1 CiBio guest Pectrum ProcPars AcguPars Title PulseProg Peaks Integrals Sample Structure Fid ACHU S M E Pulse program zgpqs0 l ze dll pllz fz 30m do fz Lawi plls f2 Jll cpd f2 DELTA du do
56. a Shell 3 Enter 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 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 17 2 Configuration The main configuration steps are performed by the commands cf and expinstall They can be started from the e Command line e Options gt Spectrometer tools menu 317 Configuration Automation Spectrometer gt Setup menu However the Spectrometer menu is only available after cf has been per formed 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 TOPSPIN on a new computer a new disk or in anew 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 configu ration is sufficient If however you want to use AU programs you must execute expinstall once selecting nstallation for Datastation Default How to Perform a Customized Configuration on a Datastation If you want to configur
57. an internal user and his password To log off the internal user Enter logoff on the command line Or Click Options gt Administration gt Log off and enter the user name and password as requested If TOPSPIN internal user is not mandatory i e the entry Enforce login for working with TopSpin is disabled you are not prompted to login after TOP SPIN startup You can however still login as internal user with the com mand login Locking TOPSPIN s Graphical User Interface TOPSPIN can be locked such that it does no longer accept user input via mouse or keyboard To do that enter lockgui on the command line Or Click Options gt Administration gt Lock TopSpin user interface A window will appear see Fig 18 6 indicating the locked status and offer Regulatory Compliance ing buttons to unlock TopSpin locked by user carol at Wed Jul 13 16 53 52 BST 2005 Please press a button to unlock carol to unlock MMR administrator to unlock Figure 18 6 Only the current user or the NMR Administrator can unlock the user inter face While TOPSPIN is locked all background activities such as data acqui sition and processing continue For safety reasons TOPSPIN can be forced to execute Lockgui automati cally when no commands from the command line menus or toolbar buttons have been entered for a certain period of time for instance because the current user has left In order to enable automatic locking
58. and move the mouse see Fig 13 2 b Right click at the peak position and choose Add from the popup menu exam2d HC 1 1 Cibio quest O x ASR c a a a ra Click the right mouse button to select the peaks for phase correction Ei T LL m cs T 135 75 7 4 7 3 7 2 7 1 F2 ppm Figure 13 2 c Click the a 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 13 3 shows an example of three selected peaks 240 2D Interactive Manipulation exam d_HC 1 1 Cjbio guest x a Click the right mouse button re fy 08 FE E kH EL a E S T PE m tT m 12 10 g 6 4 2 F2 ppm Figure 13 3 2 Click the button C to phase correct the columns F1 A new data window called Phase 2D will appear showing the columns of the selected peaks see Fig 13 4 Wi Phase 2D exam2d_HC 1 1 Cbio guest l oj x A lo 1 R mja s n e l al e pivot 126 44 ppu Phase increment 0 20 ph 0 00 phl 0 00 Figure 13 4 241 2D Interactive Manipulation 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 W 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 but
59. 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 ti 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 12 21 A red cursor line will appear at the nearest peak whose intensity is be tween MI and MAXI 5 Right click to add the selected peak to the peak list see Fig 12 21 234 Add Peak Ta List Pick Backward Figure 12 21 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 2 Choose Delete peak under cursor from the popup menu see Fig 12 22 Delete All Peaks Delete Peak Under Cursor Delete All Regions Delete Region Under Cursor Pick Peaks On Ranges Show Peak List Set Ml Set MAxI Figure 12 22 To delete all peaks Click the X button in the data window toolbar Or Right click
60. com mand cmdhist see Fig 3 3 EY Command History cmdhist Figure 3 3 It shows all commands that have been entered on the command line since TOPSPIN was started You can select one or more commands and apply one of the following functions Execute Execute the selected command s Append Append the first selected command to the command line The ap pended command can be edited and executed Useful for com mands with many arguments such as re Save as The selected command s are stored as a macro You will be prompted for the macro name To edit this macro enter edmac lt macro name gt o execute it just enter its name on the command line 3 5 Starting TOPSPIN commands from a Command Prompt TOPSPIN Commands can be executed outside of the TOPSPIN interface from a Windows Command Prompt or Linux Shell The TOPSPIN Interface Under Windows 1 Open a Windows Command Prompt 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 Examples C ts2 1 prog bin sendgui ft executes a 1D Fourier transform C ts2 1 prog bin sendgui re examld 1H 1 1 C bio joe reads the dataset C bio joe nmr exam1d_1H 1 pdata 1 Under Linux 1 Open a Linux Shell 2 Enter a TOPSPIN command in the following format lt tshome gt prog bin scripts sendgui lt topspincommand gt where lt tshome gt is the TOPSPIN in
61. 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 available RASmol commands are described in the Jmol Help menu Multiple molecules or multiple aspects of one molecule can be dis played 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 1D Display How to Display the FID Click the Fid tab fid examid_1H 1 1 Cobio guest 1 Spectrum ProcPars AcguPars Title PulseProg Peaks Integrals Sample Structure Fid Accu 200 rel 1e3 1 2 3 4 5 s displays the raw data If these do not exist the text No raw data available appears The following additional buttons appear at the right of the lower toolbar jw Show FID in shuffled mode Ww Show FID in unshuffled mode If you open a new dataset the Spectrum tab is activated no matter which tab was selected before If you enter any interactive mode for example phase correction mode the Tab bar is replaced by a toolbar for that mode 9 5 1D Display Options How to Toggle between Hertz and ppm Axis Units Click th
62. data stored in special formats select the desired file type see Fig 5 18 and click OK A dialog will appear which depends on the chosen file type Just follow the instructions on the screen The following file types are supported JCAMP DxX Bruker Topspin data stored in JCAMP DX format Zipped TOPSPIN Bruker TOPSPIN data stored in ZIP format WINNMR Bruker WINNMR data A3000 Bruker Aspect 3000 data VNMR data acquired on a Varian spectrometer JNMR data acquired on a Jeol spectrometer Felix 1D data FID or spectrum which are stored in FELIX format 1 Note that the TOPSPIN data format is identical to the XWIN NMR data format 82 Dataset Handling Note that in all cases the data are stored in a single data file which is un packed converted to standard Bruker format i e to a data directory tree Ey Open fromjdx Options O Open MMF data stored in standard Bruker format CO Open other file Required parameters File type JICAMP Dx we Figure 5 18 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 in one of the tree following ways Drag amp drop Click hold a file with the extension dx or zip and drag it into the TOPSPIN data area or data window Copy amp paste 1 Right click a file with the extension dx or zip and choose copy from the popup
63. efp 21 lb 0 8 em ftipk 3 cmnymacrosimac etp ta full path indicates a macro 4 cAmypysipoy efp py Ca full path with py indicates a Python script Click on gt Browse For Macro locate a Topspin macro gt Browse For Python locate a Topspin Python program gt Execute start processing the dataset list gt Back return to list definition gt Show show datsets while processing Figure 7 5 Continue with command definition for example for Macros or Python programs You can even Browse for Macros or Python programs The 113 Data Processing following dialog will appear dependent from your selection EN Python Programs File Options Help Source F Bruker T OPSPIN2 1 alpha exp stan nmripy Search in names search exam sum real py inadph py inadph2 py ineptrdsp py y test suite py ser_ef_apk py ser_efp py tir py Cursor2d py exam em ft apk py exam multi efp py lexam pulsprog py presepy igure 7 6 After having chosen a Python program or a Macro push the button ex ecute for finishing serial processing command In Figure 114 Data Processing 115 Abbildung 7 7 you can see the look of the actual dialog Senal Processing Define Command Please define the command to be executed on the datasets Examples 1 efp 2 Ib 0 8 em ft pk 3 CAmymacros mac etp a full path indicates a macro 4 cAmypys py etp py a full path with py indicates a Python sc
64. feature list which stays open with one click and all functionality concerning this process are available and can be started with one click Furthermore a mouse contact of the functionality opens a balloon help and one click leads to the continuative menu The yellow data button in the upper left corner replaces the File menu Accesorily all buttons appear in a new design and can be detached from the default position The Topspin Window The TOPSPIN window consists of a data area a data browser toolbars and a menubar Note that the browser can be inactive hit Ctr1 d or displayed The TOPSPIN Interface as a separate window Fig 3 2 shows the Topspin window with two data windows in the data area and the browser as an integral part l minimize maximize title bar button button menu bar tA Bruker TOPSPIN 2 0 on NMR datastation as Jos van Bo pm ak upper File Edit View Spectrometer Processing Analysis Options Window Help oolbar eH Ale Bl a4 44 5 4 ES lower toolbar G aaa N AERA Browser PFolio Alias p D E Cbi a z 4 guest H esamid_ 136 H examid 1H E exam2d_CH Eg examed HC _ examzd_HH GE E examad i an H E Cobia g EJ cts13 Loe oa close button command line status bar 1D data window 2D data window Figure 3 2 Note that the menus and toolbars depend on the data dimensionality The descriptions below holds for 1D data For 2D and 3D data the menus and
65. for example look like 178 2D Display exam d HC 1 1 Chio guest Sle spectrum ProcPars AcauPars Title PulseProg Peaks Integrals Sample Structure Fid ACU 5 0 F2 ppm How to Switch on off the Projection display Click the following toggle button in the upper toolbar 4 Switch the projection display on off pr With the projections displayed a 2D dataset looks like this exam2d HC 1 1 Cibio quest Sele spectrum ProcPars AcquPars Title PuleeProg Peaks Integrals sarple Structure Fig Acqu F2 ppm 179 In this example the F1 projection is selected as indicated by the filled blue square 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 projection area of the data window the following pop up menu appears External Projection Internal Projection Baseline At Center Baseline At Bottom Clicking External Projection opens the a dialog box where you can spec ify 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 projec tion and displays it along with the 2D spectrum Clicking Baseline at Bottom or Baseline at Center allows you to put the projection baseline at the respective positions Alternative ways to calculate display projections ar
66. for the keys Alt PageUP and Alt PageDown However when used with the control key they work on all windows for example Hit Ctrl Ctr1 Altt PageUp or Ctr1 Alt PageDown 126 1D Display 9 3 Changing the Display of a 1D Spectrum or FID TOPSPIN offers buttons to scale or shift the spectrum vertically and horizon tally How to Change the Vertical Scaling of the FID or Spectrum 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 AlttEnter Reset the intensity or Click one of the following buttons 2 Increase the intensity by a factor of 2 2 g Increase the intensity by a factor of 8 8 2 Decrease the intensity by a factor of 2 2 8 Decrease the intensity by a factor of 8 8 Reset the intensity vr Alternatively you can enter the corresponding commands as specified be tween square brackets To manipulate all data windows press the Ctrl key while clicking one of the above buttons How to Smoothly Change the Vertical Scaling of the FID Spec trum Click hold the button and move the mouse or Turn the mouse wheel while the cursor is in the data window 127 1D Display How to Change the Horizontal Scaling of the FID or Spectrum Click hold the button and move the mouse a Zoom in out smoothly or Click one of the following buttons i Zoom in to the center spectrum or
67. 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 installa tion 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 NMRSUPERUSER will be stored in the file lt tshome gt conf nmrsuperuser the NMR Administration password to be used for TOPSPIN configura tion commands This password can be freely chosen and is not con nected to any user It is asked for by TOPSPIN commands like cf expinstall 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 Administra tion password have different purposes and are totally independent Configuration Automation Changing one of them does not affect the other 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 NMRSUPERUS ER 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
68. grams 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 a new AU program is to select a Bruker AU program save it under a new name and modify it to your needs The cho sen name is now available as a new TOPSPIN command Alternatively you can open a new file from the AU dialog box and write your AU program from scratch For details on Bruker AU programs and writing your own AU programs click Help gt Manuals gt Programming Manuals AU Programming How to Create Python Programs Writing a Python program is yet another way of creating a new TOPSPIN command Python is a new generation scripting and object oriented pro gramming language Python programs are even more powerful than AU programs They are easy to use and allow you to execute TOPSPIN com mands handle NMR data and parameters generate graphics and inter act with the TOPSPIN user interface via dialogs windows etc To create a Python program enter the command edpy select a file and insert your Python statements Graphics and interface features programmed in Py thon look and work the same as regular TOPSPIN features For details on Python programming click Help gt Manuals gt Program ming Manuals Python Programming The examples mentioned there like pycmd7 are delivered with TOPSPIN Just enter their
69. highlighted How to Show Hide Pulse program and Title in the browser Right click the data name folder button and choose 69 Dataset Handling Show PULPROG Title from the popup menu see Fig 5 8 Display Display in Mew Window Display As 2D Projection Scroll to active dataset Fully Expand Selection Show PLULPROG Title Show Date Sort by Date Copy File Properties Delete Rename Files Add New Data Dir Remove Selected Data Dirs Figure 5 8 How to Show Dataset Dates in the Browser Right click the data name folder button and choose Show Date The last modified date is shown to the right of the dataset NAME where as the acquisition date is shown to the right of the dataset EXPNO see Fig 5 9 70 Dataset Handling Browser Last50 Groups Alias ECG CAbio Se quest a examid_13C 2007 04 12 12 08 59 GE examid_1H 2006 05 16 15 13 27 BG 1 2g 2004 03 30 15 00 44 i 1 1H Cyclosporin i 99999 1H Cyclosporin H 0 exam2d_CH Figure 5 9 How to change the default Top Level Data Directory By default the browser shows the TOPSPIN installation directory with the Bruker example datasets To suppress this feature click Options gt Preferences set click Administration and uncheck Show TOPSPIN data examples directory in data browser How to Add Remove or Interpret Alias Names To add an alias name 1 Click the Alias tab in the browser 2 Right click in the Alias
70. lock in procedure or as shown above after lock in has been successful At the top of the lock window the following buttons are available Open the user preferences window set 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 a Close the lock display window Note that an external lock display window is independent from the TOPSPIN window You can for example minimize TOPSPIN while keeping the lock dis play open The lock display can also be opened by double clicking the lock field in the 300 Acquisition acquisition status bar See par 16 4 The lock process can be started by entering Lock on the command line This command is described in the Acquisition Reference manual 16 8 BSMS Control Panel The BSMS control panel allows shimming locking sample handling and helium level measurement To open this panel E bsmsdisp on the command line The BSMS Control Suite window will appear see Fig 16 12 bes 301 Acquisition ESMS Control Suite Main Lock Sample amp Level Shim Autoshim Service AUTO Phaze Power ain Lack Lock Praise Poy er ain SAMPLE LIFT SFIN SHIM fa VALUE Previous Actua
71. menu 2 In TOPSPIN click Edit gt Paste paste Associate JCAMP DxX files with a script 1 Create a file with the extension cmd e g j camp cmd with a text editor 2 Enter the following line lt tshome gt prog bin sendgui cmd fromjdx 1 83 Dataset Handling and store the file 3 Open the Explorer and find the JCAMP DxX file 4 Right click the filename and choose Open with gt Choose pro gram gt Browse 5 Find and select the script and click OK Now every file with the extension dx will automatically be opened in TOPSPIN when double clicked 5 4 Saving Copying Data How to Save or Copy Data You can save the current dataset as follows 1 Click File gt Save Ctr1ts This will open a dialog box see Fig 5 19 Please specify destination data set MAME examid_14C EXPNO 1 PROCNO 1 DIF CABruikenTOPSPIN USER quest Ok Cancel Help Figure 5 19 2 Select an option and if applicable a file type 3 Click OK to execute the option The options correspond to the following command line commands e wrpa copies the current data to a new data name or expno 84 Dataset Handling 85 e toccpn convert experiment information to ccpn format 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 filter
72. names on the command line to execute them The Python dialog window is also available from the TOPSPIN menu Click File gt Open and select Open other file gt Python pro gram 2 15 How to Automate Data Acquisition TOPSPIN provides special user interfaces for automation walk up bio molecular experiments etc To open these interfaces Type iconnmr or click Spectrometer gt ICONNMR Getting Started 33 The TOPSPIN Interface Chapter 3 The TOPSPIN Interface 3 1 New Flow User Interface with TopSpin 3 0 Beginning with TopSpin 3 0 a new flow user interface is introduced to allevi ate all user processes Per default the known TopSpin user interface is activated but the new flow user interface can be enabled in the User Preferences The new workflow based interface with its applicable arrangement of all 34 The TOPSPIN Interface 35 working processes allows the user to control intuitional the workflows TU vier Toppe LEBA on LANIR ws Ona n E sani 3 Stat Acquire Process Analyse Pubish View Manage amp m eee e eee i ranno Y rere amp es 3 2 i Open Dataset E Find Dataset Create Dataset Paste Dataset PS QD BY ar a Lasso Groups ff Meant 41 17 pa a Ost Specie ProcPars AcquPars Tie PulseProg Peaks integrals Sampie Structure Pict Fio 10 t DRE E 3 4 4 2 8 2 0 ppm Figure 3 1 The Flow menu opens a horizontal
73. not display the contained information correctly Particularly when you re size the imported graphics sections of the text the spectrum or the axis sometimes have disappeared Usually this is only a display problem When you print the respective page the representation is correct 120 Printing Exporting Data How to Store Export a Data Window as Graphics File The clipboard and metafile formats are resizable vector formats In addi tion to this TOPSPIN allows you to save the contents of a data window in a graphics file of selectable type Supported formats are png jpg jpeg omp emf wmf and pdf 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 Note that exporting a data window to PDF format is only supported in TOPSPIN 2 1 and newer How to export projections of peak lists Certain situations may require that the user wants to store a projection of a peak list e g in order to evaluate an assignment in a 3D by verifying the annotated projected 2D HSQC peak list on the respective 2D spec trum Therefore it is useful and timesaving to use the option export pro jections of peak lists In order to create such a peak list
74. phase correction 1D 193 2D 231 90 degree phase correction 1D 193 2D 231 A abs command 99 103 194 195 198 214 absd command 214 absorption mode 192 193 229 230 231 acqu command 275 acquisition commands 274 278 mode 300 parameters 93 94 287 status bar 276 289 toolbar 273 275 Acquisition Reference Manual 21 97 282 283 300 AcquPars tab 93 123 165 287 activate a data window 251 the next data window 256 add comment to audit file 308 directory to the browser 22 functionalities to Topspin 29 peak in 2D phase correction 227 peak to peak list 222 add increment in 2D levels 174 align intensities in multiple display 212 peak positions in multiple display 212 Alt F11 key 118 158 Alt F4 key 41 47 Alt F6 key 47 Analysis menu 25 26 33 apk command 99 103 191 apks command 191 arrange data windows 252 data windows horizontally 254 data windows vertically 253 rows columns in 2D phase correction 232 ascii files 86 153 ased command 96 123 Aspect 3000 data 75 ATM probehead 279 280 atma command 280 AU macros 29 354 355 AU program reference manual 104 2 AU programs 20 29 103 300 354 359 362 audit trail check 307 automate data acquisition 30 automatic 1D baseline correction 99 1D calibration 99 205 1D integration 194 1D peak picking 220 1D phase correction 99 191 2D calibration 246 compilation of an AU program 303 configuration of a datastation 299 selection of the first expno procno
75. procno gt lt PathToDataset2 gt lt expno2 gt pdata lt procno gt 2 The command md no load ignores the datasets stored in the last multiple display session and enters the multiple display 3 The command md write writes only the assoc file containing the data set list for multiple display Please note that the multiple display module is not started with this command Enter command and full pathname of specified dataset in the TopSpin command line md write lt PathToDataset1 gt lt expnol gt pdata lt procno gt lt PathToDataset2 gt lt expno2 gt pdata lt procno gt Multiple display mode is supported for 1D and 2D spectra For spectra with a dimension gt 2 the selected slice subplane is shown How to Select Deselect Datasets To select a dataset 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 In the lower part of the browser you can Click one dataset to select it or Hold down the Ctrl key and click multiple datasets to select them 221 1D Interactive Manipulation 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 12 12 and its entry in the lower part of the browser is highlighted see Fig 12 13 Note that e no spectrum selected all spe
76. projection the following steps must be executed 1 Switch to the peaks tab of the data set from which the peak list pro jection should be used 121 Printing Exporting Data 2 Choose Export from the peak table context menu right click E exam3a 1 1 C Bruker TOPSPINidata guestinmr spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Peak v F3 ppm F2 ppm wF1 ippm intensityjabsy 44 4 4727 54 4986 5 9786 18274835 00 55 4 4727 12 4340 2 3521 21623906 00 77 4 4727 16 3169 2 4916 30606920 00 24 4 3913 31 8484 3 3750 14197056 00 53 4 3913 55 7929 5 8856 21066445 00 58 4 3913 19 5526 2 3986 22570729 00 5 4 3100 46 7328 4 6303 1129378400 9 4 3100 46 7328 4 3978 11652460 00 16 4 3100 21 4941 3 0030 12404568 00 18 4 3100 21 4941 2 2126 1309088200 61 4 3100 31 8484 3 4214 23242869 00 BA 4 3100 60 3229 5 7926 35436298 00 15 4 0984 38 3199 2 9100 12354004 00 52 4 0984 60 3229 5 6066 20964817 00 68 4 0984 15 6698 2 3521 24912674 00 72 4 0740 36 3785 4 3048 27304293 00 88 4 0740 36 3785 4 5838 43406665 00 6 3 9357 47 3800 4 9557 11414718 00 Figure 8 4 export dialogue Please note that the active flag Project Peak envokes the export of the entire projections peak list If seperate peaks should be exported they must be selected in the peak table and the flag Export selected data must be set Annotation Show spectrum Ex
77. 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 20 1 1 Define User Preferences Location for all Users User Preferences are by default stored in the current users home direc tory lt userhome gt topspin lt hostname gt During the first TOPSPIN session files with default settings are created there They can then be modified with the set command and used in later sessions You can however also store user preferences at one central location 349 User Preferences which are then used by all users This location can even be a remote drive allowing you to use the same preferences on all computers in the network To do that 1 Make a backup copy of the file lt t shome gt javaenv cmd 2 Open the file lt t shome gt javaenv cmd using a text editor 3 Locate the line set SYSTEM PROPS DXWIN NMRHOME XWINNMRHOME DCOMPUTERNAME COM PUT estes near the beginning of the file 4 Append a white space character and then DPROPDIR lt dir gt to the end of this line where lt dir gt is the definition of the storage directory consisting of one or more parts see below 5 Close the editor The definition of the storage directory for User Preferences can take three forms DPROPDIR lt mydir gt Stores the user properties in lt mydir gt prop Example DPROPDIR x y z DPROPDIR lt mydir gt USER 2
78. sum of all integrals and adjusting individual integral values accordingly To do that 209 1D Interactive Manipulation 1 Right click in the reference integral region 2 Choose Normalize from the popup menu see Fig 12 6 3 Enter the desired sum of all integrals and click OK Select Deselect Calibrate Normalize Lastscal Delete Figure 12 6 Calibrating and normalizing only effects the current dataset To scale inte grals 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 integrat ed interactively To do that 1 Right click in the reference integral region 2 Choose Use Lastscal for Calibration from the popup menu see Fig 12 6 As such you can compare integrals of different spectra Note that this only make sense for spectra which have been acquired under the same exper imental conditions 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 the selected integral regions from the display Click the following button t Delete selected integral regions from the display To delete a single integral region from the display 1 Right click in the integral region 210 1D Interactive Manipulation 2 Choose Delete from the popup me
79. tabs 4 Column Allows you to select the columns to be displayed set the column e width and the number of fraction digits Furthermore you can switch on off scientific notation of values for each individual col umn e Colours Allows you to set various colours of the table 148 1D Display e Spacings Allows you to set various spacings of the table Table properties Column Colours Spacings d Column properties Column width Fraction digits Scientific notation integral rel Peaks Fange F1 trom Fange F1 to WF 1 pem Intensity abs Shortcuts Apply Figure 9 10 Enter key zoom into spectrum i e show region around selected in tegral s Delete key delete the selected integral s from the integral list 149 1D Display Ctrl c copy selected integrals to the Clipboard Ctrl a select all integrals Home select the first integral End select the last integral Shift Home select current and first integral and all in between ShifttEnd select current and last integral and all in between Double clicking an integral will show the peaks within the integral re gion if they exist It they do not exist it will Zoom into spectrum show ing the integral region Note that these keys only work when the cursor focus is in the data win dow 150 1D Display How to view Sample Information Click the Sample tab edsam P
80. that when you import a graphics file into another program and resize it you loose information Therefore we recommend to resample rather than resize graphics 2 9 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 correction etc 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 Processing gt Fourier Transform e entering an interactive mode by clicking a tool button e g p e entering a user defined command usually an AU or a Python pro gram see Help gt Manuals Programming Manuals Processing and analysis commands require certain parameters to be set correctly Most commands in the Processing or Analysis menu like wm and ftf open a dialog 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 parame ters from the parameter editor To do that enter edp or click the ProcPars Tab of the data window If 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 gt Data gt Processi
81. the current MDI window such that all selected obejcts are visi ble Ctrl E Starts the annotation editor of the currently anchored peak Opens the rotate peaks dialog Ctrl Shift S Opens the shift peaks dialog Ctrl Shift D Opens a window displaying detailed informa tion of the current selection of peaks Ctrl Shift A Opens the annotate by reference dialog Focus in the Browser elect previous dataset DownArrow Select next dataset next dataset _ ae Seika oleied eOEnd Rode or user name expno selected expand node or collapse node depending on the current state ss Entter procno selected display this dataset name expno selected display this dataset Enter multiple procnos selected show in multiple dis ee eens Delete one or more name expno procno nodes ee selected delete these datasets The TOPSPIN Interface Focus anywhere in TOPSPIN AlttPageDown Scale down the data by a factor 2 72 Cer I Alt PageUp Scale up by a facior of 2 in all data windows C rI Aalt PageDown Scale down by a factor of 2 in all data windows AlttEnter Perform a vertical rest lt C rI alttEnter Perform a vertical reset in all data windows AletPIus Zoomin zi OOOO Alt Minus Zoom out zo SS Cer1 alt Plus Zoom in in all data windows CerI Alt Minus Zoom out in all data windows 48 The TOPSPIN Interface 49 Focus in a Table e g peaks integrals nuclei solvents
82. the data window and choose Display Properties dopt 2 Check Contour Levels Bar in the appearing dialog box and click OK see Fig 10 2 168 2D Display exam d HC 1 1 CBio guest Sele spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample structure Fid EL E Lael qm LL o co a T F2 ppm Figure 10 2 How to Switch on off Square 2D layout Right click inside the data field and click Square Layout On Off Era 1 1 Chio guest BHA Spectrum ProcPars AcquPars Title PulseFrog Peaks Integrals Sample Structure Fid Acgu 120 80 F1 ppm 6 F2 ppm Figure 10 3 The F2 scaling will be adjusted to reach a square display 169 2D Display How to Zoom a 2D spectrum in out Click one of the following buttons 1 Zoom in to the center spectrum or left edge FID of the dis played region increasing the horizontal scaling zi Zoom out from the center spectrum or left edge FID of the dis played region decreasing horizontal scaling zo El Perform an exact zoom via a dialog box zx EA exacizoom Please enter the exact coordinates of the desired expansion omo Figure 10 4 a Enter the coordinates of the desired region in the dialog box b Click OK Undo last zoom z1 W Show full spectral width in F2 2r Show f
83. tise Om TITLE 1D Processing Panel TTT COLOR 06 0S 255 Toggle button definition TOGGLE BUTTON To 2D TOGGLE CMD bpan bproczd TOGGLE TIP Switch to 2D processing Top row button definition TOP BUTTONS EMS SFIS SPRES 1 To locate this enter hist and look for the entry User properties directory 3 6 User Extensions 377 TOP COLORS YELLONLS YELLOW1S YELLOW1 TOP CMDS em t pk TOP TIPS Exponential multiplication Fourier transtorme Phase correction Panel button definitions LAYOUT format rows columns hgap vgap PAN LAYOUT 1 Bo 65 36 PAN BUTTONS P rims EXPORTS SSEND TOS S PAN COLORS BLUE1 BLUE1S BLUE1 PAN CMDS prnt exportfileS smail PAN TIPS Print the spectrum lt br gt as it appears on the screen Export the dataset lt br gt to pro AG Oae See Sh Send the dataset by email If you type bpan exam a panel with 75 buttons will appear 5 rows and 15 columns The corresponding panel file is called cmdpanel exam prop which resides in the directory lt tshome gt classes prop English In the same directory you can find the files cndpanel bnmr prop and cmdpanel bnmrsel prop which are used to display the bumr and bnmr sel panel described above The texts displayed on the buttons can be graphically adjusted in various ways because the text may optionally be specified in html format In the example above the PAN BUTTONS property has no html tags therefore the text
84. 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 Click in the desired data window or click its title bar Or Click one of the colored radio buttons above the data area The pressed radio button the green one in the example below corre sponds to the current dataset M2 3 examid TH 2 1 CAbio 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 264 Data Window Handling Click Window gt x dataname expno procno dir user where x is the number of the desired window and dataname expno procno dir and user refer to the dataset displayed in that window Or Hit the F6 key to activate the next window Repeat that until the de sired window is the active window How to Open a New empty Data Window Click Window gt New window Al ttw n 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 5 3 How to Arrange Data Windows If the data area contains multiple data windows you can arrange them in various ways
85. window list see Abbildung 7 4 Searching will be performed in all data directories marked in the data directories list below The checkboxes at the right will enforce exact matching if enabled NAME 13 O EXPNO PROCNO USER Title Pulse Prog 4 Search result Found 9 Data Sets Please right click In a list for more options Dimension Data type Date from mmddyy Date till mm dd yy TERRE zgpg30 2004 03 30 11 43 33 rgpg30 2004 03 30 11 43 35 zgpg30 2004 03 30 11 43 33 jmod 2004 03 30 12 01 05 depti35 2004 03 30 12 16 36 depts 2004 09 30 12 53 06 neptao 2004 03 30 13 27 39 zgig3D 2004 03 30 14 35 54 Sian lossedeuslelaese lice ode Ole eet examid_i3C 1 2 F BrukeriTopSpin guest examid_i8C 1 6 F BrukeriTopSpin guest examid_13C 11 1 F BrukenTopspin guest y examid_i38C 2 1 F BrukeriTopSpin guest examid_13C 3 1 F BrukeriTopSpin quest Data directories examid_i3C 4 1 F BrukeriTopSpin guest examid_13C 5 1 Fi BrukenTopSpin quest examid_18C 6 1 F BrukeriTopSpin quest eo et eo eB Figure 7 4 Edit List This button will open a texteditor in which you can edit the current or 112 Data Processing a new dataset list Next After having defined the full datasetpath and clicking next the follow ing dialog will appear Senal Processing Define Command Please define the command to be executed on the datasets Examples 1
86. 1 Click Options gt Preferences set 362 User Preferences oF O N 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 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 O a fF ON Click Options gt Preferences set Click Fonts Dialogs Icons in the left part of the dialog box 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 How to Change the Font of the Status Line oa fF ON Click Options gt 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 Select the desired name style and or size in the appearing dialog box Click OK to store the new font Click Apply 20 1 6 Changing Acquisition settings 363 How to Auto Archive existing expnos 1 Click Options gt Preferences set 2 Click Acquisition in the left part of the dialog box 3 Click the Change button to the right of the item Configure Accounting amp 4 Data Ar
87. 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 pre viously exported list from the current dataset Note that integration commands store the integral list in the processed data directory under the name integrals 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 177 2D Display How to Display the FID Click the Fid tab fid 2D raw data consist of a series of FIDs which are displayed in a row In dividual FIDs can be displayed by zooming in To do that click co re peatedly Now you can shift and zoom in out the data to display different FIDs see Fig 10 12 Pxam d HC 1 1 Chio guest Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acgu fid Figure 10 12 10 5 2D Display Options How to Switch between Hertz and ppm Axis Units in F2 and F1 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 Click the following toggle button in the upper toolbar 1 Switch the spectrum overview display on off ov With the spectrum overview on the data window will
