0.5 General Description of Vnmr(J) Softwares

Vnmr^TM and VnmrJ^TM are similar in prompt commands but use considerably different interfaces. The Vnmr^TM interface buttons can do a few commands, but many can only be entered from the prompt. At VnmrJ^TM the window buttons do more, but these extra functionality can be done by prompt line commands in Vnmr^TM . Here we emphasize the prompt usage since it's common for both of them and is much stable over time, ie it does not chante much. The interface buttons, on the other hand, have changed a lot from Vnmr^TM to VnmrJ^TM and are still changing considerably between versions of VnmrJ^TM. Another advantage of learning the prompt commands is that it is much faster to operate and often allows input artuments, which I am not sure one can always input in the GUI interface. If you are running Vnmr(J) remotely, then it can make a difference in speed using prompt commands. The prompt commands are entered at the top pannel, or command panel of Vnmr^TM , as shows Figure .

Figure: the command panel of Vnmr^TM , also called here top panel. In this picture the user is in the experimet library number 5 (Exp:5); the pulse sequence is called mrev8 (this is the name of the variable seqfil; and the first spectrum of an array is observed (Index: 1, if we do not have an array Index will be always 1).

The prompt syntax for any command is like ds(5) where ds is the command (display spectrum) and 5 is the argument (5th spectrum). When the argument is a string (not a number), it must be single-quoted, e.g. tn('H1') to tell that the 1st channel is for proton. To get information about a prompt command, type man('name_of_command').

Vnmr(J) line commands can be standard commands or macros. The macros, written in the Magical II language, can be found in /vnmr/maclib. You can also create your own macros and place them in $HOME/vnmrsys/maclib. To know which command/macro you are using type . Any macro that runs in Vnmr^TM should run also in VnmrJ^TM and vice-versa.

The DPS panel is shown in Figure 2. In this panel can be shown spectra, pulse sequence or directory contents (for browsing). In this case a pulse sequence is shown.

When showing a pulse sequence (the case in Figure 2), you can click the mouse at the top right and get the DPS accessory panel.

Figure: the DPS panel of Vnmr^TM , also called middle panel here. Here spectra, pulse sequence or directory contents can be shown. In this case a pulse sequence is shown. Tx is the transmiter channel and Z is the gradient at the Z direction. If you right click the mouse at the top right you get the DPS accessory window. If you now click the gradient at the DPS panel, you get an explanation, as shown in Figure 

Figure 3: the DPS accessory panel of Vnmr^TM and VnmrJ^TM. Here the gradient in Figure  was clicked, what brings explanation about this pulse sequence event at this DPS accessory panel.

The text panel is shown in Figure .

Figure: the text panel of Vnmr^TM. In VnmrJ^TM you have to click in Process $\rightarrow$ Text Output to get this window. Here important parameters of the pulse sequence are shown when you type dg. Your comments to the experiment are shown if you type text, or set them as text('my best experiment'). The contents of the working directory are shown if you type ls. Any man output, as well as errors or analysis results will appear here.