NMR Spectroscopy Short Course 2006
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VNMRJ Operation Instruction Updated(5/12/06)
DO NOT REMOVE THIS INSTRUCTION FROM THIS TABLE 1. Login
2. Start vnmrj By click the vnmrj icon on the top of the screen Drag the proton icon and drop it to the black area to start a proton experiment.
3. Eject STD sample and Insert your sample. Click icons to change your samples. You could type your sample ID, and select solvent on this page. Also you could type few words in the comment box. These words will be printed on the spectrum (pap)
4. Lock on your sample
Click Lock, Click Lock Scan; Change the ZO value for your solvent. Change the Power, gain and phase to meet the requirement of your solvent.
5. Shim Change Z1 Z2 etc. to shim on your sample. Click loadshim to load default shim file.
5. Acquire Spectrum
Click acquire tag. To change acquisition parameters. Click Process tag and type dg to check the current acquisition parameters. You change nt by type nt=16 for 16 scans then type dg to update the parameter. Then type ga to start acquisition.
6. Processing.
After the acquisition complete, the spectrum should be displayed on the screen.
Using the processing icon to process the spectrum. Or use command to process and plot the data as before. All the commands such as wft, pl pscale pap page work on this software.
7. Save the data: svf(‘file_name’) you could change the directory by cd(‘/home/your_ID/my_new_dir’) Also you could use Linux window to move the file around. For retrieve the data, Find the data and then drag/drop it to the processing window. To find your data: FileàOpenà
8. Plot the spectrum: pl pscale pir pap page. All other commands work too. 9. Completion: Eject your sample, put STD sample in the magent. Type loadshim to load our standard shim file. Lock, Shim as required. File àExit VnmrJ ActionàLogout Click OK.
If you are OK with 1H acquisition. Then you could proceed the following:
10. Acquire a 13C spectrum. Drag the Carbon icon to the black window. Then check the acquisition parameters,such as nt. and type ga.
To acquire an APT or DEPT spectrum, Drag the APT icon or DEPT icon to the window. Then check the acquisition parameters. Type ga.
There are lots of NMR experiments could be setup in this way. Such as COSY,TOCSY, HETCOR,HMQC and HMBC. Please let me know what kind of experiments you may need in the future research. I will gradually improve the capability of this machine. Please feel free to talk to me.
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Add the printer for a new user:
In the vnmrj window: File à printerà select plotter à HPplotter Select Printer à HPprinter then click close
Add an icon on the top of the window:
Edit à Tool Bar then drag the New Tool icon to the top of the window. Type the macro or commands in the command box. Type the name of icon in the Tool Label Box. Then click close. By click icon, it will replace the macro or commands that typed on the command line.
To remove the icon: Edit à Tool Bar, then click the icon that you want to remove, the box will change to red, then drag it to trash can. Then click close.
This is not for normal NMR users: Setup Proton Exp. Protocol: Vnmr1 control the Proton parameter: /vnmr/parlib/Proton.par/procpar is the file should be updated by vnmr1. All other experiments could be updated in the same way. Before change the file, cp –r DEPT.par DEPT.par_original, to back the original file.
login vnmr1 Setup a normal Proton exp. Change parameters as need. Run a proton exp. After complete, type Cd(‘/vnmr/parlib’) change the directory for save the parameters.
Svp(‘Proton’) .par is not required
The parameters will be saved in /vnmr/parlib as Proton.par. this file will be accessed by all other users who are going to use std protocol experiment.
Current Proton Parameters: P90 9.5 Tpwr 60 Dmf=10100 Dpwr=40 Pp=10.2 Pplvl=60 Tpwr_cf=1.10185 Dmm=w Dseq=waltz16 Dres=90 Date 07-apr-2006
Note: Can not change default setting for sw, since it is linked to the menu set from the panel.
To Remove STD protocol on the Walkup account: Login as vnmr1 /vnmr/adm/users modify the file: protocolListWalkup.xml Remove the line: <protocol name=”exp_name” label=”exp name”/> save the file, Esc à shift : à wq .
Backup files: protocolListWalkup.xml current in use by all walkup users protocolListWalkup.xml_current backup protocolListWalkup.xml_org original file from Varian.
Add an New Protocol Experiment for All Walkup Users: Setup an new experiment, then save the parameters in: /vnmr/parlib remember the name of the experiment. Then Tools à Create protocols à type the name. The new protocol will be in the file of protocolListWalkup.xml.
Add an New protocol Experiment in an walkup account: In the individual account: setup an experiment that will be saved as a protocol experiment. Toolsà create protocols à make a New Protocol type the proton name, then click make protocol. The name of the protocol will be in the tag called Local. To remove the local protocol: The file is in: /~/vnmrsys/templates/vnmrj/protocols/name_protocol.xml Remove the file in this directory. Also remove the parameter file in: /~/vnmrsys/parlib/name_protocol.par
Add an New Account: Login as vnmr1 #vnmrj adm in the window add user for walkup check the path etc.
login new user’s account: setup the passwd move the dot. Move the window wysiwyg=’n’
Clear the un-wanted icons in the operation pages: in the vnmrj window: 1. Edit à Parameter page… à Select the blue box, double click, it will change to yellow, then move it to trash can. After delete the icons, make sure the new setting is saved by click the save button on the above window. 2. vp=0 wysiwyg=’n’ 3. reset the ZO power level, gain and phase for the lock.
Save Layout:
Setup the layout, then put the curser on the L1 icon and press for 3 seconds. The layout will be saved.
Current VNMRS 400 Configure File:
New Probe Files: /vnmr/Probes/Name_probe
NMR Patches: /vnmr/adm/Patch: Current installed:
Protocol Experiments Parameters:
/vnmr/parlib/experiment_name.par No longer in STDlib Change standard parameter for an experiment: Run experiment and then svp(‘name’) in the parlib.
Loadshim: Rts(‘/home/vnmr1/vnmrsys/shims/goodshim’) Load=’y’ Su
Questions: How to mount and umount an external USB disk for Lunix 3 and vnmrj 1.1D
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