88. 1 Startup TOPSPIN 4 5 die dediicd sob ded et Hedin 8 he Gh bate Se had ard 20 22 JCOMIGUIANON erenneren Sart and Se Bae oe BROS Dems G ae AS 2 21 2 3 How to Display DCCs ieee couse be fete eek gees 22 How to Locate nmr data in any arbitrary directory 22 How to Open Data from the Menu 0 0005 23 How to Open Data from the Browser 00 23 How to Define Alias Names for Data 0 4 24 How to Open Data in Archive Data Directories 24 How to Open Data in Other Ways 0 0000 eae 24 2 4 How to Expand a Spectral Region 000008 24 2 5 How to Display Peaks Integrals together with the Spectrum 25 2 6 How to Display Projections 1D Spectra with 2D Spectra 25 2 7 Howto Superimpose Spectra in Multiple Display 26 2 8 How to Print or Export the Contents of a Data Window 26 FOWO TGA Abe esis 2 ike och eA dae wh sree AVE oo allel Meredith ae 26 How to Copy a Data Window to Clipboard 26 How to Store Export a Data Window as Graphics File 2 2 9 Howto Process Data 0 cc ee es 27 2 10 How to Archive Data si sia ite ge fen eek fae wh ae ele a eG A 29 2 11 How to Import NMR Data Stored in Special Formats 30 2 12 How to Fit Peaks and Deconvolve Overlapping Peaks 30 2 13 How to Compute Fids by Simulating Experiments 31 2 14 How to Add Your Own Functi
89. 140 4 ppm 17657 5 He Index lDefine new region Drag with left mouse button F2 ppm Figure 13 7 Data window in interactive integration mode Bg The yellow button indicates that you are in integration mode x tH E Define integral region mode active when green Move integral region green when active Copy a region Delete all integral regions 246 2D Interactive Manipulation Read import integral regions Save Export integral regions Save integral regions and return a B I Integrate current regions define reference J Return without save 13 2 2 2D Interactive Integration Procedure 247 When you switch to 2D integration mode the Define integral region mode is active by default This means you can immediately start defining the inte gral regions To do that 1 Click and hold the left mouse button at any corner of a region to be defined move the mouse to draw a box around that region and release the mouse 2 Choose one of the following options from the appearing popup menu Integrate a to add up all intensities in the region Integrate to add up all positive intensities in the region Integrate to add up all negative intensities in the region Integrate a to add up all intensities in the region and store sepa rate entries for all positive and negative intensities Integrate a to add up all intensities in the region and store separate entries for all and pos
90. 2 Figure 8 1 In the Print dialog box a Select Print active window prnt b Click OK Before printing starts the operating system print dialog box will ap pear Here you can for example select the printer name and the print er properties The Print dialog box see Fig 8 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 Printing Exporting Data the desired layout and click OK to print Standard layouts are deliv ered with TOPSPIN They use the Windows default printer User defined layouts use the printer defined in the Plot Editor On a 1D dataset only 1D layouts are listed on a 2D dataset only 2D layouts are listed etc For the last two options the following Required Parameters are available 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 e from Plot Editor Reset Actions The plot limits and maximum intensity are set according to the Plot Editor Reset Actions right click inside the Plot Editor data field and choose Automation to set the Reset Actions e as saved in Plot Editor The plot limits and
91. 2 52 4673 45 9670 9 1 5 31659 5 15089 47 3599 41 3238 5 8 5 02122 4 81230 47 3599 41 3238 5 8 5 02122 4 81230 47 3599 41 3238 5 8 5 02122 4 81230 76 6116 70 11130 8 4 38726 4 23598 76 6116 70 11130 8 4 38726 4 23598 Table 13 1 Abs Int 9 2529e 00 8 1 1135e 00 9 3 699e 00 7 1 0072e 00 9 1 064e 009 9 6725e 00 7 1 2637e 00 9 1 2911e 00 9 Inte gral 882 42 1062 35 953 960 57 1014 7 54 097 1205 2 1231 3 2D Interactive Manipulation Alternatively you can define a reference integral and integrate the defined regions of the same or of a different dataset relative to this integral For this purpose the I button offers the following menu items Integrate current regions rel to reference You will be prompted for the reference integral number and value e List integral values The output list will now show an additional column with the normal ized integral values e Define current dataset as reference You will be prompted for the reference integral number and value Integrate and use ref dataset for calibration The integral value defined on the reference dataset is used for cali bration How to Move an Integral region 1 Click the button m it turns green 2 Move the mouse into the region to be moved 3 Left click hold and move the mouse to move the region 4 Release the mouse at the desired position How to Copy an Integral region 1 Click the button
92. 215 position of a Topspin window 257 position of a Topspin window 256 position the baseline of a row column in 2D 245 positive 2D levels 178 pp command 133 149 150 PPARMOD parameter 92 97 122 ppl command 222 ppm axis units 145 169 pps command 220 preferences 33 329 pre scan delay 300 preview the baseline corrected spectrum 216 previous commands 37 dataset in browser 42 parameter field 92 96 plane in 3D 181 row column in 2D phase correction 231 243 print 1D peak list 133 active window 25 110 colors 337 data from the menu 109 data from the Processing Guide 111 integral list 112 metafiles 113 peak list 112 the current dataset 41 print command 34 41 109 112 133 printer colors 336 prnt command 110 probehead solvent dependent parameters 96 proc_1d AU program 103 process data 25 33 from the command line 99 from the Processing Guide 100 with AU programs 103 with composite commands 100 processing parameters 89 90 parameters 1D 122 parameters 2D 165 Processing Guide 26 101 103 Processing menu 25 26 33 Processing Reference Manual 23 procno 69 74 78 86 152 ProcPars tab 26 89 90 122 165 projections of a 2D spectrum 23 170 properties of a dataset 150 of a printer 110 prosol parameters 287 pseudo raw data 78 pulse program 20 29 62 125 display 125 parameters 96 123 287 PulsProg tab 125 Python programs 30 355 359 362 Q QUIT AU macro 104 QUITMSG AU macro 104 R re command 22 73
93. 297 298 299 300 expl command 73 86 87 153 Explorer 72 86 153 expno 65 69 72 78 151 exponential baseline correction 216 window multiplication 99 100 export data 24 114 expt command 275 extend the Topspin functionality 353 external projection 24 extract a row column in 2D 244 F F1 dimension 162 169 225 F1 key Ill 41 F1 F2 plane 180 183 F2 dimension 162 169 225 F2 key 41 61 F2 F3 plane 181 183 F3 key 47 F3 F1 plane 179 181 183 F5 key 47 F6 key 41 47 252 fid command 145 169 FID display 274 278 284 288 Fid tab 145 151 169 File Chooser 21 File menu 21 33 file size of raw data 275 files of a dataset 73 78 86 151 153 find command 41 82 find data 33 82 first order phase correction 1D 193 2D 229 231 fitting peaks 28 fmc command 100 focus 37 41 61 62 font of dialog windows 343 of the browser 343 of the command line 344 of the interface 340 of the menu 341 of the status line 344 of the tab bar 342 forward peak picking 222 Fourier transform 99 100 fp command 100 fromjdx command 28 fromzip command 27 ft command 25 26 99 ftf command 26 348 function keys 40 G Gaussian deconvolution 28 Gaussian window multiplication 100 genfid command 78 79 genser command 79 geometric sequence of levels 174 geometry of a Topspin window 256 257 getprosol command 96 123 gf command 100 gfp command 100 Gnome Mozilla 86 grab rows columns in 2D 242 gradient enhanced spectroscopy
94. 346 MC2 parameter 93 menu bar 33 commands 33 configuration table 348 350 entries 33 348 font 341 342 settings 329 MI parameter 222 minimize data window 254 minimum command line size 346 Minus key 42 mixtures 29 molecule structure viewer 143 mouse sensitivity in 1D baseline correction 217 in 1D integration 200 in 1D phase correction 194 in 2D phase correction 231 move data window 250 Mozilla 86 153 multiple display 1D 35 207 238 1D 2D 24 69 74 2D 24 238 in deconvolution 28 multiple display mode 69 207 multiple window display 116 multiplet 196 multiply with increment in 2D levels 174 N nbook command 353 negative 2D levels 178 new command 34 41 65 286 newtop command 48 next channel for wobbling 280 command 41 dataset in Browser 42 parameter field 92 96 plane in 3D 181 row column in 2D phase correction 231 243 window in data area 41 252 256 NMR ADMINISTRATION password 297 NMR SUPERUSER 297 nmradminpassword file 297 nmrsim command 29 nmrsuperuser file 297 noise region 260 261 NOISF1 parameter 260 NOISF2 parameter 260 notebook 353 NS parameter 274 O O1 parameter 275 O2 parameter 275 O3 parameter 275 objects of a dataset 24 116 250 329 335 336 337 oblique display of 2D spectra 176 178 of 3D planes 180 online help 45 online manual plot editor 112 Topspin 44 open browser portfolio 61 data 34 41 57 68 70 data from the browser 21 data from the command line 73 76
95. 4 ppm 4 fare 4 5617 2 O44 2 toe 4 5035 1 0025 1 9022 1 0025 1 1590 Intensity abs 11773060 00 1165631 00 93947450 996713 50 1739361 50 galala rs 1163631 25 2310150 75 1037 7060 25 The chemical shift in each of the three dimensions is shown in a separate column 195 nD Display To show the nD integral list click the Integrals tab of the data window or enter ints on the command line Fig 11 7 shows the integral list of a 3D dataset exam3d 1 1 CBrukeri TOPSPIN quest integral 1 502432597 00 0 1011 2 1 571 Integral 2 266808232 25 0 0537 4 471 eIntegral 3 1439384326 OO 0 2884 3 0 86 integral 4 533366464 00 0 1073 1 0 98 sIntegral 6 328194 187 25 0 0660 4 39 Integral 6 116979144 00 0 0235 3 14 Integral 7 124751045 00 0 0251 2 92 Integral 8 204916237 50 0 0412 1 0 72 Figure 11 8 The chemical shift in each of the three dimensions is shown in a separate column Peaks and integrals only appear if they have been calculated commands pp and int respectively 196 nD Display 197 Chapter 12 1D Interactive Manipulation The upper toolbar of the 1D menu offers various buttons for interactive manipulation If you click such a button the active data window will switch to the corresponding mode An interactive manipulation mode is data win dow specific i e it only applies to the active window 12 1 1D Interactive Window multiplication TOPSPIN 2 0 and newer suppor
96. 4 0 00028 Figure 15 5 After closing the editor window which shows the deconvolution result Top Spin switches automatically to multiple display mode to show the original 2 8 Analysis spectrum and the sum of the comuputed line shapes superimposed amp Bruker TopSpin on merlin as sycu File Edit View Spectrometer Processing Analysis Options Window Help est 2 999 F Bruker TopSpin guest 2 1 F Bruker TopSpin guest Figure 15 6 With the option Display the Lorentz Gauss curves of the last Deconvolution of the Deconvolution window Fig 15 4 it is possible to display the results of the deconvolution also graphically B e EMA QAQQAo QB eo oe 4 tte icon test 2 1 F Bruker TopSpin guest Deconvolution result 4 lines shapes and their sum Figure 15 7 2719 Analysis 15 5 Please note that the results of deconvolution are approximated achieve ments to interprete complex spectra These amounts are acoording to real ity if the signal is an ideal Gauss or Lorentzian shape and if the complete region of the signals is deconvolved Relaxation Analysis Typically relaxation data consist of a series of 1D FIDs measured with var ying 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 Click Analysis
97. 4 03 30 10 55 36 171 0200 gt where the last value represents the offset in hours to Universal Time UTC WHO The user logged in at the time the entry was generated It has one of the two forms lt user1 gt or lt user1 user2 gt lt user1 gt is always the user who Is logged into the operating system Windows or Linux user and who started TOPSPIN lt user2 gt only appears if the NMR adminis trator has setup an internal TOPSPIN user administration and the op 327 Regulatory Compliance 18 1 5 18 1 6 tion Enforce login for working with TOPSPIN in the User Administration dialog is enabled see below command uadmin In this case lt user2 gt is the current internal TOPSPIN user WHERE The network name of the current computer e g lt EOS2 gt PROCESS The TOPSPIN process module which performed the acquisition or processing VERSION The TopSpin version which performed the acquisition or orocessing WHAT The type of acquisition or data manipulation performed Note that if only the entries NUMBER WHEN WHO WHERE WHAT are present then the audit trail was created by TOPSPIN 1 3 or older Adding a comment to an audit trail Audit trail entries are normally generated automatically by a respective acquisition or processing command However a user can also add a com ment manually using the audit command This will generate a regular entry the comment will appear under the WHAT section and is preceded
98. 4 2 5 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 entry 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 gt 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 Create a Stack Trace If TOPSPIN hangs it can be useful to sent Bruker a stack trace about a possi ble cause You can create a stack trace as follows 1 Move the cursor into the TOPSPIN startup window 2 Under Windows hit Ctr1 Break Ctrl Pause Under Linux hit Ctr1 Control backslash 3 Copy the appearing text into a text file Store complete log with gt savelogs A complete set of TOPSPIN log files can be made automatically with the command savelogs if the user assertively confirms Trouble Shooting For saving logfiles with the command savelogs do the following Under Windows e Click the Bruker Utilities lt tops
99. 62 of the data window 24 145 of the FID display window 288 tips 45 usage 34 tooltips 44 45 top level directory 21 22 57 64 Topspin color schemes 338 data area 73 6 fonts 341 help 44 installation 299 installation directory 299 startup V 19 tailoring 329 window 31 topspin command 19 Topspin icon 19 totxt command 78 tozip command 27 78 tshome directory 19 45 299 tuning the probehead 279 U undo last parameter change 92 96 last region operation 204 unzip utility 28 Up Arrow key 38 41 upper toolbar 1D 34 189 2D 225 user defined AU programs 300 buttons 359 362 364 commands 26 29 functions keys 47 plot layouts 111 User Interface functions 355 user preferences 329 user properties directory 47 V Varian spectrometer 75 vertical scaling 118 159 View menu 33 148 virtual spectrometer 29 VNMR data 75 W walk up 30 wbst command 280 wbsw command 280 wildcards 81 window layout 256 Window menu 33 257 WINNMR data 75 wm command 26 89 wmisc command 78 wobb command 276 279 wobble display 277 frequency 280 procedure 279 steps 280 sweep width 280 window 279 wpar command 78 wra command 78 wrp command 78 wrpa command 27 77 78 X xau command 303 x axis rotation in 3D 178 182 xmac command 29 Y y axis display 35 146 y axis rotation in 3D 178 182 Z z axis rotation in 3D 182 zero order phase correction 1D 193 2D 229 230 zg command 274 276 287 ZIP data format 27 75
100. 69 tuning and matching 280 automatic mode of the Acquisition Guide 272 of the Processing Guide 26 101 automation 29 30 300 autoplot command 103 110 autostart mac file 332 Avance spectrometers IV 299 axis units 35 145 169 206 247 B background of a data window 338 Backspace key 38 backward peak picking 222 baseline correction 1D 99 214 mode 35 214 bcm command 217 bias correction 199 bio molecular experiments 30 bnmr command 356 bnmrsel command 356 bpan command 357 browser 31 32 41 57 68 font 343 in multiple display mode 209 240 Bruker AU programs 30 302 data format 21 27 28 71 75 76 85 example datasets 22 64 BSMS control panel 282 BSMS display window 256 bsmsdisp command 282 C calibration 99 1D interactive 205 2D interactive 246 mode 35 205 246 cf command 20 49 297 298 299 chemical shift 212 chemical shift distance 1D 260 2D 247 CHEMSTR parameter 143 C language 29 103 354 355 clevels file 176 clipboard 25 41 close active data window 255 lock display window 281 282 the active data window 41 close command 41 cmdhist command 38 cmdindex command 46 cmdtab_user prop file 47 collapse a data directory 57 62 color scheme 337 colors of data objects 336 of the lock display 337 on the printer 336 command definition 47 dialog box 89 help 44 index 46 line 37 38 345 command line commands 274 focus 37 41 font 344 history 37 38 preferences 345 resi
101. 9 1D zooming 40 128 1D 2D shifting 41 2D shifting 171 scaling of 1D integrals 211 scanning of planes in 3D 190 shifting of 1D integrals 212 solvent 72 spec command 130 special format data 30 spectrometer frequency 292 spectrometer hardware 21 22 Spectrometer menu 37 290 spectrum display 1D 130 objects 348 349 overview 1D 154 overview 2D 178 Spectrum tab 130 154 161 square 2D layout 169 square brackets 37 51 125 130 sref command 106 110 217 259 stacked multiple display 224 Start button 79 startup actions 348 status line font 363 status parameter change 100 display 103 158 display 1D 131 132 stdisp command 311 stop an acquisition 291 stop command 291 293 307 store 2D contour levels 184 structure file 152 Structure tab 152 sum spectrum in multiple display 222 superimpose 1D spectra 218 cursor information 157 electronic signature 159 integral trails labels 158 l 27 main status parameters 158 peak labels 158 spectra 26 title of a dataset 158 SW parameter 292 swap data windows 270 sweep width 292 swin command 270 switch to the last 2D data 38 to the last 3D data 38 T T1 calculation 16 T1 T2 Relaxation 280 tiguide command 280 T2 calculation 16 Tab bar 1D 125 130 2D 167 174 configuration 130 354 font 361 usage 130 Tab key 99 103 tabbed pane 174 354 TCP IP port 340 temperature unit window 269 Terminal Window 20 time domain signal 31 title bar 124 125 166 263 264 267 268 269
102. 9562402 r6 pk3 5 3677 S0300 0509930 29 pk Figure 10 9 gt This displays list of peaks if these have been calculated command pp 2D Display The list is basically the same as for 1D spectra The only difference is that there are two columns for the two directions V F2 ppm the chemical shift in the F2 direction V F1 ppm the chemical shift in the F1 direction To 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 10 10 exam2d_HC 1 1 Crbio guest 1 _ O x 30 F1 ppm ad a8 3 4 3 0 F2 ppm Figure 10 10 How to Display the Integral list Click the Integrals tab 176 2D Display exam2d_HC 1 1 Cibio guest loj x 0 00 1 0 00 0 0000 1 i EPEE 3 0 00 0 0000 1 Hntegral 4 1971145050 1 0000 1 EHntegral 5 0 00 0 0000 1 Peake 55751 126 2371 3446703 37 I peak 7 56356 126 2227 4532891 75 EHrtegral 7 0 00 0 0000 1 Figure 10 11 This displays the list of integrals if these have been calculated command int The listis 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
103. Aliases gt Show all data names expnos etc Remove Selected Aliases gt Remove selected aliases from list List Available Alias Commands gt Show available alias commands Figure 5 7 How to Open the Browser in a separate window The browser can be opened in a separate window as follows Click Options gt Preferences set click Window settings and check Display dataset browser in a separate window You must restart TOPSPIN for the change to take effect How to Put the Focus in the Browser Hit the F2 key or Click inside the browser 68 Dataset Handling How to Select Folders in the Browser To select a particular folder Left click the folder button or Hit the arrow up down keys while the focus is in the browser To select multiple folders Hold the Ctrl key and left click multiple folders to select them or 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 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 To fully expand a collapsed folder Right click the DIR NAME or EXPNO node and choose Fully Ex pand Selection To collapse an expanded folder Click the button to the left of the folder button or Double click the folder button or Hit the Left Arrow key while the folder is
104. Click the button or double click the title bar How to Maximize a Data Window Click the m button or double click the title bar The window will cover the entire data area Note that a maximized window cannot 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 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 Click File gt Close Crt1 w Or Click the xj button in the windows title bar To close any data window Click the x button in the data windows title bar Or Click the title bar and then click File gt Close Crtl w To close all data windows Click File gt Closeall closea11 268 How to Iconify all Data Windows Click Window gt Iconify all How to Maximize all Data Windows Click Window gt Maximicze all The active window will be displayed on top all other windows are hidden How to Activate the Next Data Window Click Window gt Next window F6 The windows title bar will become highlighted 14 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 dis
105. 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 formats such as JCAMP DX and ZIP E mailing data Processing 1D 6D fids and spectra window multiplication various transforms Fourier Hilbert DOSY phase correction baseline cor rection integration peak picking linear prediction smoothing add ing 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 16 Introduction TOPSPIN 2 1 e Fitting peaks with Lorentzian and Gaussian line shape models deconvolve overlapping peaks e Multiplet analysis e Automatic 1D 2D and 3D peak picking e Automatic 1D 2D and 3D integration e Line shape analysis of solids spectra e Data acquisition with Bruker Avance type spectrometers e Supporting automated and walk up spectrometers ICON NmR e Remote spectrometer control including web enabled ICON NMR e Adding user defined functionalities to TOPSPIN AU programs Macros and Python programs Available Documentation In TOPSPIN 2 1 and newer the Help gt Manuals submenu contains list of available manuals for the following items General Beginners Guides Acquisition Users Guides Acquisition Application Manual
106. IN USER quest Solvent coc Experiment Use current params TITLE 1301H Av 300 6 Cholesterylacetate 1 Receivers 1 2 8 ok Cancel more Info Help Figure 5 10 A dataset will be created and initialized with the parameters of the chosen experiment No fid or spectrum are available yet They can be created by data acquisition and data processing respectively 5 3 Opening Data TOPSPIN allows you to open data in several ways from the browser the menu the Windows Explorer or the command line Furthermore data can be opened e in an existing data window replacing the current dataset e ina data window which is in multiple display mode being superim posed on the current spectra e in anew data window which becomes the active window 73 Dataset Handling Note that if a dataset is already displayed in one window and it is opened in a second 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 com mand reopen How to Open Data Windows Cascaded By default a new data window appears maximized filling the entire data field and covering possibly existing windows You can however configure TOPSPIN to open new windows cascaded This is convenient if you want to open several data windows and then select one To open new windows cascaded 1 Click Options gt Preferences set 2 Click Window Settings in th
107. PIN 2 1 and newer the file autostart mac Is a regular Topspin macro In older versions however the file autostart prop was used with a different format How to Define Auto Termination after Idle Time TOPSPIN can be configured to be terminated after a user specified idle time To do that 1 Click Options gt Preferences set 2 Click the Change button to the right of the object 351 User Preferences Automatic termination of TOPSPIN when idle time has exceeded enter the NMR Administration password as requested and enter the number of minutes of allowed idle time 3 Click OK to close the dialog click OK to close the Preferences dia log 4 Restart TOPSPIN to activate the change If the user does not execute any commands from the command line menu or toolbar buttons a dialog will appear with an OK button to ter minate immediately and or Cancel button to continue Automatic termination frees the license used by this TOPSPIN in stance for other users This solves the problem of users leaving TOPSPIN Open and blocking a floating license although they do not currently use it How to Define Auto Locking after Idle Time TOPSPIN can be configured to lock the interface after a user specified idle time To do that 1 Click Options gt Preferences set 2 Click the Change button to the right of the object Automatic locking of TOPSPIN when idle time has exceeded enter the NMR Administration password as re
108. PSPIN 2 1 and newer support data dimen sionalities up to 8D The parameter editor does not allow you to modify status parameters Processing status parameters reflect the status of the processed 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 s mc2 Note that the command s is used for 1D 2D and 3D dataset TOPSPIN auto matically recognizes the dimensionality of the data and displays the param eter in all relevant dimensions Note that for example the parameter MC2 only exists in F1 6 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 domain size 1 Enter td for 1D data the following dialog box will appear Cn x Size of fid TD e5536 JRK Cancel Parameter Handling for 2D data the following dialog box will appear TT x Size of fid F2 F1 TD fi 024
109. Peak Labels on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Peak labels 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 1 These are the status parameters that also appear on the plot 1D Display How to Show Peak Annotations on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Peak labels and Peak Annotations in the appearing dialog box and click OK Peak annotations appear on peaks for which annotations have been de fined instead of regular peak labels showing chemical shift values If no peak labels or annotations 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 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 How to Superimpose the Electronic Signature on the Spectrum 1 Right click in the data window and choose Display Properties dopt 2 Check Electronic Signature in the appearing dialog box and click OK The electronic signature entered with esign will appear below the title How to Display the Main Dataset Properties Right click inside the data window and choose File
110. Picking Ranges 234 How to Define Peaks Manually 000 5 234 How to Pick Peaks Semi Automatically 234 How to Delete Peaks from the Peak List 235 How to Return from Peak Picking Mode with without Save 236 How to save Peaklists and Regions in 1D interactive mode 236 Chapter 13 2D Interactive Manipulation 000000 eu 238 13 1 2D Interactive Phase Correction 000 0 eae 238 How to Switch to 2D Interactive Phase Correction 238 How to Perform a Typical 2D Interactive Phase Correction 239 How to Scale or Shift Individual Rows Columns 242 How to Perform Smooth Phase Correction 243 How to Perform 90 90 or 180 Zero Order Phase Correction 244 How to Reset the Phase to the Original Values 244 How to Change the Mouse Sensitivity 244 How to Show the Next Previous Row or Column 244 How to Arrange Rows or Columns 0000005 245 How to Return from Multi 1D Phase to 2D Phase Display 245 251 257 How to Return from 2D Phase Mode 245 13 2 2D Interactive Integration nnana anaana 245 How to Move an Integral region 0000 eee 250 How to Copy an Integral region 00 cee ee 250 How to Delete all Integral Regions 4 6 250 How to Read Import Integra
111. Print Ctrl F Export gend To Run Delete Figure 5 14 2 In the appearing dialog box see Fig 5 15 EA Open re O Open NMR data stored in special formats O Open other file Required parameters Browser type RE Dialog hl Figure 5 15 a Select the option Open NMR data stored in standard Bruker format b Select the browser type RE Dialog 78 Dataset Handling c Click OK 3 In the appearing dialog box see Fig 5 16 Options G Display data in same window O Display data in newe window MAME examid_ 137 ExXPNO PROCMO OIR USER Figure 5 16 a Specify the dataset name expno etc b Click OK Note that the dataset specification 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 from the Windows Start button Navigate to the data name exp no or procno or 19 Dataset Handling by entering the command exp1 in TOPSPIN The Explorer shows the contents 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
112. Select the desired entries while pressing the Ctrl or Shift key 2 Right click a peak entry to open the popup menu see Fig 9 4 3 Click Export to export the selected peaks 4 This opens a dialog box where you can specify the filename and file type For the latter you can choose from Auremol peaklist ml Comma Separated Values cvs Mixed Shape deconvolution peak list peaklist TOPSPIN peak list xml XEASY peak list peaks XWIN NMR peak list txt Important Check the box in the lower left corner to export the se lected peaks only or uncheck it to export the entire list Then click Export Delete remove peaks from the peak list To delete one peak Right click the peak and choose Delete from the popup menu 137 1D Display 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 Right click any entry and choose Remove gt Duplicate peaks To remove possible peaks outside of the spectrum Right click any entry and choose Remove gt Peaks positioned outside of the spectrum To remove solvent peaks Right click any entry and choose Remove gt Solvent Peaks Copy the peak List Instead of exporting entries of the peak list they can also be copied to the Clipboard and pasted to another application like Excel To do that 1 For multiple peaks Se
113. 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 1 Click Options gt 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 Spectrum TABS font object 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 Fig 20 7 and Fig 20 8 shows a Tab bar with font size 10 and 14 respec tively Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Figure 20 7 Tab bar with font size 10 361 User Preferences spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Struct Figure 20 8 Tab bar with font size 14 How to Change the Font of Dialog Boxes Click Options gt 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 Fig 20 9 shows an example of a dialog box with the font Times New Roman Italic oh NO Cnions Display data in same window O Display dafa in new window How to Change the Font of the Browser To change the font of the browser
114. TONCONLF PROTOMEXP PROTOMLF PROTONLFEXP PROTOMMR PROTONMREXP PROTOMMRLF PROTONT1 PROTOMinto Figure 17 1 320 Configuration Automation EA AU Programs File Options Help iny au piy a2 E e nn Figure 17 2 List with two User defined AU programs Note that Bruker AU programs are only shown if the command expin stall has been executed once after the installation of TOPSPIN How to Switch to the List of User defined AU Programs Click Options gt Preferences gt direcotries gt Manage Source Directories in the menu bar to open the AU program dialog box How to Switch to the List of Bruker defined AU Programs Click Options gt Preferences gt Directories gt Manage Source Directo ries in the menu bar to open the AU program dialog box How to Define the AU Programs Source Directory 1 Click Options gt Manage Source Directories in the AU program dialog box 2 In the field AU Programs Add or modify AU program source directo ries How to Create an AU Program 1 Click File gt New in the AU program dialog box 2 Enter the AU program name in the field New name and click OK 3 Enter the AU program lines in the edit field of the appearing dialog Dox 321 Configuration Automation 4 Click Compile to compile the AU program 5 Click File gt Save to store the AU program 6 Click File gt Close to close the editor Alternatively you can enter edau l
115. TOPSPIN commands like EFP and RPAR and AU macros like IEX PNO are written in upper case letters whereas C language statements like max 10 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 Click Help gt Manuals gt Programming Manuals AU programming 21 4 Python Programs A Python program may contain TOPSPIN commands User Interface func tions 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 374 User Extensions open testdata don t display testdata examid_13C 1 1 c Bruker topspin guest 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 EXIT 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 Click Help gt Manuals gt Programming Manuals Python program ming 21 5 Button Panels A button panel i
116. The browser in multiple display is split in two parts see Fig 13 11 The ad ditional lower part shows e which datasets are displayed in the active data window e which datasets are selected they are highlighted Figure 13 11 253 2D Interactive Manipulation 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 f button and move the mouse Fig 13 12 shows a region of two comparable 1H 13C inverse 2D data sets which are shifted relative to each other Clicking the R button resets individual scaling and shifting exam2d HC 3 1 Cobio guest DER y Ro w t A GE Ee Ei 3 s ts s jaf At H F2 ppm Figure 13 12 How to Display the Next Previous Name Expno To compare a series of spectra you can interactively increment or decre ment the dataset name or expno A dataset name is incremented accord ing to the ICON NMR naming convention of increasing extensions e g name 001 name 002 etc Click one of the following button button turns green E Show the previous name expno procno of the last dataset 254 2D Interactive Manipulation E Show the previous name expno procno of the last dataset Ei Set the increment options Clicking this button will open the fol lowing dialog where you can choose to increment the procno ex pno or name set the expno increment and sw
117. 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 gt Preferences select Directory path names 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 e The following structure file types are supported xyz mol pdb SCHL Ole MMLOD eS Cim 0P nin IWO 152 1D Display 153 Secondary structure elements of proteins backbone cartoons rib bons 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 com mand to the currently displayed molecule enter jmol lt RASmol command gt Here are some example jmol zoom 400 jmol ribbon 200 jmol color ribbon yellow You may create TOPSPIN macros containing RASmol
118. Type The best fit is calculated by varying I 0 P and T1 in an iterative process accord 284 Analysis 285 ing to the Levenberg Marquardt algorithm Clicking and exe cutes 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 Set Pick data points to PD or PDO see below A T2 fitting function is defined by the func tion I t Px exp where J is Intensity or Area according to the Fitting Type The best fit is calculated by varying P and T2 in an iterative process according to the Levenberg Marquardt algorithm Clicking and executes the commands ct2 current peak and dat2 all peaks respectively invrec satrec cptirho expdec gaussdec lorgauss linear var bigdel varlitdel vargrad vardamp these functions can be used for various experiments with up to 6 components except for cpt1rho and lorgauss which allow only 4 and 3 components respectively They all use the simplex algorithm and require some parameters to be set e Enter the Number of components 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 0 must be selected such that the sum of all components does not exceed 1 If there is only one component I O is usually set to 1 The step rate is usually se
119. a Linux Shell or Terminal Window 2 In the Shell Terminal a Enter cd lt tshome gt b Enter topspin Getting Started where lt tshome gt is the directory where TOPSPIN is installed Startup TOPSPIN specifying dataset Topspin can be started with a dataset option 1 Open a Windows Command Prompt or Linux Shell 2 Enter topspin j TOP_DATA lt dataset path gt The specified dataset is automatically displayed after startup Examples topspin j TOP_DATA c bio data guest nmr exam1d_1H 1 pdata 1 topspin j TOP_DATA c bio data guest nmr exam1d_1H 1 pda ta 1 1r topspin j TOP_DATA c jcamp dx topspin j TOP_DATA c data archive zip 2 2 Configuration 21 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 hardware Just type this command and follow the instructions on the screen At the end of the dialog further configuration commands like expinstall are offered and can be started from there on a computer which is used as datastation The only configuration command to be executed is expinstall This allows you to install pulse programs AU programs lists etc Just type this command and follow the instructions on the screen selecting Installa tion for Datastation default Note that the commands cf and expinstall can be started from the command l
