2.2 Preparing a new experiment or opening an old one

Preparing a new experiment in Vnmr(J):

To load a new experiment type the pulse sequence name (e.g. s2pul for the 1 or 2-pulse pulse sequence) in the Vnmr(J) prompt. There must be a macro /vnmr/maclib/s2pul or in $HOME/vnmrsys/maclib/s2pul that sets a lot of variables for the sequence and then calls it. If you want to see which pulse sequences are available in your system, try ls /vnmr/seqlib $HOME/vnmrsys/seqlib to find the compiled versions, and search for the corresponding macros that call these pulse sequences by typing ls /vnmr/maclib $HOME/vnmrsys/maclib. Don't forget that the Varian userpage hast a lot of pulse sequence for download. The address is http://www.varianinc.com/cgi-bin/nav?products/nmr/apps/usergroup/userlib (requires login). Examples would be s2pul, dept, hsqc etc. The desktop in Vnmr^TM also offers options to set up a 1-pulse pulse sequence. They are in $\rightarrow$ , and then choose your pair nucleus/solvent, eg . In VnmrJ^TM you also find options in the button on the top. Check bellow for the most important parameters to set up before you run an experiment.

Opening a saved experiment in Vnmr^TM :

If the experiment is saved in, say, $HOME/data/myoldexpt.fid, click in the Vnmr^TM main command window $\rightarrow$ . The middle window will show you the files in your working directory. Type pwd in the Vnmr^TM command prompt to know where you are. From inside Vnmr^TM you can browse a directory tree in order to reach your experiment. One way is to type cd(´$HOME/data). Another way is to click $\rightarrow$ $\rightarrow$ . Then the Vnmr^TM top window will give you some browsing options. changes your position to the upper directory (corresponds to cd .. in a Unix shell). switches back to the previous bottons in the top window. You can also type cd to change to the $HOME directory. Type again to have the contents of your $HOME directory printet in the middle window. Click on the directory you want to change to, in this example, click in the middle window. Click in the top panel to change to this directory. Now the middle window shows you the contents of the data directory. Click $\rightarrow$ $\rightarrow$ to load this experiment.

Opening a saved experiment in VnmrJ^TM :

First of all make sure you configured the Unix user you are logged in as VnmrJ^TM User (see Section 1.3 for details). Second, make sure you ran dbupdate after adding each user (see Section 1.3 for details). Then open VnmrJ^TM and search for the saved experiment in the library window, button left side of the VnmrJ^TM window. This ``sub-window'' can also browse directory trees. Find your experiment file and click on it.

If you loaded, say, the s2pul experiment, try man('s2pul') to get some more info about this pulse sequence. Type dg to see the parameters of the experiment (in VnmrJ^TM you have to click $\rightarrow$ to see this text).

Type dps to see the pulse sequence diagram.

Set all the variables like pw=5 in the prompt.

Parameters to ajust (set this variables in the prompt, eg. nt=8):

tn

Nucleus for channel 1 (e.g. tn='H1' )

tof

transmission frequency ofset. This is set to the middle of the spectral window. You can set it also from the prompt (tof=1000) or by right clicking a position at the spectrum and witting movetof.

sw

the spectral width. For a very first spectrum set it to a high value, eg sw=60000, so that you have surely the desired signal in your spectrum. sw is measured in points for a fixed dewel time. Once you have your very first spectrum, you can select the interesting part of it with left-right click and type movesw to select a new spectral window.

tpwr

the transmiter power. Ranges: -16 to 63dB or 79dB, depending on the configuration. Type display('tpwr') to see the limits. For the very first spectrum in a new system start with low values of tpwr. Increase its value till you start having a signal. It normally ranges around 58 for liquids (using liquids amplifiers) and above 40 for solids, depending on the intended use.

pw

the pulse width (in microsec).

nt

number of scans

Set values for the variables appearing in the pulse sequence diagram (command dps). For ex. d1=2. Type time to see the time of your experiment. It can be high if you set bs to a lower value (e.g. bs=16, or other multiple of 2).

Type go

Type text('Your name, other comments, sample name, temperature, parameters etc')

Stoping, Saving and Retrieving an Experiment

aa

Abort aquisition. Stops expt. and you can save.

sa

Stop aquisition, used if you want to exclude an experiment from the queue when anoter experiment is already running. Type jexp7 sa, for example, if you want to exclude Exp7 from the aquisition queue.

ra

Resume aquisition, if you stoped in the midle.

svf

Save file (ie, the FID, processing and etc). Atention, go first to the appropriate directory (for ex: $HOME/data) in order to save it. See Section 2.1 to know how to go to the right directory. If you saved your expt in the wrong directory, use command mv (Section 0.3) to move it to the right place.