120. a spec trum expansions of a spectrum superimposed spectra spectrum compo nents such as parameters peaks integrals cross sections etc Whatever the content of the data window is it can be printed as follows type Ctrl p or click File gt Print select 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 lay outs Details on this can be found in the Plot Editor manual to be found un der Help gt Manuals gt Plotting The colors of the printed data can be chosen in the User Preferences dia log box Just enter the command set or click Options gt 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 oth er applications To do that type copy or click Edit gt Copy This will copy 26 Getting Started 2 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 addi tion to this TOPSPIN allows you to save the contents of a data 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
121. able the system for network access 1 Log in on the remote system 2 Start TOPSPIN 3 Click Options gt Preferences set 4 Click Miscellaneous in the left part of the dialog box 5 Click the Change button to the right of the object Configure remote access 6 Enter the Administration password as requested 7 In the appearing dialog box see Fig 19 1 a Click Remote Access Enabled b Click Add and enter the data directories that you want to export for remote access e g C bio and click OK c Click OK to close the dialog Ey Configure remote access Enable or disable remote access to TopSpin Select Remote access enabled to allow remote access to this Topspin installation select Remote access disabled to prevent remote access default Warning ou must restart Topspin to activate the modification Any previous modifications in the file omnmiork cont will be lost Directories must be exported in order to enable remote access to these directories Use INSTDIR tor the data directory in the Topspin horne directory Remote access O Remote access disabled Exported directories AMS TOR Figure 19 1 8 Click OK to save and close the preferences dialog 9 Restart TOPSPIN A list of exported directories is stored the file lt tshome gt prog server export conf Now a running TOPSPIN on this system can be accessed from any com puter in the network Identify the port number To identify the TCP IP port n
122. active integration mode The highest peak in each region will be used for relaxation analy sis e Manual Peak Picking The selected peaks will be used for relaxa tion analysis EA Define Peaks and or Intervals lf you choose manual integration module you can define integration regions 2 Most intensive peaks within the intervals will be found automatically lf you choose manual peak picking module you can define peaks without intervals or peaks within integration regions Manual Integration Manual Peak Picking Figure 15 10 Peaks Ranges Switches to interactive integration or peak picking mode as chosen 283 Analysis above Here you can define the ranges or peaks to be included in the re laxation analysis Then use button to export regions peaks to Relax ation Module and quit the interactive mode Relaxation Window Switches the 1D data window to relaxation analysis mode see Fig 15 11 Relaxation titest 1 1 Chiodi jos Misebanm OM FESMOi Pact Tt Peak iat e227 oom Pf fGa4rs 19 4 3 Curent Peak 1 of 1 Brief Report Peak at 7 221 ppr Pos 2241e 000 0 T1 sO 3 692e 003 1 216e 000 19 4672 Figure 15 11 and performs a default fitting By default this is one component T1 in tensity fitting Function type uxnmrt1 for peak 1 If the dataset was al ready fitted the previous type of fitting is performed The fitting curve is displayed in the data section and a Brief Report
123. ad 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 Alttw n e Add the data in the currently selected window if this is in multiple dis play mode whereas rew and repw e Always open the dataset in a new window Topspin 2 0 and newer allows opening datasets stored in the following di rectories structures lt mydata gt lt dataname gt lt expno gt pdata lt procno gt To do that Dataset Handling Enter reb on the command line browse to the desired dataset and click the Display button Or Open the Operating System File Browser browse to the desired da taset and open it in Topspin with Copy amp Paste or Drag amp Drop Note that this will create a copy of the dataset in the standard Topspin da tapath lt tshome gt data lt user gt nmr lt dataname gt lt expno gt pdata lt procno gt where lt user gt is the current internal Topspin user This copy can be proc essed deleted or overwritten even if the original dataset is write protect ed The original data set is left unchanged 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 Click File gt Open open Ctrl o select the option Open NMR
124. ak list Ctrl1 c copy selected peaks to the Clipboard Ctrlta select all peaks Home select the first peak End select the last peak Shift Home select current and first peak and all in between 139 1D Display Shift t End select current and last peak and all in between Note that these keys only work when the cursor focus is in the data win dow Table properties Various properties of the peak table can be configured To do that 1 Right click an entry to open the popup menu see Fig 9 4 2 Click Table properties 3 In the appearing dialog box with 3 tabs e Column Allows you to select the columns to be displayed set the col umn width and the number of fraction digits Furthermore you can switch on off scientific notation of values for each column individually e Colours Allows you to set various colours of the table e Spacings Allows you to set various spacings of the table 140 1D Display 141 Table properties Region Type index F1 WF 1 pem WF 14 Hz Intensity abs k OO d intensity rel rColumn properties Column width Scientific notation Figure 9 5 When you move the cursor over the peak list the active peak will by de fault be highlighted in blue See peak 3 in Fig 9 6 If the correlated spec trum is also displayed a vertical line moves along showing corresponding position in the spectrum see Fig
125. aks or ex panded 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 147 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 9 9 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 Right click the integral 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 Note that these keys only work when the cursor focus is in the data win dow Table properties Various properties of the integral table can be configured To do that 1 Right click an entry to open the popup menu see Fig 9 10 2 Click Table properties 3 In the appearing dialog box with 3
126. alal puke ngih uses 1136 Gel Garmas imas gii 1762m Coresi 90 dag S75 i upctate p parane ale is p aneia nf Vi fl ei Ta rv mT i 2 m0 ance eon j o Figure 16 22 4 Store the results e Pressing the save button writes the waveform on the disk an saves the necessary parameters pulse length power level to the target data set Used parameters are set in Options gt Define Param eter Table The target dataset may differ from the current data e g the spectrum on which Shape Tool started All regions and corresponding parameters rotation type waveform name are stored on the disk in the directory where the acquisition parameters reside Following simple text format is used by the file Region File 314 Acquisition Topspin excitation region list FMon Aor 20 Oe 5974S CEST 2007 Used format Left ppm Rigth ppm RotationType Waveform RotationAngle Field RotationAngle is not mandatory S248380 6 259606 O EBurOZ 93 6 Ze4958 Z2Zadlotoa Or EBUrpZ Jsp This region definition is stored automatically after each change The defini tion is also read automatically when starting Shape Tool For further information about Shape Tool and its functionalities please refer to the Shapetool Manual 315 Chapter 17 Configuration Automation 17 1 NMR Superuser and NMR Administration password During TOPSPIN installation you are prompted to define the username
127. alog box 96 help 50 index 52 l 17 line 41 42 364 command line commands 291 focus 41 45 font 363 history 42 preferences 364 resize 365 usage 41 Command Prompt 20 317 compile AU program 322 components of aspectrum 26 composite commands 107 configuration commands 21 customized 318 default 318 directory 318 name 318 of a datastation 21 of a spectrometer 21 of the acquisition status bar 294 of the tab bar 354 of the Topspin menu 367 password 316 consistency check 326 contour display 239 of 2D spectra 182 of 3D planes 189 contour levels 167 183 control keys 45 convdta command 85 convert data to JCAMP DX 85 data to text 85 data to ZIP 85 copy amp paste data 37 80 83 copy command 26 38 120 copy data 84 C program 110 create an AU program 31 111 321 373 an empty data window 75 data window color scheme 356 dataset 38 macro 31 373 new data window 23 new dataset 72 305 plot layouts 26 119 Python program 32 374 set of user preferences 348 user defined command 31 user notebook 372 C statements 31 Ctrl key 69 76 88 127 168 219 221 Ctrl c key 42 45 142 Ctrl d key 35 45 Ctrl f key 45 Ctrl F3 key 53 Ctrl F5 key 53 Ctrl F6 key 53 Ctrl n key 38 45 72 305 Ctrl o key 38 45 77 82 Ctrl p key 26 38 45 119 142 Ctrl s key 29 38 45 84 85 Ctrl v key 42 45 Ctrl w key 45 cube display 188 cubic spline baseline correction 230 cursor information 157 cu
128. als gt General User Manual To open the Avance Beginners Guide Click Help gt Manuals gt Beginners Guides lt language gt To open the Processing Reference guide Click Help gt Manuals gt Acquisition amp Processing Referenc es Proc Commands and Parameters Note that most manuals are stored in the directory lt tshome gt prog docu english xwinproc pdf 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 cursor over the interactive phase correction button you will see the follow ing 4 eM Ay Interactive phase correction ph The corresponding command line command in this case ph is indicated between square brackets Note that the tooltip also appears in the status bar at the bottom of the TOP SPIN window 51 The TOPSPIN Interface How to Get Help on Individual Commands To get help on an individual command for example ft Enter ft or 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 di alog box Options E Display data in s
129. ame window P Display data in newe window MAME e a a EXPHCO PROCMO DIF USER opens the same HTML file as entering help re or re How to Use the Command Index To open the TOPSPIN command index Enter cmdindex Or 52 The TOPSPIN Interface Click Help gt Command Index From there you can search for and click any command and jump to the corresponding help page 3 8 User Defined Functions Keys The default assignment of functions keys is described in chapter 3 6 and in the document Click Help gt Manuals gt General Control amp Function Keys You may assign your own commands to functions keys Here is an exam ple of how to do that 1 Open the file cmdtab user prop located in the subdirectory userdefined 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 _ 3 Sem sLOCUE Lore _f3alt Spk bo ohalt JEOCEE I 5 FSO J Salt Spope 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 commands ft pk halt reb and popt respectively You can as sign any command macro AU program or Python program to any func tion keys Only the keys Altt F4 F6 Ctrl F6 and Al
130. anual Click Help gt Manuals gt Programming Manuals AU Program ming As an alternative to AU programs you can also write Python programs which allow you to use TOPSPIN commands User Interface functions and Graphic functions For more information Click Help gt Manuals gt Programming Manuals Python Pro gramming 7 4 Serial Processing 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 TOP SPIN interface as follows Enter the command serial on the command line This will open the dialog window shown in Fig 7 3 Serial Processing Define Datasets Please define the full path name of the dataset list to be processed Click on gt Browse For List locate an existing dataset list gt Find Datasets search for datasets and use the selected ones as the list gt Edit List edit the current or a new dataset list gt Next continue with command definition Figure 7 3 1 Before you can use any Bruker AU program expinstall must have been exe cuted once 111 Data Processing The same dialog window will be shown by using the menu bar Processing Serial Processing The dialog offers you the following options Browse for list This buttons opens an Explorer in which you can locate an existing datset list Find Datasets You can for Datasets in all data directories marked in the appearing dialog
131. ar or command line 293 Acquisition 16 4 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 Preferences window To do that 1 Click Options gt 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 16 6 Administration items pane T i nns Spectrum Tree table colours e g integral table Change Contour plot Directories Spectrum title Dir of structure files for structure viewer Spectrum cursor Global search path for plot layouts Change Spectrum parameters Manage source directories for edpul edau etc Change Printer Fonts Dialogs Icons Window settings Miscellaneous Directories Acquisition status bar Auto open acquisition status bar Include spooler Include time aes Include sample temperature Acquisition status bar a S Include acquisition status Acquisition eee nna nclude acquisition indicator BSMS display we Include lock signal Lock display Include MAS spinning rate Include peak power check POWCHK indicator Include sample state Include BSMS status Include amplifier control Figure 16 6 3 Check the desired entries To switch the acquisition status bar on Click Spectrometer gt Acquisition Status Bar On Off Or Right click in the statu
132. 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 exponential 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 228 1D Interactive Manipulation To do that 1 Click the following button button turns green Preview corrected spectrum show difference The corrected spectrum will be displayed in red 2 If the baseline is correct click the H button to save the correction If further correction is needed click the pe button to show the original spectrum and the red correction line How to Reset the Baseline Correction Line 1 Click the following butto
133. bias correction values e Save Regions to reg Save the integral regions to the file reg Export Regions To Relaxation Module and sret Used on relaxation data only Exports the integral regions for T1 T2 relaxation analysis and exits from integration mode e Save amp show list Save the currently displayed integral regions including the slope and bias correction values and show the integrals on the screen How to Undo the Last Region Operation Click the following button 1 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 Click the following button Hj Save integrals and return sret 213 1D Interactive Manipulation As such you will e save the integral regions and corresponding slope and bias corrections to the file intrng e save the integral regions slope and bias corrections and inte gral values to the file integrals txt This file is displayed when you click the Integrals Tab e leave the integration mode To return without save Click the following button a Return discarding any changes ret How to deconvolve overlapping peaks from integration mode Deconvolution the line shape tool to interprete complex 1D and 2D spec tra with overlapping peaks can be started directly from within integration mode As described in the Analysis chapter deconvolution calculates the oretical signa
134. both the F2 and F1 direction by selecting certain rows and or columns and phase correct them 13 1 1 2D Interactive Phase Correction Procedure How to Switch to 2D Interactive Phase Correction Click the corresponding button in the upper toolbar as indicated below Id 3d 4 4 Ta or enter phon the command line The Tab bar of the active data window will be replaced by a toolbar Fig 238 2D Interactive Manipulation 13 1 shows an example of an unphased 2D inverse spectrum exam2d_HC 1 1 Cxbio guest O x ABH ct eb a p Click the right mouse button to select the peaks for phase correction f TE a we Lael LL g Tm 12 10 8 6 4 2 Fe ppm Figure 13 1 Data window in phase correction mode A The yellow button indicates that you are in phase correction mode tc Toggle the contour display on off p Switch to phase row mode to display rows of selected peaks ct Switch to phase columns mode to display columns of selected peaks Save the phase values to the 3D data from which this 2D was ex tracted Return a How to Perform a Typical 2D Interactive Phase Correction In this example we will perform F1 phase correction columns only Take the following steps 1 Select two or more peaks in different parts of the spectrum To do 239 2D Interactive Manipulation that a Zoom in on a peak by drawing a box around it To do that click hold the left mouse button
135. cessing status parameters 1D 122 projections 23 rows in 2D phase correction 226 settings 34 special data formats 75 spectra 21 spectrum overview in 2D 169 status parameters 92 96 sum difference spectrum 210 superimposed 1D spectra 207 superimposed 2D spectra 238 y axis 35 146 zipped data 27 display properties 23 distance measurement 1D 260 2D 247 mode 35 double headed arrow 250 261 Down Arrow key 38 41 42 dpa command 123 dpp command 92 96 122 drag amp drop data 73 76 E eda command 93 94 123 165 edasp command 97 123 edau command 30 104 300 302 354 edcpul command 125 edit AU program 303 commands 38 contour levels 174 integral ranges 199 pulse program 125 signal noise regions 262 title of a dataset 124 Edit menu 33 edlev command 158 174 edlock command 97 edmac command 29 354 edp command 26 89 90 122 165 edprosol command 96 edpul command 125 edpy command 30 355 edti command 124 ef command 100 103 efp command 100 289 em command 26 99 email data 28 empty data window 68 enable disabled commands 350 menus commands 346 Enter key 42 59 l 6 equidistant sequence of levels 174 Esc key 37 execute AU program 300 303 macro 29 354 Python program 30 exit command 41 48 expand a data directory 42 data directory 21 22 57 data directory in the browser 62 individual spectra in multiple display 212 spectrum 28 expand a region 23 experiment time 275 expinstall command 20 49 274
136. chiving after zg see Fig 20 10 In the appearing dialog see Fig 20 11 configure archiving as described in the dialog 5 Click OK Overwrite existing FID without inquiry 2 safety off Display digital resolution in FID display window Auto open acquisition window after zg Configure accounting amp data archiving after zg Figure 20 10 PH Setup Auto Archiving amp Accounting When acquisition 295 is finished Topspin allows you ta write accounting info to be evaluated by the command account to copy the acquired dataset to a desired archiving directory When zg is executed multiple times on the same dataset Topspin will increment the EXPNO while archiving s0 as to never override already archived data You may specify an additional EXPNQ offset for this case The accounting info i stored in the folowing directory one file per day stopepin homedir pragicurdiracghistory Auto archive after zy Archiving directory EXPHO offset Write accounting info after zg Figure 20 11 20 2 Command Line Preferences How to Resize the Command Line By default the TOPSPIN command line shows one command the com User Preferences mand that is currently entered e g apk However you can resize the command line to show the currently entered command plus the last and second last command e g em apk You can toggle between the two different command line sizes as follows
137. command removes all regions Single region can be removed using the region pop up menu 311 Acquisition ShapeTool examid_iH 2 1 c pavel guest aa m i Sot ne 6 EAB Gauss p 2 857 ppa y LOSPIRES He Parameters Ires 2000 5 Sones Falie i eL 158 Ha of Shana 10 Truncation Lewa 4 1 a A wc Figure 16 20 2 Edit the excitation parameters a opens a region editor The region extent the excitation type and the waveform assigned to 312 Acquisition the region can be edited Selection Use same shape for all regions button assigns the same rotation type and waveform to all regions x Use same Shape for all Regions Left Limit ppm Right Limit ppm Type of rotation Shape 5 4936 5 2588 Excitation iz gt ty el ema 2 4758 2 1678 Ok Apply Cancel Figure 16 21 The setting of available waveforms depends on the selected rotation type The following itemization explains the rotation types e Excitation Used for selective excitation the magnetization rotates from Iz to horizontal plane e Inversion Inverts the magnetization vector in the vertical plane Iz to Iz e Refocusing Inverts the magnetization in the transversal plane ly to ly 3 Calculate the pulse and display the excitation profile see Fig 16 22 e The resulting waveform is generated and the excitation pro file is calculated 313 Acquisition Shape ragion regan y Re cus TATED T
138. ction 208 How to Set the Limit for Bias Determination 209 How to Change the Mouse Sensitivity 209 How to Calibrate Normalize Integrals 0 209 How to Scale Integrals with respect to Different Spectra 210 How to Delete Integral Regions from the Display 210 How to Scale Selected Integrals 006 211 How to Move the Integral Trails Up Down 212 How to Cut Integral Regions 0 00 212 How to Save Integral Regions 00 000 213 How to Undo the Last Region Operation 213 How to Return from the Integration Mode with without Save 213 How to deconvolve overlapping peaks from integration mode 214 1D Interactive Calibration 0 0 0 ee 217 How to Switch to Calibration Mode 06 217 How to Calibrate a Spectrum Interactively 217 1D Multiple Display n nanana Gee oad oo Gee nee Pees 218 How to Switch to Multiple Display Mode and Read Multiple Spectra How to work with multiple display command md 221 How to Select Deselect Datasets 006 221 How to Remove a Dataset from Multiple Display 222 How to Display the Sum or Difference Spectra 222 How to Save the Sum or Difference Spectra 222 How to Display the Next Previous Name Expno 223 How to Toggle between Superimpose
139. ctra in tandem with a 2D spectrum 1 Open a 2D spectrum 2 If no projections are shown click the 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 Projec tion 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 dis played An alternate way to calculate projections is the following Click Processing gt Display Projections projd 25 Getting Started Or Right click on a 1D dataset in the browser and choose Display As 2D Projection 2 How to Superimpose Spectra in Multiple Display TOPSPIN allows you to compare multiple spectra in Multiple Display mode To enter this mode click the it button in the upper toolbar or enter on the command 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 2 8 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
140. ctra selected e scale shift buttons of the data window toolbar only work on selected spectra To deselect a dataset Select a different dataset To deselect all datasets Click the following button 4 Deselect all datasets How to Remove a Dataset from Multiple Display 1 Select the dataset s you want to remove 2 Click the following button iti Remove selected data from the screen Note that the data on disk are not affected Furthermore the first soectrum cannot be removed from the screen How to Display the Sum or Difference Spectra 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 222 1D Interactive Manipulation 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 decre ment the dataset name or expno A dataset name is incremented accord ing to the ICON NMR naming convention of increasing extensions e g name 001 name 002 etc Click one of the following button button turns green E Show the previous name expno procno of the last dataset E Show the previous name expno procno of the last dataset E Se
141. ctrum Figure 10 1 TOPSPIN offers various buttons to scale or shift a 2D spectrum both verti cally and horizontally How to Change the Intensity Scaling contour levels Click the button Change the intensity scaling contour levels edlev or Hit one of the keys e Altt PageUp Increase the intensity by a factor of 2 e Alt PageDown Decrease the intensity by a factor of 2 e AlttEnter Reset the intensity or 167 2D Display Click one of the following buttons 2 Increase the intensity decrease the levels by 2 2 G Increase the intensity decrease the levels by 8 8 2 Decrease the intensity increase the levels by 2 2 8 Decrease the intensity increase the levels by 8 8 Reset the intensity to the last saved intensity contour levels vr Alternatively you can enter the corresponding commands as specified be tween square brackets To manipulate all data windows press the Ctrl key while clicking one of the above buttons How to Smoothly Change the Vertical Scaling contour levels To change levels multiplying all levels with the same factor Click hold the button and move the mouse or Turn the mouse wheel while the cursor is in the data window To change the level distance increment leaving the base level the same Click hold the button and move the mouse How to Display a Contour Levels Bar in the Data Window 1 Right click in
142. ctrum print color 356 Topspin window 270 selective excitation 31 semi automatic peak picking 234 processing 107 sensitivity of the GS slider 303 of the mouse 203 209 229 244 serial command 111 serial processing 111 l 26 Server ID 341 set 1D acquisition parameters 132 2D acquisition parameters 174 2D processing parameters 174 colors for multiple display 226 contour levels 183 lock parameters 104 phase pivot point 201 processing parameters 96 processing parameters 1D 131 routing parameters 104 user preferences 349 set command 130 348 SFO1 parameter 292 Shell 20 shift 1D data down 129 1D data smoothly 129 1D data to the extreme left 129 1D data to the extreme right 129 1D data to the left 129 1D data to the right 129 1D data up 129 1D 2D data 41 48 2D data down 171 2D data smoothly 171 2D data to the left 171 2D data to the right 171 2D data up 171 data in multiple windows 126 individual spectra in multiple display 26 218 224 row column in 2D phase 243 Shift key 69 76 88 219 222 Shift Tab key 99 103 short description of an AU program 322 shortcuts for processing 107 show command 60 SIGF1 parameter 273 SIGF2 parameter 273 signal region 273 274 signal to noise calculation 273 Simplex algorithm 285 simulating experiments 31 sine baseline correction 228 single commands 106 slider sensitivity 303 slope correction 208 smail command 30 38 smooth 1D phase correction 243 1D scaling 40 1D shifting 12
143. d and Stacked Display 224 How to Shift and Scale Individual Spectra 224 226 231 How to move the selected spectrum one place up down 225 How to Switch on off the Display of Datapaths and Scaling Factors How to Return from Multiple Display mode 226 How to Set the Colors of the 19t 2 Dataset 226 12 6 1D Interactive Baseline Correction 008 226 How to Switch to Baseline Correction Mode 226 How to Perform Polynomial Baseline Correction 22 How to Perform Sine Baseline Correction 228 How to Perform Exponential Baseline Correction 228 How to Preview the Baseline Corrected Spectrum 228 How to Reset the Baseline Correction Line 229 How to Change the Mouse Sensitivity 229 How to Save the Baseline Correction and or Return 229 How to Perform Cubic Spline Baseline correction 230 How to Delete Spline Baseline Points from the screen 231 How to Return from Cubic Spline Baseline mode with without Save 12 7 1D Interactive Peak Picking 0 0 0 0 0c cee eee 232 How to Switch to Peak Picking Mode 232 How to Define New Peak Picking Ranges 233 How to Change Peak Picking Ranges 233 How to Pick Peaks in Peak Picking Ranges only 233 How to Delete all Peak
144. delete AU program 303 data 79 integrals from display 201 noise region S N 262 peaks from a peak list 223 signal region S N 262 spline baseline points 219 Delete key 38 depth cueing in 3D 183 deselect data in multiple display 209 210 integral regions 197 dialog box font 343 difference spectrum in baseline correction 217 in multiple display 210 dimensionality of a dataset 32 92 93 97 122 dir command 22 disable commands 348 menus 348 toolbar buttons 347 Display button 21 74 84 menu item 68 69 208 display 1D acquisition status parameters 123 1D data 115 1D FID 145 1D integral list 134 1D peak list 125 1D processed data 121 1D raw data 145 1D spectrum 121 1D spectrum overview 145 2D contours 173 2D data 157 2D FID 169 2D grid 172 2D integral list 167 2D peak list 166 2D projections 170 2D spectrum in contour mode 173 2D spectrum in oblique mode 176 2D spectrum in pseudo color mode 176 3D cube 182 3D data 179 columns in 2D phase correction 226 contours in 2D phase 226 data from the browser 22 59 data from the portfolio 59 data in multiple windows 116 dataset file list 151 dataset properties 150 expno procno list 69 found dataset 83 full spectrum in 2D phase correction 227 integrals 23 JCAMP data 28 manipulation 117 manipulations 35 mode of the lock window 281 molecule structure 143 options 35 options 1D 145 peaks 23 planes of 3D data 179 180 positive negative 2D levels 178 pro
145. described below How to Switch to Calibration Mode Click the indicated button in the upper toolbar 2d 3d A AM a a or enter ca1 onthe command line The Tab bar of the active data window will be replaced by a toolbar Ol x A ul E z 0 005 ppm 3736 He 75 40469965 MHz DEFINE REFERENCE FREQUENCY Define Lett click inside data window 0 2 0 1 0 0 0 1 ppm Figure 12 11 Data window in calibration mode The yellow button indicates that the data window is in calibration 4 mode How to Calibrate a Spectrum Interactively In calibration mode 217 1D Interactive Manipulation 1 Position the red cursor line at the reference peak 2 Left click at that position The following dialog box will appear Ey calibrate Spectrum calibration frequency Cursor Trequency In ppr ai Note that the units Hz or ppm correspond to the axis units of the dis play 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 automati cally leave calibration mode 12 5 1D Multiple Display The multiple display mode allows you to display multiple superimposed spectra 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 alignment of corresponding peaks in different spectra The number of superimposed spectra is un
146. described in the following manuals Click Help gt Manuals gt Analysis and Simulation Structure Analysis Tools except for Daisy which is described in the separate manual Click Help gt Manuals gt Analysis and Simulation Daisy 15 2 Chemical Shift Distance Measurement How to Measure a Chemical Shift Distance 1 Click the following button button turns green 4 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 win dow to leave distance measurement mode button turns grey 15 3 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 re gion parameters NOISF1 NOISF2 are displayed 273 Analysis SIGREG 7 70 ppm 2311 87 Hz gt WOISEREG 1 94 ppm 581 90 Hz 10 0 5 0 0 0 Figure 15 1 Data window in S 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
147. djustments can be made 17 Lorentz Gauss deconvolution Idcon Options Use Lorentzian shape Use Gaussian shape Use mixed shape auto peak pick into file peaklist Use mixed shape use peaks from file peakilist Generate file peaklist no deconvolution Display result of the last deconvolution Display the Lorentz Gauss curves of the last deconvolution Required parameters Left deconvolution limit F1P ppm 7 4059 Right deconvolution limit F2P ppm 7 3606 Minimum intensity MI rel 1 Maximum intensity MAXI rel 10000 Detection sensitivity PC 0 001 Peak overlapping factor AZFW ppm 0 06 Destination PROCNO for fitted data 999 Figure 15 4 For further information about all deconvolution options and the parameters to be set please look up the Processing Reference Manual commands gdcon ldcon mdcon ppp dconpl and dcon TopSin shows the deconvolution result i e peak positions line widths and integrals on the screen and stores it in the file dconpeaks txt within the Analysis respective procno of the dataset look up Fig 15 5 ie Deconvolution result dconpeaks txt File Edit Search 1 pata set F Bruker TopSpin data quest nmv dcon test 2 pdata 1 Fit type Lorentzian Fit Frequency Intensity Lor ppm Hz Hz chisq 4 5e 014 2954 85 0 00438 26 064 100 00 0 06 0 00057 2952 81 0 00789 0 20 0 00182 2950 09 0 00271 0 04 0 00040 2949 00 0 00344 0 0
148. dling Chapter 5 Dataset Handling 5 1 The Topspin Browser TOPSPIN offers a data browser from which you can browse select and open data The browser dialog offers the following tabs see Fig 5 1 e Browser data browser showing the data directory hierarchy e Last50 list of the 50 last open datasets e Groups list of user defined groups of datasets e Alias list of user defined alias name The browser appears at the left of the TOPSPIN window and can be shown hidden with Ctr1 d or by clicking the arrow buttons at the upper right of the browser The Browser tab The browser shows data directory trees and allows you to expand collapse their elements Figure 5 1 shows the browser with three top level data directories and one dataset fully expanded 64 Dataset Handling 65 Browser Last50 Groups Alias E H CBio Glee Guest exanitd_13 E H exantd_1H ial 1 zg E exam2d_CH B i hxcogt H 1 CH CO Cyclosporin E examzd_HE E exam2d_HH Gey examsd 1 hechdigy3sd Chiot w Cits2 0 Figure 5 1 The dimensionality of the data is indicated with different colors e black for 1D data e blue for 2D data e magenta for 3D data Furthermore the browser shows e the pulse program with the dataset EXPNO e g 1 hxcoqf in Fig 5 1 e the title with the dataset PROCNO e g CH CO Cyclosporin in Fig 5 1 Note that the displayed pulse program is the e status pulse progra
149. e Right click on a 1D dataset in the browser and choose Display As 2D Projection or Click Processing gt Calculate projections proj This will open the dialog box shown in Fig 10 13 2D Display amp f2projp Options O Calculate postive projection Fi Calculate negative projection Calculate Sumi O Calculate disco sutr OQ Read postive projection O Read negative projection CO Update rovwsJcols from display Required parameters Projection urn of Display projection First row cal Last rowicol 4024 Destination PROCNO 999 Figure 10 13 From here you can calculate positive negative sum and disco pro jections and either show them with the 2D spectrum or display them in separate data window as a 1D data For more details on the corre sponding 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 Click the following multi state button in the upper toolbar E Switch between no grid axis aligned grid and fixed grid gr Fig 10 14 shows an example of axis aligned grid display 181 2D Display exam d HC 1 1 Cibo guest Sle Spectrur ProcPars AcquPars Title PulseProg Peaks Integrals Sample structure Fid ACHU 6 4 2 F2 ppm Figure 10 14 Axis aligned grid display How to Display a 2D Spectrum in Contour Mode Click the following button in the upper t
150. e click Spectrometer gt Acquisition Flowchart 288 Acquisition 289 MMF Data Acquisition Guide Close C Automatic mode 1H Fa 1c Mew Experiment Shir a TO m HS m Frequency Routing Acquisition Pars H Lock Prosol Pars Fin la Temperature Receiver Gain lt Probe MatchiTune Start Acquisition aie Sample Rotation To Processing Figure 16 1 In Automatic mode the Acquisition Flowchart will simply execute each com mand when you click the respective button This requires the acquisition parameters to be set correctly In interactive mode Automatic mode unchecked the Acquisition Flowchart will at each step open a dialog box Acquisition offering you the available options and required parameters Note that the last button To processing will open the processing equivalent of the Acquisi tion Flowchart the Processing Guide 16 2 Acquisition Toolbar Acquisition can be prepared started and controlled from Spectrometer menu Clicking this menu opens the pulldown menu shown in Fig 16 2 Interactive Acquisition Guide topguide Data Acquisition Flowchart Basic Selective Experiments Fast Acquisition Methods ICON NMR Adjustments Acquisition Setup sample shim control Accessories Shape Tool stdisp Excitation Profile exprof Acquisition Status Bar On Off Figure 16 2 Here you find several cathegories of acquisitio
151. e In correlated window Edit annotation Remove p Define a reference b Annotate by reference shitt peaks Show detailed information Copy Export Import Print Print preview Table properties Figure 9 4 Here you can choose from the following options Show spectrum gt In correlated window to open a new data window showing the full correlated spectrum Expand spectrum gt In current window to change the current data window to spectrum display showing the region around the selected peak Expand spectrum gt In correlated window to open a new data window showing the region around the selected peak Edit Annotation Edit the annotation of the current peak Define as reference gt Complete table Define the entire peak table as a reference for annotation Define as reference gt Selection Define the selected peaks as a reference for annotation 136 1D Display Annotate by reference Create annotations according to the peaklist of the reference data set You will be prompted for the allowed variation in chemical shift Shift peaks Shift all peaks You will be prompted for the number of ppm to be shifted Show detailed information Show peak information dataset information and peak picking pa rameters Export entries of the peak list Entries of the peak list can easily be exported to Excel or any other pro gram as follows 1 For multiple peaks
152. e com mand at Enter help qu or help at for more details on the respective commands Queued commands can be viewed in the Spooling field of the acquisition status bar Note that the spooling field must be activated in the User Pref erences window command set 16 6 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 The data window toolbar switches to the Acgu tab and the wobble win dow is opened see Fig 16 10 WOBE protona 1 1 C guest ojx Figure 16 10 The buttons of the wobble toolbar have the following functions 298 Acquisition Change the number of wobble steps wbs t Change the wobble sweep width wbsw lt I Change the wobble frequency i Switch to the next channel nucleus if available Gy Stop the wobble procedure 2 Turn the tuning and matching knobs on the probehead until the wob ble 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 16 7 Locking The lock display can be opened by clicking the button in the toolbar or entering Lockdisp on the command line The lock display window will appear see Fig 16 11 299 Acquisition x SS Weeed u Here you can view the lock signal either during the
153. e cursor into the browser area 2 Right click and choose Add New Data Dir in the popup menu 3 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 Getting Started 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 Archive Data Directories Topspin 2 0 and newer allows opening datasets that are stored in the fol lowing directory structures lt mydata gt lt name gt lt expno gt pdata lt procno gt You can do that with the TOPSPIN command reb or from the Operating System File Browser with Copy amp Paste or Drag amp Drop Actually the data are copied to the data directory lt tshome gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt where lt tshome gt is the TOPSPIN installation directory and lt user gt is the cur rent internal TOPSPIN user How to Open Data in Other Ways TOPSPIN provides various other ways of displaying da
154. e data area depends on the overall size of the TOPSPIN window and on presence of the Browser and or Processing Guide Fig 14 1 shows the TOPSPIN window with the Browser and three data windows 262 Data Window Handling PY Bruker TOPSPIN 2 0 on NMR datastation as Jos van Bo Sel File Edit View Spectrometer Processing Analysis Options Window Help US oh oe Bled 3d 4 AM 1 T Bele 272 8 ts FEM QQQRQ ag B browne esol crows aie Mean 13C 1 1 Cbio SE aa quest PERE pexantd 130 H E E exami cl 1H exam2d_CH E exarm2d HC el exam cd_HH os examd jh H E Ccbiot H E cts3 H Cts16 6 C ts2 0 Figure 14 1 Note that the three data windows show different data objects 1D process ing parameters a 1D spectrum and a 2D spectrum How to Move a Data Window 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 Depending on the position of the double headed arrow you can change the window height width or both see Fig 14 2 263 Data Window Handling fclexamid_13C 11 C bio guest TIGITA DRX 300 Cholac E F 1l06 7 ppm 8049 1 Hg Mus Index 848 850 Value 4 249047528E8 i 50 0 0 0 50 0 ppm Figure 14 2 How to Select activate a Data Window The active data window is the window of
155. e defined as dataset group File properties Show main dataset parameters like Dimension Pulse program Acquisi tion Date Nuclei Spectrometer frequency and Solvent Files Show the files in the processed data directory of the selected dataset Process Selected Datasets Perform serial processing on the selected datasets Opens a dialog where you can change or edit the dataset list and specify the command macro or Python program to be executed starts the command serial The Close button allows you to close the search result dialog 5 8 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 expno and procno subdirectories These files contain the actual data parameters lists etc Right click inside the data window and choose Files from the popup 92 Dataset Handling menu Display Properties Save Display Region To Restore Display Region From Params Fife Set plot height for current position 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 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 File gt Run
156. e displayed in the data window see Fig 12 15 and 12 16 224 1D Interactive Manipulation Rot AE p Ei ACEEA B Joo examld 13C dA sels examld 13C 4 1 C bio examld 13C 1 L Cribig examld 13C 4 1 C bio guest Scale r 1 85 Shift i 0 0028 ppm 123 3 123 2 Figure 12 16 123 0 ppm How to move the selected spectrum one place up down Click the following button Move the selected spectrum one place up in the list 225 1D Interactive Manipulation Click the following button 4 Move the selected spectrum one place down in the list Note that the first soectrum and calculated spectra sum of difference cannot be moved up down How to Switch on off the Display of Datapaths and Scaling Fac tors Click the following button 1 Switch on off display of datapaths and scaling factors How to Return from Multiple Display mode Click the following button a Return from multiple display mode ret How to Set the Colors of the 15t 2 9 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 sec ond spectrum Click Options gt Preferences and click the Change button for the item Color of 2nd ID spectrum TOPSPIN 2 0 and newer allows you to set 8 different colors for different spectra in multiple display 12 6 1D Interactive Baseline Correction Baseline correction ca
157. e following button 123 Change data dimensionality This changes the number of parameter columns and value of the acquisi tion parameter PARMODE 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 Ac quisition Reference manual or enter edlock on the command line How to Set Routing Parameters Enter the command edasp and set the routing parameters in the appear ing dialog box For a detailed description of edasp please refer to the Ac quisition Reference manual or enter edasp on the command line 104 Parameter Handling 105 Data Processing Chapter 7 Data Processing 7 1 Interactive Processing Interactive processing allows full control over the processing sequence However it requires detailed Knowledge about the required parameters see chapter 6 1 and commands Therefore it is only suitable for the advanced user New or intermediate users are recommended to use the Processing Guide for semi automatic processing see chapter 7 2 How to Process Data with Single Commands Data can be processed by entering single commands on the command line A typical 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
158. e 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 dis 154 1D Display played In the overview the displayed region is marked as a green area To switch on the spectrum overview click the following toggle button in the upper toolbar ul Switch the spectrum overview display on off ov To shift the displayed region simply click hold the green area in the over view spectrum and move the mouse see Fig 9 13 How to Switch Y axis Display Click the following toggle button in the upper toolbar Ei Switch the y axis display between abs rel off y Fig 9 13 shows a data window with the spectrum overview on ppm axis units and absolute y axis display examid 1H 1 1 Cobio guest Figure 9 13 9 6 Show Display Properties Regions Files If you right click inside the data window the following popup menu will 155 1D Display appear Display Proper save Display Region To Restore Display Region From Params F172 File Properties Files Figure 9 14 If you choose Display Properties a dialog box see Fig 9 14 will appear 156 Please select the components to be displayed together with the spectrum if availabley lt Cursor information Tit
159. e left part of the dialog box The right part of the dialog box shows the window settings see Fig 5 11 mote new internal windows cascaded rather than maximized Configure cascaded window Figure 5 11 3 Check Open new internal windows cascaded rather than max 4 Optionally you can configure the cascaded windows by clicking the respective Change button This will open the dialog box shown in Fig 5 12 74 Dataset Handling 19 Ea x 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 los Height of window E offset to previous window fo Y offset to previous window pa Use standard values instead of those above ho ng JRK Cancel Figure 5 12 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 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 da ta or Left click hold a data name expno or procno and drag it into an empty data window created with Alt w n or
160. e picked and dis played 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 de fined 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 233 1D Interactive Manipulation Alternatively you can enter pp1 on the command line This command can be entered in Interactive peak picking mode or in the normal display mode How to Delete all Peak Picking Ranges Click the button in the data window toolbar or Right click in the data field and click Delete All Regions in the popup menu How to Define Peaks Manually 1 Click the following
161. e view 192 11 3 nD parameter display 0 0 0c eee 192 11 4 nD Fid BP Es 0 f Yee ee 194 11 5 nD Peak and Integral Display 0 0008 195 Chapter 12 1D Interactive Manipulation 000002e 198 12 1 1D Interactive Window multiplication 198 How to Switch to Window Multiplication Mode 198 12 2 1D Interactive Phase Correction 0 000 eae 200 How to Switch to Phase Correction Mode 200 218 12 3 12 4 12 5 How to Perform a Typical 1D Interactive Phase Correction 201 How to Set the Phase Pivot Point 0 4 201 How to Perform Default Zero Order Phase Correction 202 How to Perform Interactive Zero Order Phase Correction 202 How to Perform Interactive First Order Phase Correction 202 How to Perform 90 90 or 180 Zero Order Phase Correction 202 How to Reset the Phase to the Original Values 202 How to Change the Mouse Sensitivity 203 How to Return from Phase Correction Mode with without Save 203 1D Interactive Integration 0 00 0 ee 203 How to Switch to Integration Mode 006 204 How to Define Integral Regions 0000005 205 How to Select Deselect Integral Regions 206 How to Read Integral Regions from Disk 207 How to Perform Interactive Bias and Slope Corre
162. e 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 is installed Note that this can be different on the spectrometer than on the dat astation lt instrum gt is the configuration name After copying the configuration directory you have to perform expin stall as follows e Click Spectrometer gt Setup gt Experiment installation or enter expinstall on the command line Follow the instructions on the screen In successive dialog boxes check select the options below and click Next to continue Installation for Datastation Customize e High Resolution Systems e The configuration name as it was copied from your spectrometer 318 Configuration Automation e The items you want to install e Select the desired printer and paper format for the parameter sets e The spectrometer frequency acquisition mode and pre scan delay In the last dialog box click Finish The installation of the selected items will start now Wait until this process has finished For more details on expinstall please refer to the description of this command in the Acquisition Reference manual 17 3 Parameter set conversion The command paracon changes the basic frequency in parameter sets This allows you to use parameter sets which w
163. ecoration is available Especially users who work with many different windows will get more space on their monitor by using this function that hides respectively shows the title of the current window and reduces the used font Data Window Handling 2 1 Analysis Chapter 15 Analysis 15 1 Introduction TOPSPIN offers various data analysis methods including chemical shift measurement signal to noise calculation and T1 T2 relaxation analysis as described in this chapter Furthermore it offers the following structure anal ysis tools Multiplet Analysis This allows you to easily define multiplets and deduce chemical shifts coupling constants multiplicities and connections Daisy TOPSPIN 2 0 and newer This allows you to simulate spectra based on chemical shifts and coupling constants Solids Line Shape Analysis This allows you to simulate and fit calculated spectra to various experimental 1D solid NMR spectra Jmol A 3D Structure Viewer for displaying chemical structures 2 2 Analysis e 2D molecule structure editor A program for drawing chemical structures offering a large number of drawing tools e DNMR Dynamic NMR Lineshape Analysis A program to simulate temperature dependent NMR spectra interac tively set up and iteratively refine the model parameters to get the best fit of the measured and simulated 1D NMR spectra Structure analysis tools can be started from the Analysis menu They are all
164. ed data as analog filtered data e wrp wra genfid wmisc write various files How to Save an Entire Dataset 1 Click File gt Save Ctr1ts 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 gt Save Ctr1ts 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 gt Save Ctr1t 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 number expno and click OK How to Save Processed Data as Pseudo Raw Data 1 Click File gt Save Ctrlts 2 Select the option Save other file 1 For detailed information about the ccpn format please refer to www ccpn ac uk Dataset Handling 3 Select File type 1r 1i as fid genfid or 2rr 2ii as ser genser 4 Click OK 5 Enter a destination expno optionally you can specify further data path specifications 6 Click OK 5 5 Deleting Data How to Delete a Specific Dataset Right click the data name expno or procno in the browser then click Delete A confirmation dialog will appear Just click OK if you are sure you want to delete Note that TOPSPIN does not allow you to delete the last available dataset e g the last procno under an expno the
165. elrool 1 Gauss Amolitude Parameters 1000 Size of Shape Truncation Level 5 Figure 16 19 By default a 1000 point Gauss shape is displayed with Truncation level 1 0 The TOPSPIN menu is changed showing the additional Shapes and Manipu late 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 is displayed and selected A full description of the interactive and non interactive Shapetool can be found under Click Help gt Manuals gt Acquisition Application Manuals Sha petool 310 Acquisition Easy definition of Shape pulses The usage of shaped pulses for the selective excitation is a nontrivial task that couples together all parameters such as the power level pulse length and the excited region TopSpin 2 1 and newer offers easy setup of selective experiments For usage Shape tool is typically started by the command stdisp on a fin ished 1D preparation experiment 1 Define the excitation regions also see Fig 16 10 a creates a new region on the display The region is put in the middle of the currently visible area By using the mouse position and width can be changed b deletes defined regions This
166. ems On a datastation a default configuration is automatically done during the installation No configuration commands are required Only if you want to use AU programs you must run expinstall once History Log Files Spooler Reports 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 run ning you can view log files with the commands hist and ptrace If TOP SPIN hangs you can create a stack trace by hitting Ctr1 Linux or Ctrl Break Windows in the TOPSPIN startup window 56 4 2 1 4 2 2 4 2 3 TOPSPIN command log By default the history protocol feature is switched on This means all TOP SPIN Commands will be protocolled and can be examined by entering hist on the command 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 TOPSPIN spooler report TOPSPIN reports all queued delayed and cron jobs in the so called spooler report file The spooler report stores all jobs since TOPSPIN installation and can become very large Therefore it should be cleaned from time to time To do that 1 Enter the command spooler 2 Click Tools gt Show spooler report 3 Mark the entries to be deleted 4 Right click in the dialog and choose Delete 5 Close the Spo
167. encrypted by TOPSPIN itself For this reason a Standard Operating Procedure SOP of the company or institution that wishes to apply TOPSPIN signatures must exist defining the role of TOPSPIN signatures For this reason companies and institutions that want to apply TOPSPIN sig natures must have a Standard Operating Procedure SOP which defines the role of these signatures Note that digital signatures complying with respective laws requires special software and the involvement of trust centers Bruker refers to the respec tive commercial software for this purpose 18 3 Password Controlled Login Identification 18 3 1 Definition of an internal user In TOPSPIN the NMR administrator may set up a list of internal TOPSPIN users An internal user need not have a user account for the operating sys tem and is only known to TOPSPIN Such a user is characterized by the fol lowing items 332 Regulatory Compliance USER ID A short unique string of characters identifying a user e g guest USER NAME A long string of characters usually the full name of a user e g Franz J Maier SIGNATURE MEANINGS A list of items separated by comma e g Approval Review an empty string or the special string NONE In the latter two cases this user cannot electronically sign data In all other cases the user is allowed to sign The esign dialog allows the user to select one of the items to specify the meaning of the signature
168. equence of TOPSPIN commands It can be created with the command edmac A simple macro for processing and plotting the cur rent dataset is em FG apk sref autop Lort 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 guest 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 Dye 2 Lae Or py gt MSG done y str y Note that commands like NEWWIN INPUT DIALOG MSG and EXIT are Bruker defined whereas x and if are original Python commands Once created a macro can be executed by entering its name on the com mand line AU Programs An AU program may contain TOPSPIN commands AU macros and C lan guage statements It can be created with the command edau A simple AU program which performs the efp command on a series of dataset expno s iS User Extensions include lt lib util h gt 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
169. equency 275 spectrometer hardware 20 21 Spectrometer menu 33 273 spectrum display 1D 121 objects 329 330 overview 1D 145 overview 2D 169 Spectrum tab 121 145 152 square 2D layout 160 square brackets 33 45 116 121 sref command 99 103 205 246 stacked multiple display 211 Start button 72 startup actions 329 status line font 344 status parameter change 93 display 96 149 display 1D 122 123 stdisp command 292 stop an acquisition 274 stop command 274 276 288 store 2D contour levels 175 structure file 143 Structure tab 143 sum spectrum in multiple display 210 superimpose 1D spectra 207 cursor information 148 electronic signature 150 integral trails labels 149 main status parameters 149 peak labels 149 spectra 24 title of a dataset 149 SW parameter 275 swap data windows 257 sweep width 275 swin command 257 switch I 14 to the last 2D data 34 to the last 3D data 34 T T1 calculation Ill T1 T2 Relaxation 263 tiguide command 263 T2 calculation Ill Tab bar 1D 116 121 2D 158 165 configuration 121 335 font 342 usage 121 Tab key 92 96 tabbed pane 165 335 TCP IP port 321 temperature unit window 256 Terminal Window 19 time domain signal 29 title bar 115 116 157 250 251 254 255 256 303 title file 124 title of a dataset 23 62 65 124 149 286 337 Title tab 124 toccpn command 78 tojdx command 28 78 toolbar 1D 189 2D 225 configuration 347 extension 359 for acquisition 273 icons 360 3
170. er the source directory for these items was fixed lt tshome gt exp stan nmr Now you can define a individual source directories for each item To do that 1 Open the dialog of any of the items e g with the command edau edlist Or edmisc 2 Click Options gt Manage Source Directories A dialog will appear showing a list of items with the current source di Cots explistaninimrAllists ppluser Cts expistaninmrllists pp Pulse Programs Colts expistaninmralistsicadius er Colts expistaninmrllistsicpd CPD Programs Figure 20 14 rectories By default two source directories are present one for user defined items and one for Bruker items This list can be modified or extended with your preferred source directories e g C my pulse programs C ts21 exp stan nmr lists pp user C ts21 exp stan nmr lists pp 370 User Preferences You can do this for each item separately Items will be searched for in the order of the directories specified 371 User Extensions Chapter 21 User Extensions TOPSPIN offers various ways to extend the standard commands buttons programs etc 21 1 User Notebook You can create your own user specific notebook with the command View gt Notebook nbook Ey Notebook File Edit Search Figure 21 1 This can be used to store and retrieve any personal notes information etc 3 2 User Extensions 21 2 21 3 373 Macros A macro contains a s
171. eractive functions refer to chapter 12 and 14 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 ill Switch the overview spectrum on off 4 Toggle grid between fixed axis oft How to Use the Lower Toolbar 1D data The lower toolbar contains buttons for display functions Buttons for vertical scaling intensity 2 8 JR 2 Increase the intensity by a factor of 2 2 39 The TOPSPIN Interface f2 Decrease the intensity by a factor of 2 2 g Increase the intensity by a factor of 8 8 8 Decrease the intensity by a factor of 8 8 Change the intensity smoothly dh Reset the intensity baseline positions remains unchanged vr Note that vertical scaling can also be changed with the mouse wheel Buttons for horizontal scaling Zooming MARAA h W Reset zooming horizontal scaling to full spectrum hr 41 Display the entire spectrum baseline position and intensity scal ing are adjusted if necessary a11 1 Zoom in to the center spectrum or left edge FID of the dis played region increasing the horizontal scaling zi a Zoom in out smoothly Zoom out from the center spectrum or left edge FID of the dis played region decreasing horizontal scaling zo iE Exact zoom via dialog box zx 4 Toggle interactive zoom mode When switched off i
172. ere created on a spectrome ter with a different frequency It opens dialog box shown in Fig 17 1 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 dialog box To start the conversion select one or more parameter sets and click OK 17 4 Automation How to Install AU Programs To install AU programs you have to run the command expinstal1 see chapter 17 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 pro grams Fig 17 2 shows a dialog box with two User defined AU programs 319 Configuration Automation Ey Parameter set conversion Parameter set conversion Select parameter sets for conversion of the basic frequency BF from the list on the right Use the checkboxes to select bruker or user definedparameter sets Use the match field to apply wildcards to the list of parameter sets Use cf to set the basic frequency BF Current basic frequency 300 15 MHz Bruker defined parameter sets F User defined parameter sets Match PROT caze Insensitive match Available parameter sets IPROT VT PROTON PROTONI 26 PROTOMN256 PRO
173. erences 0 0 0 0 ccc ee eee 348 How to Open the Last Used Dataset on Startup 351 How to Define the Startup Actions 0000 351 How to Define Auto Termination after Idle Time 351 How to Define Auto Locking after Idle Time 352 How to Change the Preferred Editor 353 How to Configure the Tab Bar 0 00000 eee 354 How to Configure the Right click Menu Function 354 How to Change Colors of Data Objects on the Screen 355 How to Change Colors of Data Objects on the Printer 355 How to Change Colors of the Lock Display 356 How to Create a New Data Window Color Scheme 356 How to Read a Different Data Window Color Scheme 357 How to Change Peak and Integral table Colour Spacings 357 How to Create Thick Lines on the Screen 359 How to Create Thick Lines on the Printer 359 How to Change All Fonts of the Topspin Interface 359 How to Change the Font of the TOPSPINmenu 360 How to Change the Font of the Tab bar 361 How to Change the Font of Dialog Boxes 362 How to Change the Font of the Browser 362 Chapter 21 20 2 20 3 20 4 20 5 User 21 1 21 2 21 3 21 4 21 5 21 6 21 7 21 8 How to Change the Font of the Command Line 363 How
174. eters 306 pseudo raw data 85 pulse program 21 31 69 134 display 134 parameters 103 132 306 PulsProg tab 134 Python programs 32 374 378 381 Q QUIT AU macro 111 QUITMSG AU macro 111 R re command 24 80 219 read color scheme 35 7 data formats 82 integrals from disk 207 the prosol parameters 306 window layout 269 reb command 23 81 re enable disabled commands 369 reference peak in 1D calibration 218 in 1D phase correction 201 202 in 2D calibration 260 in 2D phase correction 242 referencing 106 reg file 213 relaxation curve 280 remote connections 348 remove commands 367 data from multiple display 222 menus 367 toolbar buttons 366 reopen a dataset 125 reopen command 74 125 rep command 24 81 repw command 81 rescale 2D projection 180 data in multiple windows 126 reset 1D baseline correction 229 1D phase values 202 3D cube size and orientation 192 F1 zoom factor in 2D 170 F2 and F1 zoom factor 170 intensity 1D 127 intensity in 2D 168 search mask 90 zoom factor 40 128 resize I 25 command line 365 data window 263 graphics 120 resolution of a screen dump 27 121 restore adjusted acquisition parameters GS 305 size and position of a data window 268 toolbar 367 uncorrected baseline 229 retrieve previously entered commands 42 rew command 24 81 Right Arrow key 42 48 69 rotate 3D cube 187 191 routing parameters 104 S S N value 275 Sample tab 151 sav command 38 45 save 1D base
175. 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 162 1D Display 9 7 Saving Display Region The currently displayed spectral region can be stored as follows Right click in the data window and choose Save Display Region To This will open the dialog box shown in Fig 9 18 EY Save display region to Options O Parameters F172 e g used by restore display dgl Parameters ABSFUZ e g used by abst apkt OQ Parameters STSRISTSI used by strip Tt CO Parameters SISF1 2 signal region used by sino Parameters NOlSF1 2 noise region used by sino 4 text file for use with other programa Figure 9 18 Here the following options are available e Parameters F1 2 dp1 to save the displayed region for restoring the display later The region is stored in the parameters F1P and F2P To restore the saved region right click in the data window and choose Restore Display Region from Params F1 2 e Parameters ABSF1 2 to save the displayed region for baseline correction command absf or phase correction command apkf The region is stored in the processing parameters ABSF1 and ABSF2 e Parameters STSR STSI to save the displayed region for Strip FT commands like ft and trf 163 1D Display The region is stored in the process
176. f peaks within the integral range Range F1 from the left edge of the integral range 1D Display Range F1 to the right edge of the integral range Please note the difference between the following items e selected integral the entry that has been clicked last Integral 3 in Fig 9 7 If you right click an entry it is selected and you can exe cute one of the commands from the popup menu see Fig 9 8 The keys Enter and Delete work on the selected entry e active integral the entry on which the cursor resides Integral 1 in Fig 9 7 The active integral is also marked in the correlated spec trum by a black vertical line see lower part of Fig 9 7 and descrip tion below When you move the cursor over the integral list the vertical line in the correlated spectrum moves along with it and vice versa Note that the colours of the selected and active integral can be set in the table properties see below Display the spectral region around an integral To display the spectral region around a particular integral Right click the desired integral 144 1D Display This will open the popup menu shown in Fig 9 8 Expand Expand all Show spectrum b Expand spectrum P In current window Delete In correlated window Define a reference Calibrate by reference Copy Export Print Print preview Table properties Figure 9 8 Here you can choose from the following options Show spectrum g
177. formation in the curve field includ ing algorithm peak number and relaxation value FB Oo Show an extended report including the fitted intensity or area 286 Analysis 287 distribution This consists of the same information as the brief report plus a table with the intensity or area distribution Example Dataset INTENSITY ELE C bio data guest nmr tltest l1 pdata 1 I t 1 0 P exp t T1 LZ POLES Or Peak dy Cursor Poume Teed PPM Results COMO VAL L 0 ee be 61070 P 2 211E F0 00 TI 19 449s SD 3 685e 003 tau ppm integral intensity 30 000s Tsak 2e58iter009 L g737er008 LOO 00 s Lees F BeZOISSTO0S 2 90S6eT007 8 000s Teac 2852567008 6 46166700 5000s be Qed LeoZegetrOo9 l 3 LOLTEe O0s Print Export of Copy the Fitting Results To print the fitting curve Click File gt Print To export the fitting curve as a graphics file Click File gt Export To copy the fitting curve to the Windows Clipboard Click Edit gt Copy Acquisition Chapter 16 Acquisition This chapter describes TOPSPIN acquisition as far as the interface is con cerned Individual acquisition command are described in the Acquisition Reference manual 16 1 Acquisition Guide If you are a new or occasional user we recommend you to acquire your data with the TOPSPIN Acquisition Flowchart This will guide you through the typical sequence of acquisition steps To start the Acquisition Guid
178. g the button opens the following dialog window ie Configure realtime ft x Set options for realtime Tt Window function Phase correction mode Nc r Baseline correction mode quad OK Cancel The acquisition information will appear in the acquisition status bar at the bottom of the TOPSPIN window for example Acquisition information Fid Flash Sample Scar 2 16 residual time 1m27s5 jie experiments 1 1 4 When the acquisition has finished spooler 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 16 18 Acquisition protona 1 1 CiBio guest DE Ea Spectrur ProcPars AcquPars Tithe PulseProg Peaks Integrals Sample structure Fid Acqu rel O246 6 6 Figure 16 18 From here the processed data can be analysed printed and or ar chived 16 11 Shape tool The Shape tool interface allows you to create manipulate RF shapes and waveformat To start the Shape Tool interface Click Spectrometer gt Shape Tool or enter stdisp on the command line The Shape Tool window will appear see Fig 16 19 This consists of a toolbar a command line and a split pane with a data section at the right and a parameter section at the left If Shape Tool is opened with a dataset the current dataset will be displayed see Fig 16 20 309 Acquisition Shap
179. h all its functionalities to acquire process and interpret spectrometer data To find information more readily you can read selected chapters depend ing on your requirements or read the User Manual in succession for general information 1 2 Safety Regulations In order to work safely in laboratries with NMR spectrometers all users have to follow the safety regulations for magnetic electrical cryogenic and chemical safety For detailed information please refer to the safety instruc tions in the Beginners Guide Manual provided on the TopSpin DVD 1 3 User Manual Conventions The User Manual utilizes different script types in order to make selected text more transparent and explicable to users Please note that this docu ment contains the following 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 Arial bold fid filenames are in Courier name any name which is not a filename is in Arial italic Introduction TOPSPIN 2 1 File directory Conventions lt tshome gt the TOPSPIN installation home directory User Action Conventions 1 2 3 a single user action the first action of a sequence the second action of a sequence etc a the first action of a sub sequence b the second action of a sub sequence c etc 1 4 TOPSPIN Overview Functionality TOPSPIN is an integrated software package for
180. h of these two modes is applied depends on how the NMR ad ministrator configured TOPSPIN If the option Enforce login for work ing with TOPSPIN is disabled see below command uadmin the first mode is active otherwise the second What is the difference between the modes e Inthe first case the System User Windows or Linux user who started TOPSPIN signs the data set Prior to signing esign requests this user s password which is administrated by the operating system OS No internal TOPSPIN user management Regulatory Compliance plays a role Advantage This mode is entirely OS compliant Disadvantages a TOPSPIN termination restart is required when a different user wants to sign data alternatively several licenses would admit simultaneous TOPSPIN sessions b All TOPSPIN users must have an OS login e Inthe second case any TOPSPIN internal user who is enabled by the NMR administrator with uadmin may sign Advantage Convenient and easy usage Disadvantage TOPSPIN internal user management is required internal users and their pass words USER NAME The complete name of the signer as specified by the NMR administra tor during user administration command uadmin SIGNATURE MEANING The meaning of a signature e g Review or Approval A user may only select meanings that were assigned to him by the NMR administrator during user administration SIGNATURE COMMENT Any text 18 2 3 Displaying the electronic
181. hase correction 106 200 2D calibration 259 compilation of an AU program 322 configuration of a datastation 318 selection of the first expno procno 76 tuning and matching 299 automatic mode of the Acquisition Guide 289 of the Processing Guide 27 108 automation 31 32 319 autoplot command 110 117 autostart mac file 351 Avance spectrometers 17 318 axis units 39 154 178 218 260 B background of a data window 357 Backspace key 42 backward peak picking 234 baseline correction 1D 106 226 mode 39 226 bcm command 229 bias correction 208 bio molecular experiments 32 bnmr command 375 bnmrsel command 375 bpan command 376 browser 35 36 45 64 75 font 362 in multiple display mode 220 253 Bruker AU programs 32 321 data format 22 29 30 78 82 83 92 example datasets 23 71 BSMS control panel 301 BSMS display window 269 bsmsdisp command 301 C calibration 106 1D interactive 217 2D interactive 259 mode 39 217 259 cf command 21 56 316 317 318 chemical shift 224 chemical shift distance 1D 273 2D 260 CHEMSTR parameter 152 C language 31 110 373 374 clevels file 185 clipboard 26 45 close active data window 268 lock display window 300 the active data window 45 close command 45 cmdhist command 43 cmdindex command 52 cmdtab_user prop file 53 collapse a data directory 64 69 color scheme 356 colors of data objects 355 of the lock display 356 on the printer 355 command definition 53 di
182. he new certificate files must be installed on BOTH machines 19 5 How to Access ICON NMR from a Remote Web Browser 345 In TOPSPIN 1 3 and newer ICON NMR is web enabled The standard Bruker Automation Software now provides a built in website which can be acti vated to allow remote access to ICON NMR from any web browser which is networked to the spectrometer workstation Experiments may be can celled submitted the run may be paused or halted and spectra in PDF for mat are available from the browser window No additional software apart from ICON NMR and Webbrowser is required and configuration is per formed via the standard ICON NMR Configuration window For security a SSL HTTPS connection is supported Pocket PC Internet Explorer is also Remote Control supported for full spectrometer control via Windows Mobile 2003 TM or equivalent PDF files of spectra may also be viewed on this platform mak ing the mobile pocket spectrometer a reality The configuration of ICON NMR web interface is described in the ICON NMR manual accessible Help gt Manuals gt Automation and Plotting con Nmr Automation Interface Note that ICON NMR remote control does not require and is fully independent of TOPSPIN remote control 19 6 How to limit IP Addresses for Remote Control TopSpin offers the possibility of limiting the IP Addresses for remote con trol in order to permit more security for all soectrometer control This fea ture is especia
183. he size 1 Enter si 96 Parameter Handling for 1D data the following dialog box will appear CT x Size of real spectrum BI 2765 Ok cancel for 2D data the following dialog box will appear x Size of real spectrum f 024 Ok cancel 2 Specify the desired value s e g 32768 or 32k 3 Click OK ol How to Set Processing Parameters from the Parameter Editor To open the processing parameter editor Click the ProcPars tab in the Tab bar of the data window or Enter edp on the command line 97 Parameter Handling examid 1H 1 1 Cibio guest Spectrum ProacPars AcguPars Title PulseProg Peaks Integrals Sample Structure Fid Acqu oMs Va Reference Window Phase Baseline Fourier Integration Peak Automation Miscellaneous User P F Reference S 32768 Size of real spec SF MHz spectrometer tre OFFSET ppm Low field limit of SR Hz oon Spectrum reterel HZpPT Hz Spectral resolutic Window function Y Phase correction PHCO degree 411 456 Oth order correct Figure 6 1 At the left of the parameter editor window you will see a list of parameter sections The processing parameter editor supports the following functions Collapse expand a parameter section by clicking the button Note that the section Window function in Fig 6 1 is collapsed Collapse expand all parameter sections by clicking the large
184. he popup menu This will determine the calibration constant 2 Right click any integral and choose Calibrate by reference This will divide all integrals by the calibration constant setting the reference 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 refer ence 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 9 7 shows only integrals However if peak pick ing has been done the integral list also shows the peaks within each integral range see Fig 9 9 146 1D Display examid_1H 1 1 Crbio guest 1 En oj x Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals Sample Structure Fia A Object integral abs Paks Rang Rang viF1i ppm Intensity FHntegrali 21807940 16 1 6664 4 7 872 8 603 gt FHntegral 20864697 28 1 5943 4 7410 7870 Peak 5 7 7318 0 80 Peak 6 7 7062 0 84 L Peaks 7 5436 0 82 HHnteqral3 45809321 78 3 5003 1 7 056 7 408 exami1d_1H 1 1 Cibio guest 2 8 5 8 0 75 7 0 ppm Figure 9 9 Note that the integral entries can be collapsed hiding the pe
185. his purpose This opens the dialog box show in Fig 18 1 Regulatory Compliance PN Audit trail audit check Options OQ Views audit trail of processed data OQ Views audit trail of acquisition data OQ Add a comment to audit trail of processed data O Add a comment to audit trail of acquistion data y Figure 18 1 The first two entries allow you to view the audit trail files The third entry performs an audit trail check i e a data consistency check If both raw and processed data are consistent you will get the message shown in Fig 18 2 EA auditcheck audit file for acquistion OK processing OK raw data checksum OK proc data checksum OK Figure 18 2 If the data have been manipulated outside of TOPSPIN e g with third party software the checksum will be inconsistent Fig 18 3 shows the message 326 Regulatory Compliance for inconsistent processed data EA auditcheck audit file tor acquisition OK processing OK raw data checksum OF proc data Invalid data checksum Figure 18 3 The fourth and fifth entry in Fig 18 1 allow you to add a comment to the raw or processed audit trail files respectively 18 1 4 Audit trail contents The contents of an audit file is grouped in the following way NUMBER WHEN WHO WHERE PROCESS VERSION WHAT These entries have the following meaning NUMBER Running number of an entry starting with 1 WHEN Date of the entry e g lt 200
186. ick Options gt Preferences set Change any color of the objects Spectrum Spectrum title Spectrum cur sor or Spectrum parameters Click Apply Click Spectrum in the left part of the User preferences box 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 356 User Preferences 6 Click OK How to Read a Different Data Window Color Scheme 1 Click Options gt Preferences set 2 Click Spectrum in the left part of the User preferences box 3 Click in the list box to the right of the object Change spectral window color scheme and select an element from the appearing list 4 Click OK TOPSPIN is delivered wit two colors schemes e light default a white background with black axes e dark a dark blue background with a white axes How to Change Peak and Integral table Colour Spacings 1 Click Options gt Preferences set 2 Click Miscellaneous in the left part of the User preferences box 3 Click in the list box to the right of the object Table colors see Fig 20 4 for simple tables like peaks solvents nuclei tables Tree table colors 357 User Preferences for nested lists like the integral table Table properties Colours Spacings Table header Column header foreground g h6Uw Column header background E B Foreground Background Selection Restore defaults
187. ift to the right half of the displayed region sz W Shift to the extreme left edge of the spectrum s10 Shift to the extreme right edge of the spectrum sro Alternatively you can enter the corresponding commands as specified be tween square brackets How to Shift the Spectrum Up or Down To shift the FID or spectrum display up or down Click hold the button and move the mouse Smoothly shift the spectrum baseline up down or 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 be tween square brackets 129 1D Display 9 4 Using the Tab bar Tabs of the data window can be activated by clicking them or by entering the corresponding 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 How to Display the Spectrum Click the Spectrum tab spec examid_1H 1 1 Cxbio guest i l oj x Spectrum ProcPars AcquPars Title PulsFrog Peaks Integrals Sample Structure Fid en ee 15 10 5 0 ppm This displays the processed data If these do not exist the text No proc essed data available appears 130
188. ill process data without this dialog using the last settings Exponential Multiply Cert LE Hz 4 Fourier Transtorm Tt Auto Phasing tapk Set Spectrum Reference sret Auto Baseline Correction abs Plot autoplot v LAYOUT HD_Howp v Figure 7 1 How to Use the Processing Guide in Automatic mode The Processing Guide in automatic mode guides you through the entire processing sequence of data selection processing printing and archiving with minimum user interaction 1 Click Processing gt Data gt Processing Guide The Processing Guide window will appear as an integral part of the current data window see Fig 7 2 108 Data Processing MMF Data Processing Guide 7 Open Data Set amp EG Advanced Window Function i 1 ta iN Peak Picking Fourier Transtorrr gt Phase Correction a Axis Calibration E mail Archive S Baseline Corr Figure 7 2 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 109 c Click Window function gt Fourier Transform gt etc Each processing step will be executed without user interaction How to Use the Processing Guide in nteractive mode The Processing Guide in interactive mode guides you through the entire processing sequence of data selectio
189. in the FID display the right part of the window This can be manipulated with the FID display buttons as described in chapter 16 10 At the bottom of the window you find the following buttons e Save Save the value of the current parameter 304 Acquisition Save all Save the values of all changed parameters e 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 16 10 Running an Acquisition A typical acquisition is performed as follows 1 Create a new dataset a Click File gt New new Ctrltn Prepare for a new experiment by creating a new data set and initializing its MMR parameters according to the selected experiment type Solvent Experime yy Use current params immi TITLE 1H Cyclosporin Figure 16 15 b Specify the datapath variables name expno procno dir and user select the desired Solvent and Experiment enter the Title and click OK 305 Acquisition 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 1 CiBio guest DE x Spectrum ProcPars ScquPars Title PulseProg Peaks Integrals Sample Structure Fid Acqu F Experiment FPULFR OG Ars mod Acquisition mace To Size of fid MS Number of Scar DS Number of durnrr TODO
190. 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 Click the following button H Save the Peak Region and Peak List and Return sret This will e Save the peak list to the file peak xml and the peak ranges to the file peakrng e Leave the peak picking mode To return while discarding any changes Click the following button a Return discarding any changes ret How to save Peaklists and Regions in 1D interactive mode In 1D interactive Peak Picking the H Save as button opens a window in which three options of saving can be chosen a Save Peaklists and Regions b Save Peaklist for Deconvolution Peaklist will be saved in a format which is needed for deconvolution c Save Peak list and start Deconvolution The Peaklist is saved and the Deconvolution will be started after that returning to Peak Picking 1D Interactive Manipulation 237 2D Interactive Manipulation Chapter 13 2D Interactive Manipulation The upper toolbar of the 2D menu offers various buttons for interactive manipulation If you click such a button the active data window will switch to the corresponding mode An interactive manipulation mode is data win dow specific i e it only applies to the active window 13 1 2D Interactive Phase Correction 2D spectra can be phase corrected interactively in
191. ine or from the Options or Spectrometer menu However the latter menu is only available after cf has been performed once choosing Getting Started Installation for spectrometer After the configuration has finished TOPSPIN is ready to be used The con figuration 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 17 2 and the descrip tions of cf and expinstal1l1 in the Acquisition Reference Manual 2 3 How to Display Spectra In this chapter opening data in standard Bruker format is described Open ing other data formats is described in chapter 5 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 1 pdata t1 How to Locate nmr data in any arbitrary directory With TopSpin 2 5 Preview and newer nmr data can be located in any arbi trary directory As described in paragraph 2 3 the standard Bruker format can still be used The new storage format can be located in the following way lt dir gt lt name gt lt expnos gt pdata lt procnos gt e g c mydir sucrose 1 O pdata 1 Please note the following facts about the usage of the old and new storage format e The old format is still valid because it is a special case of
192. ined Menus to the Menubar 381 Adding User Defined Guides 2 000000 eee 383 Chapter 1 Introduction 1 1 About the User Manual 1 About this document The User Manual describes the main aspects of Brukers integrated soft ware package TopSpin This manual enables all users who work with Bruker software to get an overview of the various functionalities of Top Spin The main aspects outlined in here describe the possibilities and functionaries of the TopSpin interface and elucidate working processes for data acquisition and processing 2 Target audience The Bruker User Manual for TopSpin 2 1 and newer supports all Bruker users who already work with Bruker software products or who newly enter the software dimension of TopSpin The main aspect of this Man ual is to enable new TopSpin users and experienced TopSpin users to work with this software package 3 How to get the User Manual 15 Introduction TOPSPIN 2 1 The User Manual is available as a hard copy just like an electronically copy on the TopSpin DVD in the menu section Help where all other Bruker Manuals are provided too For detailed information about all Bruker software manuals please refer to chapter 1 4 The latest version of the User Manual is also provided on the Bruker Web Server http www bruker biospin com documentation_general html 4 How to read the User Manual The User Manual describes especially the TopSpin interface wit
193. ing parameters STSR and STSI Parameters NOISF1 2 to save the displayed region as the signal region for Signal to Noise calculation command sino The region is stored in the processing parameters SIGF1 and SIGF2 Parameters SIGF1 2 to save the displayed region as the noise region for Signal to Noise calculation command sino The region is stored in the processing parameters NOISF1 and NOISF2 A text file for use with other programs to save the displayed region in a text file This file can be viewed with any editor or used by external programs 9 8 Synchronize Visible Region of all Data Windows The visible region of all data windows can be synchronized as follows Zoom in or out one dataset while holding the Ctrl key or Zoom in or out one dataset and then enter the syne command 164 1D Display 165 2D Display Chapter 10 2D Display 10 1 The 2D Data Window The 2D data window consists of a data field a title bar a Tab bar and but tons Fig 10 1 shows a data window with a 2D spectrum 166 2D Display data title bar minimize maximize close field Tab bar button button button cence 1 cto pee__ Sica ae ProcPars AcquPars Title PulseProg Peaks Integrals Sample S FUC UFE Fid ACHU m 120 80 F1 pp F2 ppm 10 2 Changing the Display of a 2D spe
194. ions gt Preferences gt Acquisition gt Configure e Copying a dataset to a desired destination directory which could for instance be located on a server Type wrpa click File gt Save or type Ctrlts 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 directory tree into a single file with the extension bnmr zip To zip a dataset type tozip click File gt Save or type Ctrlts To unpack and display a zipped dataset enter fromzip Note that Getting Started bnmr zip files are fully compatible with the well Known PC zip for mat and can be unpacked with any common unzip 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 stand ard 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 Ctrl1 s To convert and dis play a JCAMP DxX file type fromjdx 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 2 11 How to Import NMR Data Stored in Special Formats TOPSPIN allows you to convert various data formats to standard Bruker for ma
195. irectory in the browser 69 individual spectra in multiple display 224 spectrum 30 expand a region 24 experiment time 292 expinstall command 21 56 291 316 317 318 319 expl command 80 93 94 162 I 20 Explorer 79 93 162 expno 72 6 79 85 160 exponential baseline correction 228 window multiplication 106 107 export data 26 121 expt command 292 extend the Topspin functionality 372 external projection 25 extract a row column in 2D 257 F F1 dimension 171 178 238 F1 key 16 45 F1 F2 plane 189 192 F2 dimension 171 178 238 F2 key 45 68 F2 F3 plane 190 192 F3 key 53 F3 F1 plane 188 190 192 F5 key 53 F6 key 45 53 265 fid command 154 178 FID display 291 295 303 307 Fid tab 154 160 178 File Chooser 23 File menu 23 37 file size of raw data 292 files of a dataset 80 85 93 160 162 find command 45 89 find data 37 89 first order phase correction 1D 202 2D 242 244 fitting peaks 30 fmc command 107 focus 41 45 68 69 font of dialog windows 362 of the browser 362 of the command line 363 of the interface 359 of the menu 360 of the status line 363 of the tab bar 361 forward peak picking 234 Fourier transform 106 107 fo command 107 fromjdx command 30 fromzip command 29 ft command 27 106 ftf command 27 367 function keys 45 G Gaussian deconvolution 30 Gaussian window multiplication 107 genfid command 85 86 genser command 86 geometric sequence of levels 183 geometry of a To
196. is selected the lowest integral is used The right edge of the selected integral is put at 3 4 of the window height If no integral is selected the highest integral is used 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 In case of overlapping integrals you must select the integral to be cut be fore you actually cut it Note that if one or more integrals are selected cut ting only works on selected integrals With TopSpin 2 2 1D Interactive Integration command cut integral can be called directly from right click context menu Right mouse click on the in tegral opens a popup menu in which cut current integral must be selected 212 1D Interactive Manipulation How to Save Integral Regions 1 Click the following button Save integral regions The following popup menu will appear Save Regions To intrag Save Regions To reg Export Regions To Relaxation Module and ret save amp Show List Figure 12 7 2 Choose one of the following entries Save regions to intrng Save the currently displayed integral regions including the slope and
197. is shown in the parameter section If this default fitting is appropriate you can view interpret and print the results as described below If not you can perform the desired fitting as described below Analysis Perform Fitting and Calculate the Relaxation Time Depending on the experiment you can perform the appropriate fitting as follows 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 Function Type and set the required parameters see below 3 Click OK 4 Perform fitting and calculate the relaxation time gt Fit the relaxation curve for the current peak Fit the relaxation curve for all peaks ast Fit data according to the ASCII file t1ascii View and interpret the results as described below Function Types and Parameters The TOPSPIN relaxation routine offers functions for various relaxation ex periments with up to 6 components uxnmrt1 for one component T1 experiments Set the parameter List file name to the list type used during the acquisition Set Pick data points to PD or PDO see below The 11 fitting function is defined by the function I t 1 0 Px exp where J is Intensity or Area according to the Fitting
198. ist and click the button Kill The command show all or kill all work like show and kill except that they also show TOPSPIN system processes Note that killing such proc esses may kill TOPSPIN 4 4 What to do if TOPSPIN hangs lf 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 gt Programs gt Bruker TOPSPIN gt TOPSPIN 2 1 gt Bruker Utilities 2 1 gt Miscellaneous 2 In the appearing window Click killtopspin Normally this kill all TOPSPIN processes including cpr corserver dataserver and java Trouble Shooting 4 5 How to Restart User Interface during Acquisition If Topspin hangs up during a data acquisition you can restart the user inter face without disturbing the acquisition To do that 1 oa h WN 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 62 Trouble Shooting 63 Dataset Han
199. ist of baseline points al ready exists you are prompted to overwrite or append to these points If you choose Append 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 posi tion 2 Do this for at least five baseline points Fig 12 18 shows a spectrum with five defined baseline points Note that here the points have been chosen at the right part of the spectrum for dis 230 1D Interactive Manipulation play reasons only Note that the actual baseline correction is only performed when you click the Hi button in the spline baselineand interactive baseline mode 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 12 19 Quit save amp Uit List baslonts Delete All Enter zoom Figure 12 19 To delete all baseline points 1 Right click any position in the data window 2 Choose Delete All from the popup menu see Fig 12 19 How to Return from Cubic Spline Baseline mode with without Save To return while saving the baseline points Click the following button H Save baseline points and Return retsab To return whi
200. itch individual scaling on off 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 amp to scan columns in the 2D spectrum Click the following button it turns green and move the mouse in the data field Lf to scan rows and columns in the 2D spectrum To scale up the displayed row column Click the left mouse button or turn the mouse wheel up To scale down the displayed row column Click the middle mouse button or turn the mouse wheel down How to Grab a Row Column You can grab a row or column i e keep it displayed in the data window as follows 1 Scan rows or columns as described above and hold at the desired position 2 Right click in the data window 3 Choose Grab Row Column from the popup menu see Fig 13 13 Note that a grabbed row column appears in the lower apart of the brows er It can be selected there and individually scaled or shifted 255 2D Interactive Manipulation Toggle Rows fColumns Extract RowlColumn Grab RowsCoalumn Baseline At Center Baseline At Bottom Figure 13 13 examzd HC 3 1 Crbio guest E IBR BE Ro wl t 4 A E E Ei 7 s s d tlag A A Row 57 746 ppm 619 of 1024 5 8 5 4 F2 ppm
201. ith the FDA 21 CFR Part 11 regulations Please read the accessible under Help gt Manuals gt Good Laboratory Practice 2 CFR Part 11 compliance This chapter describes the respective functionali ties provided by TOPSPIN in detail Audit Trails A TOPSPIN data set consists of acquisition raw data and processed data These are stored in a directory tree with the following structure lt dir gt data lt user gt nmr lt name gt lt expno gt pdata lt procno gt The acquisition data are stored in the expno subdirectory and the proc essed data are stored in the procno subdirectory The raw data audit trail Each expno sub directory contains a text file audita txt the audit trail of the raw data This reflects the acquisition state of the raw data and contains a checksum for the file itself audita txt and one for the raw data file fid or ser The latter checksum links the audit file with the raw data By means of the checksums any illegal manipulation of the audit file or the raw data file can be detected using the TOPSPIN commands audit or auditcheck 324 Regulatory Compliance 18 1 2 18 1 3 325 Whenever an acquisition is started the possibly existing audit file is over written by a new one belonging to the new raw data file By default the user is warned when the current dataset already contains raw data thus preventing accidental overwriting The option Override existing fid without inquiry is
202. itive intensities Integrate a to add up all intensities in the region and store separate entries for all and negative intensities Integrate to add up all intensities in the region and store separate entries for positive and negative intensities The integral regions will be displayed along with their storage num 2D Interactive Manipulation bers and modes see Fig 13 8 Pxam d HC 3 1 Cobio guest col 7 154 ppm 3577 739 He row 6 5 ppm olv 5 He Define new region a a Drag with lett mouse button g uerg da 5 6 s aft es 7a B 45 F2 ppm Figure 13 8 3 Click the I button and choose Integrate current regions from the pull down menu to integrate the defined regions 4 Click the I button again and choose List integral values from the pulldown menu to show the list of integrals Table 13 1 shows the list of integrals based on the regions defined in Fig 13 8 248 2D Interactive Manipulation 249 1024 1024 1024 1024 1024 1024 1024 1024 1024 1024 1024 1024 1024 1024 1024 row col 666 510 597 520 652 566 683 589 683 589 683 589 502 637 502 637 row2 col2 689 522 632 533 692 579 121 605 121 605 121 605 543 649 543 649 row1 row2 ppm ppm col pom col2 ppm 50 1458 46 4313 3 2 6 04420 5 89291 61 2893 55 7175 4 9 5 91452 5 7416
203. itle PulsProg Peaks Integrals Sample ij Object Integral abs Integral rel Range F1 from Fange F1 to m integral 1 21786348 44 1 6650 0 Tarz 8 603 integral 2 20849330 78 1 5934 0 r 410 rari Hntegral 3 4579692197 3 5000 r056 r405 integral 4 131363188 00 10 0393 0 4 491 6 158 Integral 5 20473381 47 1 5647 0 3 974 4 469 Integral 6 1068216295 19 61 6376 32 0 304 3 977 Figure 8 2 How to Print the Peak list 1 Click the Peaks tab of the data window see Fig 8 3 2 Enter print or Ctrlt p 119 Printing Exporting Data examid 1H 1 1 Cobio guest o 614 0 10 0 0092 A 1 2 6 5956 0 11 0 0044 3 6 5561 0 01 0 0007 4 6 5421 0 00 0 0007 5 6 5279 0 00 0 0015 B 6 5059 0 00 0 0000 7 5 4974 0 01 0 0018 Figure 8 3 8 2 Exporting Data How to Copy data to Other Applications Under MS Windows you can easily copy the data window contents to oth er applications To do that Click Edit gt Copy copy This will copy the data window contents to e the clipboard After that you can paste the clipboard contents to any Windows application On Windows systems the command Edit gt Copy copy saves bmp for mat whereas the command copy wmf stores the old wmf format On Linux systems the command copy stores png files into a temporary file The pathname of this file is copied to clipboard Please note Some programs when importing spectra from the clipboard or metafile do
204. l Absolute Step Difference Step Stepsize a f ia f 4 7 E ii sample down missing up QL Q Figure 16 12 The individual functions BSMS control panel are described in detail in the Acquisition Reference manual 302 Acquisition 16 9 Interactive Parameter Adjustment GS Several parameters can be adjusted interactively while observing the acquired FID To start this Enter gs on the command line A split window will appear showing e the FID display see Fig 16 13 e the GS parameter adjustment dialog see Fig 16 14 0 2 04 06 08 10 12 1 4 5 Figure 16 13 The buttons of the FID display are the same as for the acquisition com mand zg see paragraph Fig 16 10 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 mod ified in the field below the slider The sensitivity of the slider can be set in 303 Acquisition squarePower Frequency l Delay Receiver RetPhase Offset Pulse ey sensitivity a 1 r adjust max 3138 51 Offset Of Hz min 3035 51 3088 51 DAYE Save all Restore Restore all stop s ME Figure 16 14 the field Sensitivity above the slider The effect of the change can be viewed
205. l Regions 250 How to Save Export Integral Regions 251 How to Return from 2D Integration mode 251 13 3 2D Multiple Display and Row Column Handling 251 How Switch to Multiple Display mode and Read Multiple Spectra How to Align Multiple 2D Spectra 000005 204 How to Display the Next Previous Name Expno 254 How to Scan Rows Columns 0 0 0 0 cee eee 255 How to Grab a Row Column 0000 eee ees 255 How to Show the Next Previous Row or Column 256 How to Move the Selected Dataset Up Down in the Dataset List How to Extract a Row Column 0 0000 cee aes 257 How to Copy Contour Levels from First to Other Spectra 258 How to Switch on off 2D contour display 208 How to Position the Baseline of the Row Column 258 13 4 2D Interactive Calibration 0 0 0 0 eee 259 How to Switch to 2D Calibration mode 259 How to Perform 2D Calibration 0 00000 e ees 260 How to Measure a 2D Chemical Shift Distance 260 Chapter 14 Data Window Handling 0000 cee eee 262 14 1 Data Windows 0 0 0 ccc eee 262 How to Move a Data Window 0 00000 eee eee 263 How to Resize a Data Window 00 00 cee 263 How to Select activate a Data Window 264 How to Open a Ne
206. last expno under a name or the last name under a user How to Delete Types of Datasets To delete certain types of data like 1D raw data 2D processed data etc Click File gt Delete or Enter delete on the command line The dialog window shown in Fig 5 20 will appear Here you can select the data type and selection criteria 5 6 Renaming Data How to Rename a Specific Dataset 1 Right click the data name expno or procno in the browser then click Rename 2 In the appearing dialog Enter the new name expno or procno 86 Dataset Handling 8 3 Click OK Browse Options OQ An entire data set with all EXPN OSs PROCNOs G Acquisition data Processed data Data acquired at certain dates 1D raw data tid 1D processed data iri 203D raw data ser 2D processed data 2rri2ii O Imaginary processed data 1i CO Macro O AL prograrn O Python prograrn Pulse program O Parameter list O Mizcellan ous file Required parameters Marne Data directory User Figure 5 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 Dataset Handling Note that you can use the wildcards e Asterix for any character and any number of characters e Question mark for any single character 3
207. le Status parameters Acquisition parameters h integrals x integral labels s Feak labels s Feak annotations Muti pleats Show data points Electronic Signature h Molecular Structure Figure 9 14 Here you can check or uncheck the spectrum components that you want to be displayed in the data window Note that the Display Properties dialog box can also be opened from the View menu 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 Spec trum 1 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 dia log 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
208. le all or multiple inte grals are selected How to Read Integral Regions from Disk You can read integrals regions from disk which have been stored by auto matic integration command abs or by a previous interactive integration To read integrals 1 Click the following button 3 Read integral regions The following popup menu will appear 207 1D Interactive Manipulation Read intrng Read intrng Mo Slope amp Bias Corr Read intrng Use Last Slope amp Blas Import intrng trom Relaxation Experiment Edit intrig Figure 12 5 2 From the popup menu choose one of the following entries Read intrng 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 and bias correction values Read intrng from Relaxation Experiment to read the last stored integral regions of the T1 T2 relaxation experiment Edit intrng to edit the file int rng that contains the integral regions and slope and bias correction values Changes in this file are automat ically shown on the screen when the file is saved How to Perform Interactive Bias and Slope Correction To perform interactive bias correction 1
209. le discarding any changes 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 231 1D Interactive Manipulation 12 7 1D Interactive Peak Picking Peak picking can be performed automatically with the commands pps or interactively in the peak picking mode How to Switch to Peak Picking Mode Click the indicated button in the upper toolbar ad 3d 4 AMO Tjian or enter pp on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 12 20 examid_1H 1 1 Cbio guest l oj x dio xia d x s gt 10 15 20 1e6 5 0 0 97 ppm 483 04 Hz CY 20 00 rel MAXI 19 50 rel MI 0 00 rel Figure 12 20 Data window in peak picking mode The yellow button indicates that you are in peak picking mode 5 Some buttons will turn green when they are clicked As long as a button is green it is active 232 1D Interactive Manipulation Note that the button is automatically activated i e you are in Define peak picking range mode How to Define New Peak Picking Ranges 1 Put the cursor at the upper left corner of a peak picking range 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 max imum intensity are set and the peaks in the range ar
210. lect the desired entries while pressing the Ctrl or Shift key 2 Right click a peak entry to open the popup menu see Fig 9 4 3 Click Copy to copy the selected peaks to the Clipboard Print the peak List To print the peaklist Right click a peak entry and choose Print or Enter print on the command line or Press Ctrl p All actions will print the entire peaklist To preview a print 138 1D Display Right click a peak entry and choose Print preview Import a peak List A peak list from a different dataset or program can be imported as fol lows 1 Right click an entry to open the popup menu see Fig 9 4 2 Click Import 3 Inthe appearing dialog box navigate to the directory where the list resides and select the peak list choosing from e Auremol peaklist ml e MULABEL peak list labels e TOPSPIN peak list xml e XEASY peak list peaks e XWIN NMR peak list txt As such you can import a peak list from a different dataset or program or a previously exported list from the current dataset Note that peak picking commands store the peak list in the processed data directory under the name peak xml TOPSPIN 2 1 or newer or peak txt XWIN NMR and TOPSPIN 2 0 or older Shortcuts Double click a peak zoom into spectrum i e show region around that peak Enter key zoom into spectrum i e show region around selected peak s Delete key delete the selected peak s from the pe
211. left edge FID of the dis played region increasing the horizontal scaling zi Zoom out from the center spectrum or left edge FID of the dis played region decreasing horizontal scaling zo iE Perform an exact zoom via a dialog box zx a Enter the coordinates of the desired region in the dialog box EJexactzoom ue Please enter the exact coordinates of the desired expansion F1 ppr From b11 0310 To 27 4876 JR Cancel b Click OK Undo last zoom z1 W Reset horizontal scaling to show the full spectrum Ar 41 Display the entire spectrum baseline position and intensity scal ing are adjusted if necessary a11 4 Toggle interactive zoom mode When switched off interactive zooming only selects a horizontal region baseline position and intensity scaling remain the same When switched on interactive zooming draws a box selecting the corresponding area iil Retain horizontal and vertical scaling when modifying dataset or 128 1D Display changing to different dataset keep Effects all data windows Alternatively you can enter the corresponding commands as specified be tween square brackets How to Shift a Spectral Region to the Left or to the Right Click hold the following button and move the mouse Smoothly shift to left or right or Click one of the following buttons Shift to the left half of the displayed region s1 Sh
212. libration mode A The yellow button indicates that the data window is in calibration mode 259 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 Fal calibrate x Spectrum calibration frequency F2 ppr F1 per 0 1621 z4 T 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 The spectrum will be calibrated and re displayed 2D Chemical Shift Dis tance Measurement How to Measure a 2D Chemical Shift Distance 1 Click the following button button turns green 4 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 2D Interactive Manipulation examed HC 1 1 Cobiol guest e par Lal qm LL 5 F2 2 34 ppm 702 72 Hz S Fl 18 96 ppm 1431 19 Hg c Distance 19 10 ppm 1994 40 He 12 10 8 6 4 2 F2 ppm Figure 13 17 Data window in distance measurement mode 261 Data Window Handling Chapter 14 Data Window Handling 14 1 Data Windows The TOPSPIN window has a data area that may contain multiple data win dows The size of th
213. limited Although multiple display is normally used for spectra with matching nuclei it allows you to superimpose spectra with non matching nuclei You will get a warning that the nuclei do not match Just just click OK to continue How to 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 1 Read a 1D dataset 218 1D Interactive Manipulation 219 2 Click the button in the upper toolbar or type md on the com mand line The data window will switch to multiple display mode Add a dataset as follows Left click hold the dataset in the browser and drag it into the data window Or Right click the dataset in the browser and choose Display from the popup menu Or Enter re and specify the additional dataset in the appearing dialog Dox Another way to superimpose data in multiple display is to read multiple datasets simultaneously 1 In the browser 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 Right click any of the selected data Choose Display from the popup menu This will show the data in the active data window if that is in multi ple display mode or otherwise show the data in a new window Or Choose Display in new wi
214. line correction 229 1D integrals 213 1D phase correction 203 acquisition data 85 adjusted acquisition parameters GS 304 AU program 32 color scheme 356 cubic spline baseline points 231 current window layout 269 data 29 38 45 84 data in analog filtered format 85 data to a JCAMP DX file 30 data to a ZIP file 29 data window to a graphics file 27 121 entire dataset 84 85 integral regions 213 macro 31 parameters 131 132 peak list and peak ranges 236 phase correction 2D 242 245 251 processed data 85 processed data as pseudo raw data 85 pulse program 151 sum or difference spectrum 222 title of a dataset 133 scale 1D integrals 211 1D spectrum 127 2D spectrum 167 3D cube 192 individual spectra in multiple display 26 218 224 row column in 2D phase 243 scaling factor of integrals 212 scan planes of 3D data 190 rows columns in 2D 255 screen dump 27 121 scroll bar 99 103 search criteria 89 data 89 field in the parameter editor 98 102 result window 90 select AU program 322 color scheme 357 data 64 data in multiple display 219 221 data window 264 default printer 319 expno procno combination 76 first expno procno 76 folders in the browser 69 font 361 362 363 integral regions 206 208 lock signal color 356 multiple datasets 76 multiple folders 69 peaks in 2D phase correction 239 plot layout 117 printer 117 remote system 342 row column in 2D phase 242 spectra in 2D multiple display 254 spectrum color 355 spe
215. lly 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 2D Interactive Manipulation 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 multiple dis play mode see chapter 12 5 In multiple display mode the Tab bar of the active data window Is re placed by a toolbar see Fig 13 9 exam2d HC 3 1 Cibio quest DEAR ni t R t 4 A B E Er Eil Ste fts te hat a l l gt F2 ppm Figure 13 9 Multiple display with two 2D spectra superimposed 252 2D Interactive Manipulation examed HC 3 1 Cabiao guest F2 ppm Figure 13 10 Multiple display with a 1D spectrum superimposed on a 2D spectrum ae The yellow button indicates that the data window is in multiple display mode E Some buttons will turn green when they are clicked As long as a button is green it is active
216. lly useful for big companies and concerns that work with different NMR spectrometers and many members of staff respectively many PCs Please note that the functionality of limiting IP Addresses is a feature for technical experienced users and IT Experts therefore the following description is given by an example By default remote connection is disabled You have to enable remote con trol first For enabling remote control and limiting the IP Addresses the fol lowing file has to be edited lt tshome gt prog server omniorb conf In this file you have to search for the following section which enables every IP Address for remote connection To enable the Remote Connection feature using SSL en cryption the character at the beginning of the next line should be removed SserverTransportRule 0 0 0 0 0 0 0 0 ssl After removing the an unlimited number of IP Addresses may use remote control The IP Address can be limited as it is shown in the follow ing example by editing the respective IP Address line serverTransportRule 149 236 14 0 255 255 255 0 ssl After editing the IP Addresses belonging to your special requirements 346 Remote Control every IP Address of the permitted subnet may use the feature remote con trol and all other addresses have no longer permission to connect remotely 347 User Preferences Chapter 20 User Preferences 20 1 User Preferences TOPSPIN can be tailored to your
217. ls with different methods i e Gaussian Lorentzian or a mix ture of these line shapes The values are stored in the file dconpeaks txt and displayed graphically For further information please look up the Anal ysis chapter and the Processing Reference Manual commands gdcon ldcon mdcon ppp dconpl and dcon From within the integration mode after the integration of the respective peak or peak groups deconvolution can be started by right clicking on the 214 1D Interactive Manipulation peak The following window will appear amp Bruker TopSpin on merlin as svcu File Edit View Spectrometer Processing Analysis Options Window Help Select Deselect Calibrate Current Integral Normalize Sum Of Integrals Use Lastscale For Calibration Deconvolution Deconvolve amp Display Integrals Delete Current Integral Change Peak Picking Parameters For Deconvolution Edit Peak List amp Deconvolve Show Deconvolution Fit 10 5880 Figure 12 8 Choosing Deconvolution offers the following options e Deconvolve and display regions e Change Peak Picking Parameters for Deconvolution e Edit Peak List amp Deconvolve e Show Deconvolution Fit graphical display With the latter function it is possible to display results after deconvolution graphically 215 1D Interactive Manipulation EN Bruker TopSpin on merlin as sycu File Edit View Spectrometer Processing Analysis Options Window Help Deconvolution
218. ly Select the first expno procno of a dataset 76 How to Open Data from the Topspin menu 77 How to Open Data from the Explorer Konqueror or Nautilus 79 How to Open Data from the Command Line 80 How to Open Special Format Data 82 How to Open a ZIP or JCAMP DxX file from the Windows Explorer 5 4 Saving Copying Data 0 ee 84 How to Save or Copy Data 2 0 anaa ee 84 How to Save an Entire Dataset 0 0 000 ee 85 How to Save Processed Data 0 000 c eee ees 85 How to Save Acquisition Data 0 0 0 eee ee 85 How to Save Processed Data as Pseudo Raw Data 85 5 5 Deleting Palais sos wooed ei oe Sa Bde ea 68S 86 How to Delete a Specific Dataset 0 5 86 How to Delete Types of Datasets 0005 86 5 6 Renaming Dales 22 25 4 ten take tities ewe one Aes 86 How to Rename a Specific Dataset 0005 86 5 7 Searching Finding Data naana aaa aaea 89 FOW TO FNA Dala siressa a a dy oot dee dee a elk a 89 How to Display one of the Found Datasets 90 5 8 Handling Data Files nananana aaa ccc eee 92 How to List Open the Current Dataset Files 92 How to List Open the current Dataset Files in the Windows Explorer Parameter Handling 2 000 e eee eee es 96 6 1 Processing Parameters 0 0 0 0 cee eee 96 How to Set a Proce
219. m if an acquisition has been done raw data exist e setup pulse program if no acquisition has been done raw data do not exist The display of title and pulse program can be switched of see Fig 5 2 Dataset Handling Display Display in Mew window Display As 20 Projection scroll to active dataset Fully Expand Selection Show PULPROG Title show Date Sort by Date Copy File Properties Delete Rename Files Add Mew Data Dir Remove Selected Data Dirs The Last50 tab gt Display in current data window gt Display in new data window gt Display 1D data as projection of active 2D data gt Scroll to PROCNO of active data window gt Fully expand selected node gt Switch pulsprogram title display on off gt Show acq date expno or last mod date name gt Sort data by last modified date gt Copy dataset entry to clipboard gt Show dataset properties gt Delete selected entry name expno or procno gt Rename dataset name expno or procno gt Show files in selected entry expno or procno gt Add new top level data directory gt Remove selected top level data directory Figure 5 2 Clicking the Last50 tab displays the list of the last 50 displayed datasets Each dataset that you open is automatically added to the current list Fig 5 3 shows a Last50 list with four datasets As in the browser different colors are used to indicate the data dimensionality Br
220. manipulations 39 mode of the lock window 300 molecule structure 152 options 39 options 1D 154 peaks 25 planes of 3D data 188 189 positive negative 2D levels 187 processing status parameters 1D 131 projections 25 rows in 2D phase correction 239 settings 38 special data formats 82 spectra 22 spectrum overview in 2D 178 status parameters 99 103 sum difference spectrum 222 superimposed 1D spectra 218 superimposed 2D spectra 251 y axis 39 155 zipped data 29 display properties 25 distance measurement 1D 273 2D 260 mode 39 double headed arrow 263 274 Down Arrow key 42 45 47 dpa command 132 dpp command 99 103 131 drag amp drop data 80 83 E eda command 100 101 132 174 edasp command 104 132 edau command 32 111 319 322 373 edcpul command 134 edit AU program 322 commands 42 contour levels 183 integral ranges 208 pulse program 134 signal noise regions 275 title of a dataset 133 Edit menu 37 edlev command 167 183 edlock command 104 edmac command 31 373 edp command 27 96 97 131 174 edprosol command 103 edpul command 134 edpy command 32 374 edti command 133 ef command 107 110 efp command 107 308 emcommand 27 106 email data 30 empty data window 75 enable disabled commands 369 menus commands 365 Enter key 47 66 equidistant sequence of levels 183 Esc key 41 execute AU program 319 322 macro 31 373 Python program 32 exit command 45 54 expand a data directory 47 data directory 23 64 data d
221. maximum intensity are set in the specified lay out Fill dataset list e from your default portfolio The portfolio contains the current TOPSPIN dataset plus the data from the default Plot Editor portfolio e from port folio saved in dataset The portfolio contains the current TOPSPIN dataset plus the data from the portfolio stored in this dataset Override Plotter saved in Plot Editor If enabled the plotter defined in the Plot Editor layout will be overrid den by de plotter defined by the processing parameter CURPLOT 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 win dow will be printed as it appears in the screen If Automatic mode is un checked you will get the dialog box as displayed in Fig 8 1 118 Printing Exporting Data How to Plot Data with the Plot Editor The Plot Editor can be started from the Print dialog 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 as follows Click Help gt Manuals gt Automation and Plotting Plotting How to Print the Integral list 1 Click the Integrals tab of the data window see Fig 8 2 2 Enter print or Ctrl p to print it examid_1H 1 1 Cxbio guest l x Spectrum ProcPars AcquPars T
222. meter Processing Analysis Options Window Help j Danga zda A AKL Tna H a Or lS om E 2 27 B ZWAAN aW e oHe arta Browser Lastsa Groups aias J ACO protona 10 1 C BrukeriTOPSPIN nmr eee w C Bruker TOPSPIN Spectrum ProcPars AcquPars Title PulseProg Peaks integrals Sample Structure Fid Acqu S CABruker TOPSPIN_2 1pI1 j a E a J i accent im fc He e OO A fet l p augn 2 Proton experiment db final rid a b gradshim T am eerren Saab hdaereaiite ee 71 PULPROG zg30 J nmr SI 32768 a di cl 1H BU 20 618 8J 6188 12 S Ip 65536 H ANS 1 16 j TIME 1m29s 1m54s o o oOo N 4 o ow vt M T T T T T T T T T T T T T T T T T T T 5 0 5 10 ppm Amplifier Control Acquisition information Fid Flash Lock Sample POWCHK VTU Spooler BSMS status message Time scan 1 16 am i x Keni pai g 10 55 PEN ae lelayed residual time 1m29s me 297 0 cton of Autoshimx Lockedy Error APr 08 Figure 16 5 From here you can start various acquisition commands like Start acquisition zg m Halt the acquisition hal t Gy Stop the acquisition stop 42 Probe matching and tuning wobb th Interactive Parameter Adjustment gs Data specific acquisition display allows you to open multiple acquisition display windows one for each dataset Note that the Acqu tab is automatically activated when the acquisition is started from the TOPSPIN menu toolb
223. mmand 35 118 159 2d command 34 3d command 34 all command 36 119 161 basl command 215 omp files 25 ozip files 27 76 cal command 205 246 co command 173 dec command 194 200 217 231 dopt command 149 150 159 312 dx files 76 emf files 25 f1r command 161 f2r command 161 gif files 360 362 gr command 172 hr command 36 119 hz command 145 169 im command 176 inc command 194 200 217 231 nt command 195 233 jpeg files 25 360 362 Jpg files 25 360 362 kKeep command 36 120 161 is command 176 It command 178 lv command 174 md command 24 207 ov command 146 169 ph command 45 191 225 ph180 command 193 ph90 command 193 phr command 193 png files 25 114 360 362 pp command 220 pr command 24 170 prop files 256 ret command 194 205 214 218 219 224 retsab command 219 s2d command 194 sd command 37 120 162 Sino command 260 S command 37 120 162 SIl0 command 37 120 sr command 37 120 162 srO0 command 37 120 sret command 194 204 217 224 st command 176 su command 37 120 162 tif files 114 txt files 153 vr command 36 118 159 wmf files 25 114 y command 146 zi command 36 119 161 zl command 36 119 161 ZO command 36 119 161 ZX Command 36 119 161 2 command 35 42 118 159 8 command 36 118 159 command help 46 Numerics 1223 180 degree phase correction 1D 193 2D 231 3D molecule viewer 259 90 degree
224. n 0 Reset the red correction line to zero If the difference spectrum is displayed the ry button is active click ing the reset button will restore the original spectrum 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 ll Reset the Mouse Sensitivity How to Save the Baseline Correction and or Return To return while saving the baseline correction Click the following button H Save baseline correction and Return sret This will perform the following tasks e Execute the baseline correction ben e Save the baseline correction values A B C D and E e Leave the baseline correction mode To return while discarding any changes 229 1D Interactive Manipulation Click the following button a Return Discarding any changes ret How to Perform Cubic Spline Baseline correction Click the following button t4 Define points for cubic spline baseline correction The toolbar of the data window will change as shown in Fig 12 18 O x 3 examid_1H 2 1 Cobo guest 0 41 ppm 124 28 Hg DEFINE LIST OF POINTS Left click inside data window ia ae 1 426 ppm 3 634 ppm Define Delete Right click on defined peak Click right mouse button DAVE Figure 12 18 Data window in spline baseline correction mode The cursor line in the data window turns red If a l
225. n processing printing and archiving requiring some user interaction 1 Click Processing gt Data gt 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 gt Fourier Transform gt etc For each step a dialog box will appear where you can enter options pa rameters etc For details on these items please refer to the corresponding commands in the Processing Reference Guide 7 3 Processing Data with AU programs Data processing can be performed by using AU programs An AU program is actually a C program which contains TOPSPIN commands macros and or C language statements Various standard AU programs are deliv ered 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 Data Processing AU program just enter proc_1don 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 programming m
226. n a data window on the screen like 15t 209 and 30 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 A 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 color of the User Preferences corresponding object on the screen To set print colors 1 2 3 4 5 Click Options Preferences set Click Printer in the left part of the User Preferences box Click the Change button to the right of the object you want to change e g Color of title IE Change Select the desired color in the appearing dialog box and click OK Click Apply How to Change Colors of the Lock Display The colors of lock display objects can be changed as follows 1 2 3 4 5 Click Options gt Preferences set Click Lock display in the left part of the User preferences box Click the Change button to the right of the object you want to change e g Color 2 a Change Select the desired color in the appearing dialog box and click OK Click Apply How to Create a New Data Window Color Scheme To create a new data window color scheme 1 2 Cl
227. n be performed with commands like abs or absd or interactively as described below How to Switch to Baseline Correction Mode Click the indicated button in the upper toolbar 226 1D Interactive Manipulation 2d 3d A AMO OD a or enter basl1 on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 12 17 examid_1H 2 1 Crbio guest ojx IMER gt At El TERES Mouse Sensitivity 1 0 3 16 ppm 954 20 Hz Figure 12 17 Data window in baseline correction mode Ne The yellow button indicates that the data window is in baseline correction mode g 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 F 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 Dx E x4 22 1D Interactive Manipulation 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 coin cides with the entire baseline of the spectrum How to Perform Sine Baseline Correction 1 Click the following button button turns green E Perform sine baseline correction A red horizontal line will appear as well
228. n related commands Each entry give access to a submenu with various commands Fig 16 3 for example shows the Setup submenu 290 Acquisition 291 Hardware Configuration cf Ethernet addresses of hardware ha 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 edsolyv Amplifier linearization setup cortab Convert gradient field maps convfieldmaps Figure 16 3 For most entries the command line command for example expinstall is specified in square brackets Furthermore Topspin can be configured such that right clicking any menu entry will display the corresponding com mand line command To do that right click in an empty part of the menubar and choose Define Right click Action For convenience common acquisition commands can also be started from the TOPSPIN toolbar The right part of the upper toolbar shows the following buttons Start the acquisition Acquires NS scans in the current dataset over writing possibly existing data Equivalent to the command zg m Halt the acquisition This stops the acquisition after the current scan has finished All data acquired so far are saved Equivalent to the command halt amp Stop the acquisition This stops the acquisition immediately Data acquired after the last disk write if any are lost
229. n square brackets behind the corresponding menu entries Further more right clicking any menu entry will show the corresponding com mand unless right clicking is defined otherwise 1 The TOPSPIN Interface How to Use the Upper Toolbar 1D data The upper toolbar contains buttons for data handling switching to interac tive modes display settings and starting acquisition Buttons for data handling Dae 6 amp Bi2a 3a The functions of the individual buttons are Create a new dataset Ctr1 n new amp Open a dataset Ctrlt o open Save the current dataset Ctr1 s sav Email the current dataset smai1 amp Print the current dataset Ctrl p print 5 Copy the data path of the active data window to the clipboard copy f Paste the data path on the clipboard to the active data window paste 7d 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 5 3 Buttons for interactive functions fe BS oth IP e 1 Right click an entry part of the menubar and choose Define Right click Action 38 The TOPSPIN Interface The functions of the individual buttons are A Enter phase correction mode Enter calibration mode Enter baseline correction mode ii Enter peak picking mode T Enter integration mode i Enter multiple display mode 4 Enter distance measurement mode For more information on int
230. ncorrectly With the keyword PAN LAYOUT you define the number of rows and columns and the number of items will become rows cols All specifications such as PAN BUTTONS PAN COLORS etc must have this number of members otherwise you will get some kind of TOPSPIN error Please insert the separator to make sure the item count is correct 21 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 378 User Extensions Add User Defined Button Reactivate All InvisibleInactive Buttons Add User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars type SHIFT ESC to reset 3 In the appearing dialog box see Fig 21 3 a Choose between the options text label or icon The corresponding parameters are enabled disabled b Enter the command name the tool tip and the label text or icon file pathname c For a text label set its font text color and background color d For an icon label specify the icon image filename e Set the separator flag to yes or no and select the data dimension s for which the button must appear For an icon label you must stored the icon image file in
231. nd 40 48 127 168 8 command 40 127 168 Numerics 12 25 180 degree phase correction 1D 202 2D 244 3D molecule viewer 272 90 degree phase correction 1D 202 2D 244 90 degree phase correction 1D 202 2D 244 A abs command 106 110 203 204 207 226 absd command 226 absorption mode 201 202 242 243 244 acqu command 292 acquisition commands 291 296 mode 319 parameters 100 101 306 status bar 294 308 toolbar 290 292 Acquisition Reference Manual 22 104 301 302 319 AcquPars tab 100 132 174 306 activate a data window 264 the next data window 269 add comment to audit file 327 directory to the browser 23 functionalities to Topspin 31 peak in 2D phase correction 240 peak to peak list 234 add increment in 2D levels 183 align intensities in multiple display 224 peak positions in multiple display 224 Alt F11 key 127 167 I 16 Alt F4 key 45 53 Alt F6 key 53 Analysis menu 27 37 apk command 106 110 200 apks command 200 arrange data windows 265 data windows horizontally 267 data windows vertically 266 rows columns in 2D phase correction 245 ascii files 93 162 ased command 103 132 Aspect 3000 data 82 ATM probehead 298 299 atma command 299 AU macros 31 373 374 AU program reference manual 111 AU programs 21 31 110 319 373 378 381 audit trail check 326 automate data acquisition 32 automatic 1D baseline correction 106 1D calibration 106 217 1D integration 203 1D peak picking 232 1D p
232. nd line 193 nD Display Parameters of each direction are shown in a separate column Fig 11 5 examsad 1 1 Chio guest AcquPars Title PuleeProg Peaks Integrals Sample Structure Fi Os u Ea 2 Y j L Installed probe not defined Experiment F3 F2 F 1 width Experiment Receiver ete PULPROG hechdign 3d ull Durations Ad mod Da a Power FniiQDe States TFFI States TFFI Program TD 1024 120 Probe Ne ia Spectrum ProcPars Lists DS J56 pai Tot Doo Lock l Automation Width Figure 11 6 shows the acquisition parameter display of a 3D dataset 11 4 nD Fid Display nD raw data can be displayed as a series of 1D FIDs To do that click the FID tab of the data window Or enter fid on the command line 194 nD Display 11 5 nD Peak and Integral Display TOPSPIN 2 1 and newer support peak and integral display of up to 8D data To show the nD peak list Fig 11 7 shows the peak list of a 3D dataset exams3d 1 1 Chio guest Spectrum ProcPars 367 11 156 426 591 yfF 3 ppm 4 7636 4 5952 4 5947 4 5947 4 5194 4 4995 4 4995 4 4995 4 4995 WF ppr lili AcquPars Title PulseProg 50 5341 46 5005 3r 4667 a 4667 51 7756 19 4212 34 3554 2l 9103 29 9996 Figure 11 7 click the Peaks tab of the data window enter peaks on the command line WF 1
233. ndow 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 re placed by a toolbar Fig 12 12 shows three comparable 1D spectra and the sum of all three 1D Interactive Manipulation examid TC 1 1 Cobiol guest i o x Be Rom t 4 Ae E Eil Z Sg ZE OREIN examld 13c Cri biol dest examld l3C Ciri biol yest 1e9 10 examld 13C 1 l Citbigl gyest 200 150 100 50 ppm Figure 12 12 Data window in multiple display mode 4 The yellow button indicates that the data window is in multiple display mode m Some buttons will turn green when they are clicked As long as a button is green it is active Furthermore the browser is split in two parts as shown in Fig 12 13 examid 130 3 1 Cobiol guest examid 137 2 1 Cobiol guest examid 130 1 1 Cobiol quest Figure 12 13 220 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 work with multiple display command md The following arguments of md for controlling data sets from command line AU programs or Python programs are available 1 Specified data set names can be shown in the display by command md Enter command and full pathname for a specified dataset in the Top Spin command line md lt PathToDataset1 gt lt expnol gt pdata lt
234. nds are indicated in square brackets behind the corresponding menu entries e g Processing gt Fourier transform ftf Menu entries which are not used very often appear without the corre User Preferences sponding command indicated e g Options gt 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 en try Remote connection in the Options menu 1 Open the configuration table as described above 2 Scroll to the Description Remote connection 3 Set the Status to disabled 4 Click Apply Clicking the TOPSPIN Options menu will now show the following popup menu Options Window Help Preferences Spectrometer Tools P Manage configuration P Administration The entry Remote connection is greyed and can no longer be used Go back to the Configuration table change the Status of Remote connec tion to invisible and click Apply Clicking the TOPSPIN Options menu will now show following popup menu Sines Window Help Preferences Spectrometer Tools Manage configuration Administration The entry Remote connection has disappeared Note that if you disable or remove a menu entry the corresponding com mand is automatically disabled For example if you disable 368 User Preferences Analysis gt Deconvolution dcon en
235. ng Guide In Automatic mode the Getting Started 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 enter interactive phasing mode A simple way to process 1D data is the following 1 Click Processing gt Process Plot Current data 2 In the appearing dialog see Fig 2 1 a Enable the desired processing plotting steps b Set the parameter LB for Exponential multiplication c Select the desired LAYOUT for plotting d Click OK 28 Getting Started ee procid Press OF to process J plot the selected dataset using the enabled options The command procid y will process data without this dialog using the last settings Exponential Multiply Cert LE Hz 4 Fourier Transtorm Tt Auto Phasing tapk Set Spectrum Reference sret Auto Baseline Correction abs Plot autoplot LAYOUT D Hxwp v Figure 2 1 2 10 How to Archive Data 29 TOPSPIN 2 1 provides the following methods for data archiving e Automatic archiving of raw data after the acquisition as defined in the User preferences click Opt
236. ng is performed for dataset variables NAME EXPNO PROCNO and USER if the checkboxes at the right are enabled e The search is restricted to data created between the specified dates Note that this refers to the acquisition date e The Reset mask button allows you to reset the default criteria 3 Select the Data directories to be searched in the lower part of the dialog If no directories are selected all will be searched 4 Click OK to start the search A list of data that fulfil the defined criteria will appear see Fig 5 23 ee Search result Found 6 Data Sets Please right click in a list for more options Bamia 13C 11 Cobic Zgpaz0 2004 03 30 10 43 33 examid_ 13C 2 1 Cobio imod 2004 03 30 11 01 05 examid_13C 3 1 Cbig dept 35 2004 03 30 11 15 36 examid_13C 4 1 Cobio dept4s 2004 03 30 11 53 06 examld_130 5 1 Cobio deptao 2004 03 30 12 27 39 examid 130 6 1 Cobio Fqigs0 2004 03 30 13 35 54 Figure 5 23 Note that on exiting TOPSPIN the search criteria will be rest to default How to Display one of the Found Datasets In the search result window see Fig 5 23 1 Click one or more datasets to select them Dataset Handling 91 2 Click Display to display the selected dataset s in the current data window If multi ple datasets are selected they are displayed in a new data window in multiple display mode The search result window offers a right click context menu with various op tions see Fig 5 24
237. nteractive zooming only selects a horizontal region baseline position and intensity scaling remain the same When switched on interactive zooming draws a box selecting the corresponding area Undo last zoom z1 iil Retain horizontal and vertical scaling when modifying dataset or changing to different dataset Global button for all data windows 40 The TOPSPIN Interface keep Buttons for horizontal shifting 39 I So Shift to the left half of the displayed region s1 Smoothly shift to the left or to the right Shift to the right half of the displayed region sz Shift to the extreme left edge of the spectrum s10 Shift to the extreme right edge of the spectrum sro 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 Shift the spectrum baseline to the bottom of the data field sd For more information on display options please refer to chapter 9 5 1D data and 10 5 2D data 3 3 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 selecting a dataset from the browser puts the focus in the browser To put the focus on the command line Hit the Esc key or 41 The TOPSPIN Interface Click inside the command line How to Retrieve Previously Entered Commands
238. nu see Fig 12 6 To delete all integral regions from the display Click the following buttons Select all integral regions ti Delete selected integral regions from the display Note that regions are only deleted from the screen Regions which are saved on disk in the intrng file are not affected How to Scale Selected Integrals Integral scaling only manipulates selected integrals However if no inte grals are selected it works on all integrals Click one of the following buttons 2 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 amp calib 3 Click OK to apply this factor To scale all selected integrals to the same height 211 1D Interactive Manipulation Click the following button Scale unscale all integrals to the same height The individual scaling factor for each region is displayed above the in tegral Clicking this button again rescales all integrals to their original height How to Move the Integral Trails Up Down To move the integrals selected and unselected up or down Click one of the following buttons 4 The left edge of the selected integral is put just above the base line If no integral
239. o Switch Depth Cueing on off 1 Right click inside the data window 2 Choose Depth Cueing On off see Fig 11 4 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 Onfott Figure 11 4 How to Display a Cube Front or Side view Click one the following buttons 12 Show F1 F2 plane 23 Show F2 F3 plane 31 Show F3 F1 plane 11 3 nD parameter display TOPSPIN 2 1 and newer support parameter display of up to 8D data To show processing parameters click the ProcPars tab of the data window 192 nD Display Or enter edp on the command line Parameters of each direction are shown in a separate column Fig 11 5 examad 1 1 Cobio guest is Peaks Integrals Sample Structure Fir AcquPars Title PulzeProg Spectrum ProcPars F3 F2 F1 Reference winga Phase Baseline Fourier Peak Automation Miscellaneous User FY Reference Si 2048 256 SF MHz 00 1300000 150 9027490 00 1300000 OFFSET ppm 5 11956 56 91221 5 11956 SR Hz 000 oo HZpPT Hz 1 467191 46 950119 11 737530 AGIOROER k Poo window function Figure 11 5 shows the processing parameter display of a 3D dataset To show acquisition parameters click the AcquPars tab of the data window Or enter eda on the comma
240. oler report Note that the spooler report can also be opened from Spooler field if ena bled in the Acquisition Status Bar by right clicking the word Spooler and choosing Show spooler report TOPSPIN command dataserver and network log A full protocol including not only TOPSPIN commands but also dataserver and network traffic is show by the command ptrace This opens the fol lowing dialog window ptrace TopSpin Log File Tracer File iter DE sowat i Message 11 270 08 03 06 1278 52700 TOPSPIN Version 7 1 11 20 08 03 06 128 FLEX Im license is valid until 2010 11 14 11 20 08 03 06 128 52 cmd enter cprserver 11 20 08 03 06 144 3908 11 20 08 03 06 580 3908 11 20 08 03 07 0 t cprelient module cprclient 11 20 08 03 07 641 3 irt machi a_i 20 08 03 07 641 4748 cmd sent cp relient 340 Contact 340 Contact CPR ad o CprListener is corbaloc iiop E U3 10 Contact i 20 08 03 10 34011 e 20 08 03 10 605 contact m A D L C Bruker TOPSPIN prog curdir drud history CiBruker TOPSPIN progicurdir idrud stdout dataserver 3980 Figure 4 1 Here TOPSPIN log messages from various log files are displayed time sorted Messages from different log files are shown in different colours The color assignment and location of the files is shown in the lower part of the dialog window ptrace supports the following functions Trouble Shooting 59 4 2 4
241. onalities 2005 31 Chapter 3 Chapter 4 Chapter 5 How to Create Macros 0 000 eee ee eee ees 31 How to Create AU automation Programs 31 How to Create Python Programs 0000 e eee 32 2 15 How to Automate Data Acquisition 0000 32 The TOPSPIN Interface 0 0 0 cece eee eee 34 3 1 New Flow User Interface with TopSpin 3 0 34 3 2 The Topspin Window 0 0 0 cee eee 35 How to Use Multiple Data Windows 37 How to Use the Menu bar 2 0 0 es 37 How to Use the Upper Toolbar 1D data 38 How to Use the Lower Toolbar 1D data 39 3 3 Command Line Usage 2 0 00 eee 41 How to Put the Focus in the Command Line 41 How to Retrieve Previously Entered Commands 42 How to Change Previously Entered Commands 42 How to Enter a Series of Commands 005 42 3 4 Command Line History 2 0 0 0 ee 42 3 5 Starting TOPSPIN commands from a Command Prompt 43 3 6 Function Keys and Control Keys 0 0 0 00 0 ce eae 45 Our HCIDIT TOOS risas ninan Abe oa wate Saves ad wie et eed BE 50 How to Open Online Help documents 51 How to Get Tooltips anaana aaa 51 How to Get Help on Individual Commands 52 How to Use the Command Index
242. one of the following directories e lt user home gt topspin lt hostname gt prop userdefined only available for this user e lt tshome gt classes prop available for any user e any directory the full pathname must be specified in the icon label field The formats gif jpg jpeg and png are supported Standard TOP SPIN 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 stand ard size 379 User Extensions EA Add tool button Options Add a button with a text label Add a button vith an icon Required parameters Assign this command to button Button tool tip Fourier Tf Button label text Font of button label text Button label text color Button background color Append separator to button Show button only for data of this dimension Figure 21 3 In the example above a button FT is created with a separator which only appears for 1D datasets and executes the command ft How do 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 21 4 How do Shift a User Defined Toolbar Button to the left right Right click the toolbar button and click Shift left or Shift right 380 User Extensions 381 in the appearing popup menu see Fig 21 4
243. oolbar 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 182 2D Display How to Set the 2D Contour Levels Click the following button in the lower toolbar Edit contour levels edlev 1v This will open the following dialog box shown in Fig 10 15 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 e Multiply with increment to create a geometric sequence of levels e Add increment to create a equidistant sequence of levels Enter the desired Base level Level increment and Number of lev els Click Fill to display and activate the sequence 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 183 2D Display PY exam2d_HC 1 1 C bio guest oo OO fo oo 4 to ey amp w if y Required parameters Calculation method O biultiply wi
244. or FID will be automatically adjusted as you change the window function and parameters 3 Click H to store the window settings and return Now you can perform further processing steps like Fourier transform phase correction etc 12 2 1D Interactive Phase Correction Manually acquired spectra can be phase corrected automatically with com mands like apk or apks or interactively in phase correction mode 12 2 1 1D Interactive Phase Correction Procedure How to Switch to Phase Correction Mode Click the indicated button in the upper toolbar 2d 3d A A A OD a or enter phon the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 12 2 200 1D Interactive Manipulation exam1d_1H 1 1 Crbio guest a ojx o 1 R wila s lS A al CELE pivot 1 2508 ppu Phase increment 0 20 ph 0 00 phl 0 00 Set Pivot Point 10 rel Calculate pho O 5 Figure 12 2 Data window in phase correction mode ae The yellow button indicates that you are in phase correction mode a 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 refer ence peak is exactly in absorption mode 2 Click hold the button 1 and move the mouse until the entire spec t
245. or removed as fol lows 1 Right click a toolbar button 2 Choose one of the entries Make this button invisible to remove the button from the toolbar Make this button inactive to disable the button it will appear greyed To restore the complete toolbars click 366 User Preferences 367 Reactivate all invisible or inactive buttons to restore the default tool bar 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 re move commands or menus This is typically done by system administra tors who want to disable certain functions for standard users Open the Menu Configuration table as follows 1 Click Options gt 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 com mands The table consists of the following columns Command Description Menu Status You can disable remove e Menus e g Options to be found in the column Menu e Sub menus g Options gt Administration tools to be found in the column Menu e Menu entries e g Options gt 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 cer tain command In the TOPSPIN menu most comma
246. order phase correction phm90 180 Perform 180 zero order phase correction ph180 How to Reset the Phase to the Original Values Click the following button R Reset zero and first order phase values phr 202 1D Interactive Manipulation How to Change the Mouse Sensitivity Click one of the following buttons Increase double the mouse sensitivity inc t Decrease halve the mouse sensitivity dec IIl 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 Click the following button H 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 Click the following button a Return discarding any changes ret To return while saving the phase correction to the source 2D dataset 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 cur rent 1D dataset was extracted 12 3 1D Interactive Integration Integration of 1D data can be done automatically with the commands abs 203 1D Interactive Manipulation and 1i or interactively as described in this paragraph How to Switch to Integration Mode
247. orm Smooth Phase Correction To perform zero order phase correction 1 Click hold the following button it turns green and move the mouse 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 243 2D Interactive Manipulation To perform first order phase correction 1 Click hold the following button it turns green and move the mouse 1 First order phase correction until the reference peak of the second and further rows columns is ex actly 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 gj 90 zero order phase correction 90 zero order phase correction 18 180 zero order phase correction How to Reset the Phase to the Original Values Click the following button R 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 II Reset the mouse sensitivity to 2 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
248. ot data from the menu 116 data from the Plot Editor 119 data from the Processing Guide 118 layouts 26 plot command 117 119 Plot Editor 26 117 Plus key 48 polynomial baseline correction 227 position of a Topspin window 270 position of a Topspin window 269 position the baseline of a row column in 2D 258 positive 2D levels 187 pp command 142 158 159 PPARMOD parameter 99 104 131 ppl command 234 ppm axis units 154 178 24 pps command 232 preferences 37 348 pre scan delay 319 preview the baseline corrected spectrum 228 previous commands 42 dataset in browser 47 parameter field 99 103 plane in 3D 190 row column in 2D phase correction 244 256 print 1D peak list 142 active window 26 117 colors 356 data from the menu 116 data from the Processing Guide 118 integral list 119 metafiles 120 peak list 119 the current dataset 45 print command 38 45 116 119 142 printer colors 355 prnt command 117 probehead solvent dependent parameters 103 proc_1d AU program 110 process data 27 37 from the command line 106 from the Processing Guide 107 with AU programs 110 with composite commands 107 processing parameters 96 97 parameters 1D 131 parameters 2D 174 Processing Guide 27 108 110 Processing menu 27 37 Processing Reference Manual 24 procno 76 81 85 93 161 ProcPars tab 27 96 97 131 174 projections of a 2D spectrum 25 179 properties of a dataset 159 of a printer 117 prosol param
249. over each individual processing step 106 Data Processing How to Process data with Composite Commands Data can also be processed with so called composite commands These are combinations of single processing commands The following compos ite commands are available e ef Exponential multiplication Fourier transform e efp Exponential multiplication Fourier transform phase correc tion 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 correc tion They can be entered on the command line or clicked from the menu For the latter option Click Processing gt More transforms gt Shortcuts Just like single commands composite commands can be used in Macros AU programs and Python programs 7 2 Semi automatic Processing How to Use the 1D Processing Dialog 1D data processing often involves the same sequence of steps which can easily be performed as follows 1 Click Processing gt Process Plot Current data 2 In the appearing dialog see Fig 2 1 a Enable the desired processing plotting steps b Set the parameter LB for exponential multiplication c Select the desired LAYOUT for plotting d Click OK 107 Data Processing ee procid Press OF to process J plot the selected dataset using the enabled options The command procid y w
250. ow F3 F1 planes How to Display various Plane Positions numbers Click one of the following buttons Show the next plane Show the previous plane Scan planes smoothly E Enter the exact plane number This will open the dialog shown in Fig 11 2 Here you can specify the desired plane number as well as switch to a different plane orientation Valid plane indexes F3 1 2048 4H 6 12 0 11 ppm F2 1 128 143C 56 91 17 09 pom F1 1 256 TH 5 12 0 11 pom Select the visible plane O F2 F3 F1 F3 O F1 F2 Use pom for plane selection Figure 11 2 190 nD Display 11 2 3D Cube Display Mode How to Display the 3D Cube Click the following button A Show 3d cube see Fig 11 3 examad 2 1 Cobia quest DER Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample structure Fid ACU F3 ppm Figure 11 3 How to Rotate the 3D Cube Click hold one the following buttons and move the mouse up down Rotate cube around x axis g Rotate cube around y axis z5 Rotate cube around z axis 191 nD Display 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 11 4 How to Reset the Cube Size and Orientation Click the following button R Reset to default size and orientation How t
251. owser Lasti Groups Alias at zgpgal 1301H AY 300 Automation Cholesterylacetate E exam 11 CoBio guest hechdiggsd exam2d HCO 1 1 CoBio quest Amagcgpat Hat Cyclosporin examid 1H 1 1 CoBio quest zg 1H Cyclosporin Figure 5 3 Hit the Enter key to display the highlighted dataset in the current window Double click a dataset to display it in the current window 66 Dataset Handling Remove Selected Items From List gt Remove the selected dataset from the list Open Saved Last50 List save Last50 List AS gt Open a dialog to select a Last50 list gt Open a dialog for saving the current Last50 list Figure 5 4 Each line displays one dataset showing its name expno procno top level directory and user The Groups tab Clicking the Groups tab displays the list of user defined dataset groups Here you can create modify and display groups of datasets Defining a group is useful is you work on projects where each project involves multiple datasets It allows you to easily organizes your projects and access all data belonging to a certain project Display Display In Mews Window Display Group Add Selected Data Window Add All Open Data windows Update Window Bounds amp Display Limits Remove Selected Datasets From Group Collapse All Groups Toggle DimPulprog Title Add new Dataset Group Close All Group windows Process Selected Datasets File Properties Files co
252. p 51 online manual I 23 plot editor 119 Topspin 50 open browser portfolio 68 data 38 45 64 75 77 data from the browser 23 data from the command line 80 83 data from the Explorer 79 data from the menu 23 IconNmr interfaces 32 Linux Shell 20 new data window 265 new procno 81 online help documents 51 special format data 82 Topspin command index 52 open command 38 45 77 82 Options menu 37 overview spectrum 1D 154 2D 178 P paper format 319 paracon command 319 parameter adjustment window 100 303 change 99 103 104 display 25 editor 96 97 100 101 field 98 99 102 103 files 92 handling 96 name 96 100 search 131 132 value 98 102 parameter set 72 85 PARMODE parameter 132 paste command 38 80 83 peak alignment 26 224 display 25 fitting 30 group 30 labels 158 159 234 list 235 236 list 1D 134 234 list 2D 175 picking mode 232 position 273 position alignment 224 ranges 236 peak picking 1D automatic 232 1D interactive 232 mode 39 mode 1D 232 ranges in 1D 233 234 peak txt file 236 peakrng file 236 Peaks tab 119 134 175 phase correction 1D automatic 106 107 1D interactive 200 2D interactive 238 first order 1D 202 mode 39 mode 1D 201 mode 2D 239 pivot point in 1D 201 values 1D 203 zero order 1D 202 PHCO parameter 98 202 243 PHC1 parameter 202 244 pivot point in 1D phase correction 201 in 2D phase correction 242 pk command 203 plane display in 3D 189 pl
253. pand spectrum gt Delete Edit annotation Remove Define as reference Annotate by reference Shift peaks Rotate peaks Show detailed information Copy Export Import Print Print preview Table properties Select the Project Peaks flag in the options panel of the appearing axe 4 Export Lookin B drud BRUKER i lt b be jmol Zuletzt J topspin drudn verwendet AppData IE Kontakte Desktop Desktop E Download I Favoriten X IM Links NMRSIM_SESSION Dokumente I Gespeicherte Spiele Au IIB Suchvorg nge Computer PGE May Filename 3D testdatase Netzwerk Files of type AUREMOL peak list ml Options v Export selected data v Project peaks ar Figure 8 5 122 Printing Exporting Data In the dialogue box the file format can be changed acoording to the the required application 4 Define the desired options in the upcoming projections dialogue win dow i e target dimension and axis mapping Peak list projection Dimension of projected data Target dimension 2 dimensional gt RILA 2 dimensional Projection Original peak list VFI V F2 FF w a ro q a cS q o o pa oa Figure 8 6 The exported peak list is now of the specified dimension where the axis are projected according to the specified axis mapping 123 1D Display Chap
254. pin version gt icon on your desktop An Explorer will be opened e Double click Miscellaneous e Execute the script savelogs Under Linux e Open a shell e Type savelogs All lt tshome gt prog curdir lt user gt files will be saved with savelogs The stored files can be found under following pathname e Under Windows XP lt userhome gt AppData Local Settings Temp TopSpinSupportFiles lt Support Token gt lt operating system user gt lt year gt lt month gt lt day gt lt hour gt lt minute gt tar gz e Windows Vista lt userhome gt AppData Local Temp TopSpinSupportFiles lt Support Token gt lt operating system user gt lt year gt lt month gt lt day gt lt hour gt lt minute gt tar gz e Linux tmp TopSpinSupportFiles lt Support Token gt _ lt operating system user gt lt year gt lt month gt lt day gt lt hour gt lt minute gt tar gz For detailed information about saving all possible log files and about the upload to the Bruker FTP server please refer to the Processing Reference Command Manual 4 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 show ing the process command dataset etc 60 Trouble Shooting 61 Command Details Sort modules Kill Close i Figure 4 2 Fig 4 2 shows a list with one process command xfb To kill a process select it in the l
255. play Larger Smaller Default view From Top From Front F2 From right F 1 shift To Center shift To Bottom Properties Files Figure 10 17 How to Rotate a 2D Spectrum in Oblique Mode Click hold one of the following buttons and move the mouse up down Rotate around x axis g Rotate around y axis How to Switch between Displaying Positive and Negative levels Click the following multi state button in the lower toolbar lt Switch between positive negative and both contours 1 187 nD Display Chapter 11 nD Display 11 1 Display Planes of 3D Data 3D data can be displayed as 2D planes or as a 3D cube By default the first F3 F1 plane is displayed see Fig 11 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 10 188 O x M ezam3d 1 1 Cobo guest Spectrum ProcPars AcquPars Title PulsProg Peaks Integrals 4 F1 ppm 2 d J 2 F3 ppm Figure 11 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 E Switch to 2D image display x Switch to 2D oblique display How to Display various Plane Orientations Click one of the following buttons 12 Show F1 F2 planes nD Display 23 Show F2 F3 planes 31 Sh
256. play window e acquisition display window e BSMS display window e temperature unit window How to Save the Current Window Layout 1 Click Window gt 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 gt 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 e Each currently displayed window type gets the position and geom etry 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 If a window type is defined in the layout but not displayed the lay out definition is ignored e Multiple data windows are arbitrarily assigned to the available data window definitions How to Swap Data Windows Within a certain layout you can easily swap two TOPSPIN windows with the command swin If the data area contains exactly two windows swin sim ple 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 currently selected active window Swapping windows can also be executed from the Window menu How to Toggle Window Decoration By clicking Window gt Window Layout gt Toggle Window Decoration easy toggling of window d
257. preference in many respects This ranges from startup options to spectrum objects menu settings remote connec tions etc Every standard user can create his her own set of preferences To set user preferences e Click Options gt Preferences set A dialog box will appear with at the left side the categories that can be tai 348 User Preferences lored see Fig 20 1 Ey User preferences Administration terns pectrurn Contour plot spectrum tithe Spectrum Cursor Spectrum parameters Printer Administration terns gt Auto open last used dataset when restarting Topspin Show Topspin data examples directory in data browser Setup Users for TopSpin internal laginfagott and esign Change Automatic termination af TopSpin when idle time exceeded Charge Automatic locking of Top Spin when idle time exceeded Change Fonts Dialogs flcons Window settings Auto apooling Miscellaneous Spectrum Directory path names Tabbed pane layout Acquistion status bar Change CAE OER Change spectral window color scheme Change Acquisition BSMS display Save spectral window colors as a new color scheme Dave aS i Lock display Background color Change Color of 1st 10 spectrum Figure 20 1 Change 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
258. pspin window 269 270 getprosol command 103 132 gf command 107 gfp command 107 Gnome Mozilla 93 grab rows columns in 2D 255 gradient enhanced spectroscopy 31 graphic functions 374 graphics files 27 121 grid display 39 181 300 window arrangement 265 gs command 100 293 303 GS parameter adjustment window 303 H halt an acquisition 291 292 halt command 291 293 307 Hardware requirements 18 helium level 301 Help button 52 menu 37 51 help in Topspin 50 on commands 52 help command 52 Hertz axis units 154 178 hist command 53 57 376 381 383 history file 381 hostname of a remote system 341 HTML page 52 l iconify all data windows 269 data window 267 iconnmr command 32 l 21 image display of 2D data 185 of 3D planes 189 import data 30 inconsistent dataset 99 initial guess 285 install AU programs 21 319 pulse programs 21 Topspin 316 installation directory 71 317 318 installnmr script 317 int command 158 Integral list 2D 176 integral bias 208 display 25 label 206 list 1D 143 regions 204 205 206 207 212 scaling factor 212 slope 209 trails 158 212 values 205 Integrals tab 143 176 214 integrals txt file 214 integration 1D automatic 203 207 1D interactive 203 204 207 mode 39 204 213 214 intensity alignment in multiple display 224 decrease 1D 127 167 increase 1D 127 167 manipulation 39 reset 1D 40 127 167 scaling 2D 168 interactive 1D baseline correction 226 1D calibra
259. py gt Display selected dataset s in active window gt Display selected dataset s in new window gt Display all datasets in group in new windows gt Add selected data window to selected group gt Add all open data windows to selected group gt Update window bounds and dislay regions gt Remove selected datasets from group gt Collapse all groups gt Show hide dimension pulse program title gt Add a new empty dataset group to the list gt Close all data windows of selected group gt Process selected dataset with serial processing gt Show file properties of selected dataset gt Show file list of selected dataset gt Copy pathnames of selected data to clipboard Figure 5 5 Note that a group not only defines the datasets involved but also their data window positions and dimensions and the displayed region of each spec trum Dataset Handling The entry Update window bounds amp displays regions The Alias tab Clicking the Alias tab displays the list of user defined alias names for data sets Just right click any entry to define remove or interpret alias names Browser LastS0 Groups Alias 5 Gramicidine toxy Menthial 1H Menthal inadequat Strychnine C1 3 strychnine Cl Sdeptgo Figure 5 6 Define Alias For Data In Selected Window gt define alias for data in selected window List Selected Alias gt Show selected data name expno etc List All
260. quest Spectrum ProcPars AcquPars Title PuleeProg Peaks Integrals Sample Structure Fid Acqu row 673 Crom examed HC 1 1 C bio quest 10 15 20 25 rel Lis Figure 13 15 How to Copy Contour Levels from First to Other Spectra Click the following button 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 mi 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 13 13 To put the baseline at the bottom of the data window 258 2D Interactive Manipulation 1 Right click in the data window 2 Choose in Baseline At Bottom from the popup menu see Fig 13 13 This works both in the scan submode or on a grabbed row column 13 4 2D Interactive Calibration A 2D spectrum can be calibrated automatically with the command sref or interactively as described below How to Switch to 2D Calibration mode Click the corresponding button in the upper toolbar Id 3d 4 RO ac or enter ca1 on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 13 16 Wi exam2d_Hc 1 1 Cobo guest F2 ppm Figure 13 16 Data window in ca
261. quested and enter the number of minutes of allowed idle time 3 Click OK to close the dialog click OK to close the Preferences dia log If the user does not execute any commands from the command line menu or toobarl buttons the TOPSPIN interface will be locked see Fig 352 User Preferences 20 2 TopSpin locked by user carol at Wed Jul 13 16 53 52 BST 2005 Please press a button to unlock carol to unlock MMR administrator to unlock Figure 20 2 How to Change the Preferred Editor You can choose your preferred editor as it is used by commands like edau edpul edcpd etc To do that 1 Click Options gt 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 edi tor enter the desired Editor and its path For example for Wordpad under Windows 2000 XP this would look like EN Editor definition Please specify an ID name and the editor s path The ID is an arbitray name Editor ID Wordpad Full path C Program Files windows MTAccessoriestworgdg Remove Save Cancel 353 User Preferences 4 Click Save to save the changes If no editor is specified here the TOPSPIN internal editor is used It the file being edited is read only the TOPSPIN internal viewer is used How to Configure the Tab Bar The default Tab bar at the top of the da
262. reen 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 Enter the exact values for the region limits 3 Click OK to define the selected region 205 1D Interactive Manipulation How to Select Deselect Integral Regions To select deselect all displayed integral regions Click the button button To select a single integral region 1 Right click in the integral region 2 Choose Select Deselect from the popup menu To select the next integral region Click the button To select the previous integral region Click the amp button To select multiple integral regions 1 Click the button button to select all integrals 2 Deselect the integral that are not to be selected Selected integral regions are indicated by a color filled integral label In the Fig 12 4 the five left most regions are selected the region around 6 ppm is currently being deselected 206 1D Interactive Manipulation examid 1H 1 1 Crbio guest Sle d f ole Hj A dA lan Ixl Mouse Sensitivity 1 0 6 04 ppm 3020 776 He Calibrate Mormalize Lastscal Delete Figure 12 4 Note that e If no integral is selected the next and previous integral button select the first or last integral respectively e the select all integrals button remains green whi
263. result 4 lines shapes and their sum Exact zoom zx Figure 12 9 The integral values of each of the deconvolved signals are available in the integrals tab within the originally defined integral column Intensity abs EN Bruker TopSpin on merlin as svcu File Edit View Spectrometer Processing Analysis Options Window Help Spectrum ProcPars AcquPars Title PulseProg Peaks Integrals Sample Structure Fid Acqu Object Integral 18 Integral 17 Integral 16 Integral 15 integral 14 Integral 13 integral 12 Integral 11 Integral 10 Integral 9 Integral 8 Integral 7 integral 6 H Integral 5 Integral 4 Deconvoluted signal 18 Deconvoluted signal 19 Deconvoluted signal 20 Deconvoluted signal 21 Integral 3 Integral abs 2466361 88 21904297712 3355158 81 1420407 06 3955862 00 4635586 06 5789624 62 2272572 50 214776518 75 3705958 31 994993 31 4212755 56 1013357 38 71567626 88 121244613 81 4254401 19 Integral rel Range F1 from 4 Range F1 to 0 2154 19 1286 0 2930 0 1240 0 3456 0 4048 0 5056 0 1985 18 7560 0 3236 0 0869 0 3679 0 0886 6 2499 10 5880 eS fee fee E EI ee Oo me e Intensity abs Figure 12 10 216 1D Interactive Manipulation 12 4 1D Interactive Calibration A 1D spectrum can be calibrated referenced automatically with the com mand sref or interactively as
264. ript Click on gt Browse For Macro locate a TopSpin macro gt Browse For Python locate a TopSpin Python program gt Execute start processing the dataset list gt Back return to list definition gt Show show datsets while processing em ftrabs apk igure After executing the serial processing TopSpin 2 1 and newer displays following feedback dialog i Serial Processing Finished Data set list C Documents and Settings svcu Local Settings Temp datasets_12569 txt Serial script C DOCUME 1 svcu LOCALS 1 Tempitopmac_12570 Figure 7 8 Cancel Leave this dialog Chapter 8 Printing Exporting Data 8 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 Click the button amp in the upper toolbar or Click File gt Print or Enter print or Ctrl p All these actions are equivalent they open the Print dialog box see Fig 8 1 Printing Exporting Data 117 A Print Ctrl P plot Options C3 Print active window print Print with layout start Plot Editor plot O Print with layout plot directly autoplot Required parameters LAYOUT H D_Hocwp v Use plot limits Fill data set list s from screen lC Y irom Plot Editor Reset Actions CO as saved in Plot Editor OQ from portfolio saved in data set O from your default portfolio CURPLOT Dell Photo AIG Printer 94
265. rocessing 104 Server ID 323 set 1D acquisition parameters 123 2D acquisition parameters 165 2D processing parameters 165 colors for multiple display 214 contour levels 174 lock parameters 97 phase pivot point 192 processing parameters 89 processing parameters 1D 122 routing parameters 97 user preferences 330 set command 121 329 SFO1 parameter 275 Shell 19 shift 1D data down 120 1D data smoothly 120 1D data to the extreme left 120 1D data to the extreme right 120 1D data to the left 120 1D data to the right 120 1D data up 120 1D 2D data 37 42 2D data down 162 2D data smoothly 162 2D data to the left 162 2D data to the right 162 2D data up 162 data in multiple windows 117 individual spectra in multiple display 24 207 212 row column in 2D phase 230 Shift key 62 69 81 208 209 Shift Tab key 92 96 short description of an AU program 303 shortcuts for processing 100 show command 53 SIGF1 parameter 260 SIGF2 parameter 260 signal region 260 261 signal to noise calculation 260 Simplex algorithm 268 simulating experiments 29 sine baseline correction 216 single commands 99 slider sensitivity 284 slope correction 199 smail command 28 34 smooth 1D phase correction 230 1D scaling 36 1D shifting 120 1D zooming 36 119 1D 2D shifting 37 2D shifting 162 scaling of 1D integrals 202 scanning of planes in 3D 181 shifting of 1D integrals 203 solvent 65 spec command 121 I 13 special format data 28 spectrometer fr
266. rocno combination To do that 1 Click Options gt 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 76 Dataset Handling Tf EN examid 13C This data set contains several EXPN SPROCNO pairs corresponding to several rawwprocessed data files Open Display the selected data set Print Print the data set list Type set and navigate to Printer Printer Font in order to change the tont EXPNO SPROCNO dim pulsprog title zgpgs0 TSC AY 300 Automation Cholesterylacetate jmod 13C APT AY 300 Automation Cholesterylacetate deptiss 13C DEPT135 A 300 Automation Cholesterylacetate dept45 13C DEPTS Av 300 Automation Cholesterylacetate deptg0 13C DEPTSO A 300 Automation Cholesterylacetate zgigs0 WC AY 300 Automation Cholesterylacetate Figure 5 13 Note that the command rel also opens the dialog shown in Fig 5 13 showing the available EXPNO s under the current dataset Similarly rep1 shows the available PROCNO s under the current dataset EXPNO How to Open Data from the Topspin menu 1 To open a dataset Click the 4 button in the upper toolbar or Click File gt Open open Ctr1 o see Fig 5 14 Dataset Handling File Edit View Processing Analysis Mew Ctrl M Oper Ctrl O Reopen Close Ctrl VW Close All Save Ctrl 5
267. rum is exactly in absorption mode 3 Click the button H to save and execute the phase correction and return 12 2 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 see Fig 12 2 201 1D Interactive Manipulation How to Perform Default Zero Order Phase Correction 1 Right click in the data window 2 Choose Calculate ph0 in the popup menu see Fig 12 2 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 Click one of the following buttons 40 Perform 90 zero order phase correction ph90 4 Perform 90 zero
268. s Acquisition amp Processing Reference Automation and Plotting Analysis and Simulation Programming Manuals Technical Manuals Installation Guides Good Laboratory Practice Each document is listed with a short description of its contents Introduction TOPSPIN 2 1 1 5 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 Furthermore you can use TOPSPIN for developer purposes with restricted functionality In this case you have to start it from a Windows Command prompt or Linux shell as follows topspin developer 1 6 TopSpin program versions The TopSpin DVD 2 1 and newer contains the following program ver sions e TOPSPIN e TOPSPIN Plot Editor e ICON NMR e NMR SIM e NMR GUIDE e AUTOLINK The following programs are distributed as part of the TopSpin DVD but they must be licensed separately e AMIX e AUREMOL e PERCH NMR TOOLS only for Windows operating system 18 Chapter 2 Getting Started 2 1 Startup TOPSPIN Under Windows Click the TOPSPIN icon on the desktop or Start TOPSPIN from a Command Prompt as follows 1 Click Start gt Run enter cmd and click OK 2 In the Command Prompt a Enter cd lt tshome gt b Enter topspin where lt tshome gt is the directory where TOPSPIN is installed Under Linux 1 Open
269. s a window with user defined buttons for executing TOPSPIN commands 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 panels like bnmr and bnmrse1 To create your own button panels you can modify one this or write one from scratch In this description we will create a very simple button panel with some 1D processing commands and print export buttons see Fig 21 2 10 Processing Panel Close To 20 Tips Figure 21 2 375 User Extensions To write this button panel take the following steps 1 5 Open the Windows Explorer and navigate to the subdirectory userdefined of the users properties directory b Create a text file with the name emopanel 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 7 COLlOr GCSLini trons used in this frie RGB BLUE1 51S5 2049 255 YELLOW1 255S 2558 0 GREEN1 845 1965 20 eM he er
270. s are displayed in black using the default TOPSPIN Dialog window font as specified in the User Preferences command set If you replace the text Print by the following lt html gt lt font size 10 gt lt font color O00BFO00 gt Print lt br gt Now lt font gt lt html gt then the new text Print Now is displayed in green the color to be speci fied in RGB hex code with 10 points font size Also Now is display below Print due to the html lt br gt break line tag Note that User Extensions 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 If TOGGLE BUTTON is specified without a value i e the entry is TOGGLE BUTTON instead of TOGGLE BUTTON action text the corresponding button is not shown in the panel tems must be separated with the character button items with e A Y 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 composite commands like em nft npk Note that in the latter case the commands must be separated by n e When the bpan lt name gt command comes up with an error mes sage carefully check the syntax of your cmdpanel file A common mistake is to specify the button items i
271. s 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 294 Acquisition this quisition running Amplifier Control Acquisition information Fid Flash SCA 17 16 residual time mess Acquisition display left side see above Acquisition display right side see below 1 PACHE X TU spooler Batis status MESSAGE Kelvi n gueued T delayed T eo lil cron o Autoshimx Locked Error The acquisition status bar not only displays information it also allows you to perform various actions e g 295 Double click the Time field to view detailed time and date information Double click the Lock field to open the lock display Left click the Spooler queued delayed cron field to open the spooler main window Double click on sample field to open BSMS control suite Double click on VTU opens the edte window Right click the Fid Flash field to switch on off FID flashing or to stop the acquisition For more information about peak power check POWCHk please look up the Acquisition Reference Guide Chapter 3 Spectrometer configuration commands Within the command explanation of cf you will find the functionality of POWCHK Acquisition e Right click the Acquisition information field to open the following popup menu show acquisition display Start rga S
272. signature in the data window The electronic signature can be displayed in the data window by setting the corresponding display component To do that 1 Right click in the data window and choose Display Properties dopt 2 Check Electronic Signature in the appearing dialog box and click OK The electronic signature will appear at the upper left corner below the title 18 2 4 Plotting the electronic signature When plotting a dataset using TOPSPIN s plot editor commands plot and autoplot an electronic signature is automatically plotted unless this feature is disabled if the last entry of the audit trail of the data to be plot 331 Regulatory Compliance ted is an electronic signature This ensures that after signing no more data manipulations have been performed 18 2 5 Multiple signatures The command esign may be applied several times to a data set for instance if two persons say an operator and an administrator must sign in accordance with company regulations 18 2 6 Validity and security of signatures TOPSPIN electronic signatures of data sets must not be confused with digital signatures as defined in applicable law Digital signature laws are usually country dependent They require the administration of passwords more general electronic keys which authenticate the owner of the document to be performed by authorized trust centers In contrast TOPSPIN uses OS encrypted passwords or internal user passwords
273. ssing Parameter from the Command Line 96 How to Set Processing Parameters from the Parameter Editor 97 How to Undo the Last Processing Parameter Change 99 How to Display Processing Status Parameters 99 How to Switch to Maxent parameters 05 99 How to Change Processed Data Dimensionality 99 6 2 Acquisition Parameters 0 000 eee eee 100 How to Set Acquisition Parameters 005 100 127 Chapter 7 Chapter 8 Chapter 9 How to Set an Acquisition Parameter from the Command Line 100 How to Set Acquisition Parameters from the Parameter Editor 101 How to Undo the Last Acquisition Parameter Change 103 How to Set Pulse Program Parameters 103 How to Display Acquisition Status Parameters 103 How to Get Probehead Solvent dependent Parameters 103 How to Change Acquisition Data Dimensionality 104 How to Set Lock Parameters 0 0 00 cece eens 104 How to Set Routing Parameters 0 00005 104 Data Processing i ivcvsiie ear etewew a tea he eis ee 106 7 1 Interactive Processing 0000 cece ees 106 How to Process Data with Single Commands 106 How to Process data with Composite Commands 107 7 2 Semi automatic Processing 0 00 c eee eee 107 How to Use the 1D Processing Dialog 107 How to Use the Processing G
274. stallation directory or sendgui lt topspincommand gt if the TOPSPIN home directory is in the users search path Examples C ts2 1 prog bin scripts sendgui ft executes a 1D Fourier transform sendgui re examld 1H 1 1 C bio joe reads the dataset C bio joe nmr exam1d_1H 1 pdata 1 Note that commands are executed on the currently active TOPSPINdata win dow 44 The TOPSPIN Interface 3 6 Function Keys and Control Keys For several TOPSPIN commands or tasks you can use a control key or func tion key short cut Focus anywhere in TOPSPIN Esc Put the focus in the command line fe SG Utme TOGUS In Me command Une wee Shift Esc Display menu bar and toolbars if hidden Put the focus in the browser F1 Search for string in command help or NUR Guide help F6 Select the next window in the data area Alt F4 Terminate TOPSPIN exit CALE A Switch the browser on off Ctr1 o Open data open eer iFo Opendatalopen Find data find Newdala new Ctrl n New data new Ctrl p Print current data print Ctrl s Save current data sav Ctrlt w Close active window close LCE Cl seracive Window erosa 8 Ctrl1 c Copy a text that you selectea nignlignted In an error box dialog box pulse program title etc to the clipboard Paste text from the clipboard into any editable field Focus in the Command Line Ctrl Backspace Kill current input Ctrl Delete Kill current input elect previous command if available
275. stomized configuration 318 cut integrals 212 D data area 24 35 36 75 80 83 262 265 268 compression 30 dimensionality 36 99 104 131 132 directory 64 71 88 field 41 124 129 166 object colors 355 data window 23 36 37 75 80 83 2D 166 3D 188 color scheme 356 contents 26 120 creation 75 handling 37 262 in 1D peak picking mode 232 in 1D phase correction 201 in 2D calibration mode 259 in 2D multiple display mode 252 in 2D phase mode 239 246 in baseline correction mode 227 in calibration mode 217 in integration mode 204 in multiple display mode 220 I 18 in S N measurement mode 274 in spline baseline correction mode 230 objects 26 popup menu 155 171 printing 116 reopen 125 tab bar 1D 130 tab bar 2D 174 toolbar 26 dataset active 264 colors 226 dir 22 324 directory tree 22 79 expno 22 67 72 324 files 93 162 handling 31 64 last 2D 38 last 3D 38 last used 351 name 22 67 72 80 procno 22 67 72 324 procno directory 80 properties 159 selection in multiple display 221 specification 79 264 title 72 top level directory 67 user 22 67 72 324 variables 85 datastation configuration 318 dcon command 30 369 dconpeaks txt file 30 deconvolution 30 default color scheme 357 command line size 364 configuration 318 find criteria 90 menu font 361 pivot point in 1D phase correction 201 pivot point in 2D phase 242 plane in 3D display 188 printer 118 Tab bar 354 zero order phase correc
276. t In correlated spectrum to open a new data window showing the full correlated spectrum Expand spectrum gt In current window to change the current data window to spectrum display showing the region around the selected integral Expand spectrum gt In correlated window to open a new data window showing the region around the select ed integral lower part of Fig 9 7 Note that clicking the marked entry in the right click popup menu is equivalent to pressing 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 145 1D Display Select the desired entries while pressing the Ctrl or Shift key 2 Right click an entry to open the popup menu see Fig 9 8 3 Click one of the following menu items Copy Copy the selected integral s entry to the Clipboard Equivalent to clicking Edit gt Copy or hitting Ctr1 c Copied integrals can easily be pasted in any other application such as Excel 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 Calibrate Integrals to Compare Spectra Integrals from the current and other spectra can be calibrated with re spect to a reference integral To do that 1 Right click the reference integral and choose Define as reference from t
277. t F6 are currently fixed Their function cannot be changed 3 9 How to Open Multiple TOPSPIN Interfaces TOPSPIN allows you to open multiple User Interfaces This is for example 53 The TOPSPIN Interface useful to run an acquisition in one interface and process data in another To open an addition interface enter the command newtop on the command line or click Window gt 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 differ ent datasets or different aspects of the same dataset e g raw processed regions scalings etc When the dataset is re processed in 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 54 The TOPSPIN Interface 99 Trouble Shooting 4 1 4 2 Chapter 4 Trouble Shooting General Tips and Tricks On a spectrometer make sure the commands cf and expinstall have been executed once after installing TOPSPIN cf must be executed again if your hardware configuration has changed Sometimes executing cf is useful in case of acquisition probl
278. t for display and processing Click File gt Open and select Open NMR data stored in special formats Then follow the instructions on the screen 2 12 How to Fit Peaks and Deconvolve Overlapping Peaks Deconvolution is a useful tool to interprete complex spectra in which the peaks are not definite and clear Peaks of a 1D and 2D NMR spectrum can be approximated by a Lorentz ian Gaussian or a mixture of these line shapes Overlapping peaks may be deconvolved into a sum of such line shapes TOPSPIN shows the deconvolution result i e peak positions line widths and integrals on the screen and stores it in the file dconpeaks txt Further more 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 spectrum on the display to show the peak or peak group of interest Then type dcon or click Analysis gt Line Shape Fitting gt Deconvolution 30 Getting Started 2 13 How to Compute Fids by Simulating Experiments TOPSPIN includes a virtual spectrometer that computes fids of any dimen sion 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 task mathematically by solving the quantum mechanical Liouville equation The sample must be entered in form of a spin system description For the computation
279. t name gt 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 gt Delete or click the Delete button How to Show Comments short descriptions in the AU Program List To switch on off the comments in the AU program list 322 Configuration Automation inthe AU program dialog box Click Options and select the entry Comment A comment is a short description of the AU program which is also part of the AU program header 323 Regulatory Compliance 18 1 18 1 1 Chapter 18 Regulatory Compliance TopSpin complies w
280. t the increment options Clicking this button will open the fol lowing dialog Data set increment options Increment Procna Expno C Marne Expno increment Preserve individual scaling Figure 12 14 Here you can choose to increment the procno expno or name set the expno increment and switch individual scaling on off 223 1D Interactive Manipulation How to Toggle between Superimposed and Stacked Display 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 2 3 Display the spectra in multiple display mode as described above Expand the spectra to display the desired region or peak Select one of the spectra e g by clicking it in the lower part of the browser Click hold the g button and move the mouse to align the intensi ties Click hold the button and move the mouse to align the peak posi tions The alignment can be facilitated by showing the difference spectrum A button and minimize that Note that you can also scale the selected spec tra up down with the buttons 2 and 4 The button allows you to move the selected spectra vertically Clicking the p button resets individ ual scaling and shifting The performed scaling and shifting ar
281. t 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 itera tions Note that the initial guesses can also be set with the toolbar button Clicking and executes the commands simfit current peak and simfit all all peaks respec tively Analysis The Fitting Function to pick data points can be e pd pick data points for relaxation analysis Drift value interpreted T e pdO pick data points for relaxation analysis at constant peak positions drift value ignored e pft2 pick data points for T2 calculation of 1D raw data View the Fitting Results When the fitting procedure has finished the fitting curve is displayed in the data section and a Brief Report appears in the parameter section see Fig 15 11 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 Switch x axis to logarithmic scaling E Switch x axis to square root scaling H Switch y axis to logarithmic scaling Note that this only works for curves with positive intensities areas only E Import integrals from dataset TEMP Export integrals to dataset TEMP Toggle button to hide show in
282. t user properties directory gt userdefined To identify this directory enter the command hist in TOPSPIN The file toolbar user prop contains the guide definition If the file does not exist it must be created Here is an example of a user modified 11 T2 guide MyT1T2Toolbar NM tiliid 40 917 NM2 SExtract fid TIP Do0 rser CMD tl fid END NM tlispec 40 gif NM2 Transform TIP Do ef apk CMD t1 spec END NM tliranges 40 gif NM2 SRanges TIP S Enter integ mode CMD tl ranges END NM tiscreen 40 gif NM2 SRelax Window TIP SEnter Relax mode CMD t1 relax END NM END NM myicon gif NM2 Fit Methods TIP Select fit funcs CMD t1_ func END NM c myicons myicon1 gif NM2 Start TIP ct1 ct2 simfit User Extensions CMD 1t1_ start END NM c myicons myicon2 gif NU2 Show Report TIP report CMD t1_report END NM tlprint 40 918 NMZ SPrint 1t TLP oprinc CMDS tl export END Notes to this guide definition 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 The bold lines in the example above are user modified lines NM t1fid 40 gif a Bruker defined icon with a size of 40x40 pixels NM myicon gif a user defined icon which must be located in the user properties directory Caution not in its subdirectory userdefined NM C
283. tOPSAPIN Bruker BioSpin e User Manual TopSpin 3 0 Version 3 0 0 NMR Spectroscopy think forward Copyright C by Bruker BiosSpin GmbH All rights reserved No part of this publication may be reproduced stored in a retrieval system or transmitted in any form or by any means without prior consent of the publisher Product names used are trademarks or registered trademarks of their respective holders C Bruker BioSpin GmbH printed in Federal Republic of Germany 25 03 2010 Part No Variant H9469SA3 10 Document No SM User3 0 0 Document Part No 03 Contents Chapter 1 Chapter 2 IN FOQUCTION 6 ac5srs ieee ee tear eee ee ee 14 1 1 About the User Manual 0 0 0 eee 14 1 2 Safety Regulations 4 5 ed ya eed hewn d cack ol elles ees 15 1 3 User Manual Conventions 0 00 0 cee ee ee 15 Font Conventions 0 0 0 ee eee 15 File directory Conventions 0 00 cece eee eee 16 User Action Conventions 00 0 eee 16 1 4 TOPSPIN OvervieW 0 0 cc ee eee 16 FUNCION ANE a ct ster da td a Gove an a th vee ae et a Scheer ee Gat aiaa 16 Available Documentation 0 0 0 0 eee ees 17 leo TOPSPINMIGCNSC tf iewGtiecd vec ley Ghd arse wearers ath Sane Mawes 18 1 6 TopSpin program versions 000 eee ee eee 18 a dis iy Sesion do it itachi topcase sme ace a God diecast nthe dept en ncaa amp 18 Getting Started 24 233 602 244 2607 iea a e eee eed 20 2
284. ta You can for ex ample use command line commands like re rew rep and dir Details on these features can be found in chapter 5 3 and in the Processing Ref erence Manual 2 4 How to Expand a Spectral Region To expand a certain spectral region Click hold the left mouse button on one side of the region drag the cursor to the other side and release the mouse If you want to cancel the expansion while dragging the mouse just move the mouse out of the data area and release it 24 Getting Started An alternative way of expanding a region is clicking the button repeat edly and then shifting the spectrum to the proper position 2 5 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 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 example peaks and integrals are only shown if peak picking and inte gration have been performed respectively see also chapter 12 The number of displayed digits for the integral and peak labels can be set in the User Preferences click Options gt Preferences gt Spectrum 2 6 How to Display Projections 1D Spectra with 2D Spectra To display projections or 1D spe
285. ta window consist of Tabs to switch between various dataset objects like Spectrum Parameters Title etc You can however configure the Tab bar to contain Tabs for interactive data manipulation like phase correction integration etc These Tabs have the same function as the corresponding buttons in the upper tool bar see chapter 2 and 14 but are easier to access You can configure the Tab bar as follows 1 Click Options gt Preferences 2 Click Spectrum in the left part of the User preferences box 3 Click the Change button to the right of the object Tabbed pane layout 4 Check the desired Tabs uncheck the others 5 Click OK Note that you can change the relative positions of a Tab by selecting it and then clicking the Up or Down button How to Configure the Right click Menu Function Right clicking a pull down or popup menu can perform various actions This can be configured as follows 1 Right click an empty part of the menubar and choose Define Right 354 User Preferences Click Action from the popup menu Define right click action on a menu tern Mo action when right button clicked OQ Display help it available O Execute menu termi O Display command assigned to menu tern i Cancel Figure 20 3 2 In the appearing dialog see Fig 20 3 select the desired action 3 Click OK 20 1 3 Changing Colors 355 How to Change Colors of Data Objects on the Screen The color of various objects i
286. table to open the popup menu see Fig 5 7 Click Define alias names for data in selected window 3 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 5 7 Furthermore the popup menu offers entries to display the dataset list its properties and print the full dataset specification 11 Dataset Handling 5 2 Creating Data How to Create a New Dataset 1 Click File gt New new Ctr1 n Or Click the button in the upper toolbar Specify the dataset name expno procno dir and user in the appear ing dialog box If one or more datasets are open the fields are initial ized with the current dataset see Fig 5 10 Click the down arrow of the Solvent box and choose a solvent from the list or type a solvent name Click the down arrow of the Experiment box and choose a parame ter set from the list or type a parameter set name Type the dataset title in the TITLE box Click OK 72 Dataset Handling Prepare for a new experiment by creating a new data set and initializing its NMP parameters according to the selected experiment type For multtreceiver experiments several datasets are created Please define the number of receivers in the box below MAME examid_ 13C EXPNO 1 PROCNO 1 DIR CABrukenvTOPSP
287. tart acquisition Start wobble start gs stop acquisition from this menu you can start various acquisition commands e Right click the VTU field to open the following popup menu Start Edte Options Clicking Options will open the following dialog box i x Temperature monitor options scale kelvin Update rate s 30 OK Cancel Figure 16 7 296 Acquisition e Right click the Lock field to opent the following popup menu Locksignal display BSMs panel Toggle lock mode Lock sample Figure 16 8 e Right click the Spooler field to open the following popup menu Show suspend Remove all jobs Show spooler report Show spooler log Figure 16 9 16 5 Command Queuing and Scheduling 297 TOPSPIN 2 0 and newer support command queuing spooling and schedul ing Acquisition commands like zg go rga and atma are automatically queued if this feature is on default off This allows you for example to enter multiple zg commands on different datasets Automatic queuing can be switched on as follows 1 Click Options gt Preferences 2 In the User Preferences dialog Enable Auto Spooling under Administration Items Processing commands can be queued with the command qu For exam ple the command sequence zg qu xfbon a 2D dataset will start an Acquisition acquisition and when this has finished process the data Acquisition and processing commands can be scheduled with th
288. ter 9 1D Display 9 1 The 1D Data Window The 1D data window consists of a data field a title bar a Tab bar and but tons Fig 9 1 shows a data window with a 1D spectrum 124 1D Display maximize data button field ae teb minimize close titie Dar Tab bar button button examid 1H 1 1 Chio guest pectrur ProcPars A guPars Title Il PulseProg Peaks Integrals Sample Structure Fid Acgu Figure 9 1 9 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 various regions or various objects spec trum 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 gt 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 9 2 125 1D Display examid_1H 1 1 Cibi o gues ojx Spectrum ProcPars ania tal PulsProg Peaks integ ij gt jox Mexam1d_1H 1 1 Crbio quest 3 ioj x Spectrum ProcPars AcquPars Tite PulsProg Peaks integ aj gt a s Ea E i IFI F Reference indow function oat LB Hz af af Figure 9 2 How to Rescale or Shift one Dataset in Multiple windows Display buttons like 2 and only work on the active data window The same counts
289. tering 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 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 20 4 Resizing Shifting Toolbar Icons How to Change the Toolbar Icon Size 1 Right click of any part of the toolbar 2 In the appearing popup menu see Fig 20 13 click Change Icon Size Reactivate All InvisibleiInactive Buttons Add User Defined Button Change Icon Size Change Toolbar Offset Hide Toolbars wpe SHIFT ESC to reset Figure 20 13 3 Enter the icon size in the appearing dialog and click OK How to Shift Toolbar Icons to the Right 1 Right click of any part of the toolbar 369 User Preferences 2 In the appearing popup menu see Fig 20 13 click Change Toolbar Offset 3 Enter the toolbar offset in the appearing dialog and click OK 20 5 Defining Source Directory for Programs Lists etc TOPSPIN 2 1 and newer allow you to define the source directories for pulse programs AU programs integral ranges various lists etc In TOPSPIN 2 0 and old
290. th increment O Add increment Contour level sign Positive amp Meqgative O Positive Negative Positive Negative Base level S691 27 1 56691 27 1 Level increment 1 800 1 600 Number of levels Figure 10 15 How to Store interactively set Contour Levels To store contour levels that were set interactively for example by clicking 184 2D Display 9 Or pressing Alt PageUp Click the following button in the lower toolbar Lj 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 Pseudo Color Mode Click the following button in the upper toolbar Switch to image color display mode im In pseudo color mode a spectral region looks like this 5 4 5 2 5 0 4 8 F2 ppm 50 48 46 F1 ppm Note that in pseudo color mode the contours are superimposed in black when you zoom in on a small region of the spectrum How to Display a 2D Spectrum in Oblique Mode 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 10 16 185 2D Display 5 4 5 2 5 0 F2 ppm Figure 10 16 In this mode you can manipulate the display in various ways Just right click inside the data window and choose one of the options from the ap pearing popup menu see Fig 10 17 186 2D Dis
291. the new storage format e The old and new style data storage must not be mixed this would confuse TopSpin data browser 22 Getting Started e The brwoser command scroll to active dataset will not work for old style data storage e The Bruker example datasets if installed at all can be found with TopSpin 2 5 and newer in lt TOPSPIN INSTALLATION DIR gt examdata This directory is automatically shown in the browser if enabled in the User Preferences command set How to Open Data from the Menu Open the File menu and click Open A dialog box appears Select the first option the Browser type File Chooser and click OK A file browser appears Navigate 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 ac tive window If no data window was displayed a new one will be created Alternatively you can first create a new window by clicking Window gt New Window Alt 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 How to Open Data from the Browser TOPSPIN has data browser which by default displays the top level data di rectory lt dir gt with Bruker example data You can add your own data di rectories local or remote as follows 1 Move th
292. the noise region 5 Right click any position in the data window The popup menu as shown in Fig 15 2 will appear Quit Clear NWOISEREG Clear SIGREG Edit Regions Change Region Widths Start S N Calculation Enter zoom Figure 15 2 214 Analysis 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 15 2 To delete the current noise region 1 Right click in the data window 2 Choose Clear NOISEREG from the popup menu see Fig 15 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 15 2 3 Enter new limit values in the appearing dialog box Define sino parameters From pern To pern SIGREG 8 6355 0 4351 NOISEREG 10 7777 9 2045 4 Click OK The S N value is automatically recalculated and displayed 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 15 2 275 Analysis 15 4 3 Enter new width values in the appearing dialog box Define sino parameters Vuictth Unit SIGREG 5 2004
293. tion 202 define cubic spline baseline points 230 integral regions 205 NMR ADMINISTRATOR password 316 NMR SUPERUSER 316 peak ranges 233 peaks 234 de iconify data window 268 delete AU program 322 data 86 integrals from display 210 noise region S N 275 peaks from a peak list 235 signal region S N 275 spline baseline points 231 Delete key 42 depth cueing in 3D 192 deselect data in multiple display 221 222 integral regions 206 dialog box font 362 difference spectrum in baseline correction 229 in multiple display 222 dimensionality of a dataset 36 99 100 104 131 dir command 24 disable commands 367 menus 367 toolbar buttons 366 Display button 23 81 91 menu item 75 76 219 display 1D acquisition status parameters 132 1D data 124 1D FID 154 1D integral list 143 1D peak list 134 1D processed data 130 1D raw data 154 1D spectrum 130 1D spectrum overview 154 2D contours 182 2D data 166 2D FID 178 2D grid 181 2D integral list 176 2D peak list 175 2D projections 179 I 19 2D spectrum in contour mode 182 2D spectrum in oblique mode 185 2D spectrum in pseudo color mode 185 3D cube 191 3D data 188 columns in 2D phase correction 239 contours in 2D phase 239 data from the browser 23 66 data from the portfolio 66 data in multiple windows 125 dataset file list 160 dataset properties 159 expno procno list 76 found dataset 90 full spectrum in 2D phase correction 240 integrals 25 JCAMP data 30 manipulation 126
294. tion 217 1D data manipulation 198 1D integration 203 1D peak picking 232 1D phase correction 198 200 1D signal to noise calculation 273 2D calibration 259 2D data manipulation 238 2D phase correction 238 data manipulation 27 38 354 modes 38 parameter adjustment 100 303 processing 106 Processing Guide mode 110 interface fonts 359 internal projection 25 Internet Browser 80 intrng file 208 211 214 IP address of a remote system 341 IUPAC standard 30 J JCAMP DX format 30 82 83 85 Jeol spectrometer 82 Jmol molecule structure viewer 152 JNMR data 82 K KDE konqueror 93 keyboard commands 37 kill command 60 Konqueror 93 162 L Left Arrow key 42 48 69 Levenberg Marquardt algorithm 285 licommand 143 204 Liouville equation 31 lipp command 143 lippf command 143 list 176 1D integrals 143 2D integrals 176 2D peaks 175 AU programs 319 baseline points 230 Bruker AU programs 321 color schemes 357 data files 92 160 EXPNOS PROCNOS 76 found data 90 integrals 119 213 macros 31 opened datasets 66 67 68 parameter sets 72 peaks 119 234 peaks 1D 134 plot layouts 117 solvents 72 22 user defined AU programs 321 local Topspin interface 338 lock parameters 104 signal 300 lock command 301 lock display colors 356 mode 300 window 269 292 295 299 lockdisp command 292 299 lock in procedure 300 Lorentzian deconvolution 30 lower toolbar 39 macros in AU programs 110 374 in Topspin 31 53
295. tion se 2 aie wach ce sees Shen eceoet he acne 9k Ss ane Rea a Peete Mine 319 How to Install AU Programs 0 00 0 319 How to Open the AU Program Dialog Box 319 How to Switch to the List of User defined AU Programs 321 322 How to Switch to the List of Bruker defined AU Programs 321 How to Define the AU Programs Source Directory 321 How to Create an AU Program 000 cece eee 321 How to Edit an Existing AU Program 045 322 How to Execute an AU Program 0 000 eae 322 How to Delete an AU Program anaana eee 322 How to Show Comments short descriptions in the AU Program List Chapter 18 Regulatory Compliance 0 00 eee eee 324 18 1 Audit Trails yc accent Mee acee a eee ae eae ke eh a a ew Sos 324 18 2 Electronic Signatures 0 0 00 ces 329 18 3 Password Controlled Login Identification 332 Chapter 19 Remote Control 00 0 ccs 338 19 1 Remote control 0 0 0 0 aaa eee 338 19 2 How to Establish a Remote Connection from yourPC 338 19 3 How to Make a Remote Connection without a Local License 344 19 4 Security of Remote Connections 0000 05 345 19 5 How to Access ICON NMR from a Remote Web Browser 345 19 6 How to limit IP Addresses for Remote Control 346 Chapter 20 User Preferences 0 ccc eee ees 348 20 1 User Pref
296. tions on the Spectrum 159 How to Show Individual Data Points of the Spectrum 159 How to Superimpose the Electronic Signature on the Spectrum 159 How to Display the Main Dataset Properties 159 How to Display a List of Files of aDataset 160 9 7 Saving Display Region anaa 00 ce eee 163 9 8 Synchronize Visible Region of all Data Windows 164 Chapter 10 2D Display 0 es 166 10 1 The 2D Data Window js 5 5 sien sean Sac ak We als alae we ae hae 166 10 2 Changing the Display of a 2D spectrum 167 How to Change the Intensity Scaling contour levels 167 How to Smoothly Change the Vertical Scaling contour levels 168 How to Display a Contour Levels Bar in the Data Window 168 How to Switch on off Square 2D layout 169 How to Zoom a 2D spectrum in out 046 170 How to Shift a Spectral Region in the F2 direction left right 171 How to Shift a Spectral Region in the F1 direction up down 171 178 187 10 3 Show Display Properties Regions Files 171 10 4 Using the Tab bar 0 0 0 0 cee 174 How to Set Processing Parameters 005 174 How to Set Acquisition Parameters 0 005 174 How to Display the Peak list 2 000008 175 How to Display the Integral list 0 8 176 How to Display the FID
297. to Change the Font of the Status Line 363 How to Auto Archive existing expnos 00006 363 Command Line Preferences 00 0c eee eee 364 How to Resize the Command Line 04 364 How to Set the Minimum and Maximum Command Line Size 365 Disabling Enabling Toolbar Buttons Menus and Commands 365 How to Hide the Upper and Lower Toolbars 365 How to Hide the Menubar 0 0 0 0 0c eee ees 366 How to Disable Remove Toolbar Buttons 366 How to Disable Remove Menus or Commands 367 How to Re enable a disabled Command Menu 369 How to Re enable All Commands Menus 369 Resizing Shifting Toolbar Icons 0 00000 eee 369 How to Change the Toolbar Icon Size 0 4 369 How to Shift Toolbar Icons to the Right 369 Defining Source Directory for Programs Lists etc 370 EXIGNSIONS 3 is3 c2402 tie init iiae 00 06 RES das 372 User Notebook f 4 6 4 did eth oe deb tee eed amp Sed deed hdewes 372 MACOS fests Ses ats tet ete eh ete deg G Seals aa ee et SRO yp Gute Gas Ae eons ns 373 PA POON aM Sese a Sk co Widnes tha tees aera Diba Me E AEA 373 Python I FOGRAING sso eiser Bette ot he eae Deane id eek ee 374 BUEOM PANGS 55 6 cn db ducaeph hoa debit dee tin aed Bit om E E ay need 375 Adding User Defined Buttons to the Toolbars 378 Adding User Def
298. ton for zero order correction and move the mouse until the reference peak of the first column is exactly in absorp tion 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 Hj button to execute save and return see Fig 13 5 WW Phase 2D exam2d_HC 1 1 Cbio guest E l O x Ajlo 1 R lame ult fu Bl gl EES pivot 1265 44 ppm Fhase increment 0 20 ph 63 356 phl 150 80 a a a Column 899 ne a ppm igure 13 50 lt Cti w SCS 13 5 13 1 2 2D Interactive Phase Correction Details How to Scale or Shift Individual Rows Columns To select one row or column 242 2D Interactive Manipulation Click in the corresponding part of the data window The selected row column will be marked with a filled blue square where as unselected rows columns will be marked with an unfilled blue square __ Selecting a single row column allows you to shift and scale it separately from the other rows columns as shown in Fig 13 6 MW Phase 2D exam2d_HC 1 1 Csbio guest l O x Ajlo 1 R fae ult jm El gl ERS pivot 126 44 ppm Fhase increment 0 20 ph 63 356 phl 180 80 7 2569 ppm SIL p44 i JE a BIT P com Column 899 9748 ppm Figure 13 6 To select all rows or columns Click the following button 4 Select all rows or columns How to Perf
299. toolbars are similar and will be discussed in the chapters 10 11 and 13 respectively 36 The TOPSPIN Interface 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 different datasets Data windows can be arranged from the Window menu One of them is the active current data window The ac tive data window e is the only data window receiving commands from the command line e can be selected by clicking inside the window or hitting F6 repeat edly e has a highlighted title bar e has the mouse focus 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 Menu bar The menu bar contains the following menus e File performing data file handling tasks e Edit copy amp paste data and finding data e View display properties browser on off notebook command his tory e Spectrometer data acquisition and acquisition related tasks e Processing data processing e Analysis data analysis e Options setting various options preferences and configurations e Window data window handling arrangement e Help access various information indices manuals etc Experienced users will usually work with keyboard commands rather than menu commands Note that the main keyboard commands are displayed i
300. tored The command auditcheck may be used to check whether the data are still consistent If for example JCAMP DX or ZIP file have been manipulated the data might not be consistent 18 2 Electronic Signatures 18 2 1 Signing a data set The command esign adds an electronic signature to the raw data or to the processed data of a data set It opens a dialog where you can select the data component to be signed the signature meaning and optionally add a comment esign requires that the NMR administrator has set up a list of users who are allowed to sign a data set along with definitions of signature meanings e g review approval See below for details command uad m n Ey esien Add Electronic signature To Data Set examigd 136 1 1 C bio guest Data component to be signed Raw amp Processed Data ha our comment Comment Figure 18 4 18 2 2 Structure of a signature In TOPSPIN an electronic signature is realized as a special entry appended to the audit trail of the raw or processed data It is therefore linked with the data and protected against manipulations just like any other audit trail entry Signatures can be viewed with the command audit An electronic signature consists of the following items USER ID The ID of the user logged in at the time esign was executed This is either the user who was logged into the operating system Windows or Linux user and who started TOPSPIN or the TOPSPIN internal user Whic
301. ts 1D interactive window multiplication 12 1 1 1D Interactive Window Multiplication Procedure How to Switch to Window Multiplication Mode Click the Processing gt Window Multiplication wm enable Manual window adjustment in the appearing dialog and click OK Or Enter winf on the command line The Tab bar of the active data window will be replaced by a toolbar see Fig 12 2 and the data window itself will be divided into three parts e aparameter part at the left 1D Interactive Manipulation e aspectrum part at the upper right e aFID part at the lower right Pxamid 1H 1 1 Cobio guest winfune Parameters WD Window function type Line broadening LE Gaussian max postion O GB 1 O Sine bell shift SSB C SSB 4 SSB 2 1 2 3 4 s Figure 12 1 t Show both spectrum and FID Ww Show FID only ul Show spectrum only i Switch cursor information on off toggle EL Save windows settings to source 2D dataset and return 1 2D data from which current 1D dataset was extracted e g with rser 199 1D Interactive Manipulation Ej Save window settings and return a Return without save You can perform interactive window manipulation as follows 1 Select the window function parameter WDW 2 Set the corresponding parameter s e g e LB for exponential e LB and GB for Gaussian e SSB for sine bell and squared sine The displayed spectrum and
302. uide in Automatic mode 108 How to Use the Processing Guide in nteractive mode 110 7 3 Processing Data with AU programs 0005 110 7 4 Serial Processing 2 4 5 2c24c 0p3 54 245606540 5dendaia dads 111 Printing Exporting Data 0 00 c ees 116 8 1 Printing plotting Data 0 0 0 0 116 How to Print Plot from the Menu 00008 116 How to Plot Data from the Processing guide 118 How to Plot Data with the Plot Editor 119 How to Print the Integral list 0 00000 eae 119 How to Print the Peak list 0 0 0 0000 cee 119 OA EXPOMING Dats 4 x25 heck tt oar a a a dae ode EM Sores 120 How to Copy data to Other Applications 120 How to Store Export a Data Window as Graphics File 121 How to export projections of peak lists 121 UD DISDIAY s 3 52c 4 ese eae Ra ee lt A ee eae ie 124 9 1 The 1D Data Window 00 ce ee 124 9 2 Displaying one Dataset in Multiple windows 125 How to Reopen a Dataset in a Second Third etc Window 125 How to Rescale or Shift one Dataset in Multiple windows 126 9 3 Changing the Display of a 1D Spectrum or FID 127 How to Change the Vertical Scaling of the FID or Spectrum 127 How to Smoothly Change the Vertical Scaling of the FID Spectrum How to Change the Horizontal Scaling of the FID or Spectr
303. ull spectral width in F1 f1r 41 Show full spectrum a11 iil 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 be tween square brackets 170 2D Display How to Shift a Spectral Region in the F2 direction left right 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 sz or Click hold the button and move the mouse Smoothly shift in any direction Alternatively you can enter the corresponding commands as specified be tween square brackets How to Shift a Spectral Region in the F1 direction up down Click one of the following buttons Shift the spectrum up half of the displayed region su 4 Shift the spectrum down half of the displayed region sd or Click hold the button and move the mouse Smoothly shift up down and left right Alternatively you can enter the corresponding commands as specified be tween square brackets 10 3 Show Display Properties Regions Files If you right click inside the data window the popup menu shown in Fig 171 2D Display 10 5 will appear Display Properti Edit Contour Levels Save Display Region To Restore Display Region From Params Fi File Properties Square
304. um 128 How to Shift a Spectral Region to the Left or to the Right 129 158 158 How to Shift the Spectrum Up or Down 129 9 4 Using the Tab bar sks sce ewrbewe bead ie ae Ae ee Re 130 How to Display the Spectrum 0 00 cee eae 130 How to Set Processing Parameters 0005 131 How to Set Acquisition Parameters 005 132 How to Edit the Title 0 0 0 cee 133 How to Edit the Pulse Program 000 0c eae 134 How to Display the Peak list 0000058 134 How to Display the Integral list 06 143 How to view Sample Information 005 151 How to Open the Jmol Molecule Structure Viewer 152 How to Display the FID 0 0 0 0 eee eee 154 9 5 1D Display OptionS s 35 2 4 euuls se ee weeded deo ewe ee ed 154 How to Toggle between Hertz and ppm Axis Units 154 How to Switch on off the Spectrum Overview display 154 How to Switch Y axis Display 0 0 00 0c 155 9 6 Show Display Properties Regions Files 155 How to Superimpose the Cursor Information 157 How to Superimpose the Title on the Spectrum 158 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 158 How to Show Peak Annota
305. umber used by TOPSPIN Remote Control 1 Start TOPSPIN 2 Enter hist 3 Look for the line To connect to this TOPSPIN use host lt xxxx gt port lt yyyy gt in the upper part of the dialog window The number at the end of this line lt yyyy is the desired port number which must be used to set up the local system see chapter 19 2 2 By default this is port number 5500 Only if this port is already used by a program other than TOPSPIN a different port is used 19 2 2 Setup the local system Define the remote system 1 Log in on the local system Start TOPSPIN Click Options gt Preferences set Click Miscellaneous in the left part of the dialog box oF O N Click the Change button at the entry Setup remote systems n the appearing dialog see Fig 19 2 ledalsottware bruker de 5500 Figure 19 2 Server ID Host name or address TCPAP port number enter the following information e Server ID an arbitrary name for the remote system e Hostname or address the hostname or IP address of the remote host e TCP IP port number of the remote TOPSPIN as identified in chapter 19 2 1 341 Remote Control 6 Click Add to add the remote host 7 Click OK to save the changes and close the dialog Note that you can define multiple remote systems for example different spectrometers in your laboratory Connect to the remote system 1 Click Options gt Remote connection
306. w empty Data Window 265 How to Arrange Data Windows 0 000000 ce 265 How to Iconify minimize a Data Window 267 How to De iconify a Data Window 005 268 How to Maximize a Data Window 0008 268 How to Restore the Size and Position of a Data Window 268 How to Close a Data Window 0000 ee eee 268 How to Iconify all Data Windows 00006 269 How to Maximize all Data Windows 269 How to Activate the Next Data Window 269 2 5 14 2 Window Layouts a a bo de a on a a2 b Seem gen ado oe x Seae se 269 How to Save the Current Window Layout 269 How to Read a Window Layout 2 0000 aes 269 How to Swap Data Windows 0 0 eee ees 270 How to Toggle Window Decoration 0 270 Chapter 15 AhalysiS 2 2 4 2 0406 s2 e seen e Cedte2ee ne tae ieee 272 Oe MITOOUCHON eo osha uiy iti a ene we sit pb at th es aes a ees Ba 212 15 2 Chemical Shift Distance Measurement 213 How to Measure a Chemical Shift Distance 213 15 3 1D Signal to Noise Calculation 000 273 How to Perform Interactive S N Calculation 213 How to Delete the Signal Region or Noise Region 215 How to Edit the Limits of the Signal Region or Noise Region 275 How to
307. ws Command Prompt or Linux Shell 2 Go to the TOPSPIN installation directory 3 Enter topspin client 344 Remote Control 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 communicate with local Just click OK to continue 5 Click Options gt Remote connection and establish a remote connection as described in chapter 19 2 Note that without a local license e TOPSPIN on the remote system must run with a licence e Local data cannot be accessed 19 4 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 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 connec tion 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 t
308. xamid 1H 1 1 CiBio guest 151 s 7 r r r Spectrum ProcPars AcquPars Title PuleeProg Peaks Integrals sample structure Fig ACEL E Eao t4 Sample Description Sample ID Origin Concentration Date Prepared Butter Contact Comment Figure 9 11 This table can be used to fill out any sample information you want to store with the dataset The table can easily be modified or extended with the fol lowing functions To select an item double click it Save the sample information table with the dataset E Save the sample information table as default x Reload the original table discarding any changes Add anew item to the table You will be prompted for an identifi cation name and the desired number of lines Remove the selected item from the table Move the selected item one place up in the table 1D Display Move the selected item one place down in the table How to Open the Jmol Molecule Structure Viewer Click the Structure tab jmo1 examid 1H 1 1 Cobio guest 1 Sele Spectrum ProcPars AcquPars Title PuleeProg Peaks Integrals Sample Structure F File Edt Display View Toole Macros Plugins Help amp ia mji BP 2p eciter oyclosporina pab cyclosporina Orme Gre Figure 9 12 opens the Jmo molecule structure viewer TOPSPIN 2 1 contains Jmol ver sion 10 This has the following features e
309. ze 346 usage 37 Command Prompt 19 298 compile AU program 302 303 components of a spectrum 24 composite commands 100 configuration commands 20 customized 299 default 299 directory 299 name 299 of a datastation 20 of a spectrometer 20 of the acquisition status bar 276 of the tab bar 335 of the Topspin menu 348 password 297 consistency check 307 contour display 226 of 2D spectra 173 of 3D planes 180 contour levels 158 174 control keys 40 convdta command 78 convert data to JCAMP DX 78 data to text 78 data to ZIP 78 copy amp paste data 33 73 76 copy command 25 34 113 copy data 77 C program 103 create an AU program 29 104 302 354 an empty data window 68 data window color scheme 337 dataset 34 macro 29 354 new data window 21 new dataset 65 286 plot layouts 25 112 Python program 30 355 set of user preferences 329 user defined command 29 user notebook 353 C statements 29 Ctrl key 62 69 81 118 159 208 209 Ctrl c key 38 41 133 Ctrl d key 31 41 Ctrl f key 41 Ctrl F3 key 47 Ctrl F5 key 47 Ctrl F6 key 47 Ctrl n key 34 41 65 286 Ctrl o key 34 41 70 75 Ctrl p key 25 34 41 112 133 Ctrl s key 27 34 41 77 78 Ctrl v key 38 41 Ctrl w key 41 cube display 179 cubic spline baseline correction 218 cursor information 148 customized configuration 299 cut integrals 203 D data area 22 31 68 73 76 249 252 255 compression 28 dimensionality 32 92 97 122 123 directory 57 64

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