VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 18 2002 - 15:23:35 CST

Dear Yufang,
  The first error message you got was due to replacing the default
"xmgr %s" command with an empty command. VMD gives this (admittedly
confusing, and soon to be improved!) error message to indicate that
it has to have a command with which to graph the data. I'll update
the new VMD code to give a more useful/understandable error message
right now.

As for your second question: VMD expects to find Xmgr or Grace on your
computer, which are the free graphing packages it knows how to support
internally. In truth, you could use any graphing program that can read
the simple one line per data point 2-d graphs that VMD normally uses.
To use another program, replace 'xmgr' with the command to run your
alternate graphing program, and leave the %s, as that's the filename
VMD will insert when it runs the graphing program.

To see what the file VMD generates looks like, try this for a graphing
command on a Unix machine :-)
  cat %s

The format of the file is:
 X0 Y0
 X1 Y1
 ...

Where the X values are the timestep indices in VMD, and the Y values
are the measured lengths, angles, and dihedrals over the trajectory.

Let us know if you need more help getting this going.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Mar 17, 2002 at 03:03:41PM -0600, Yufang Wang wrote:
> Hello,
>
> When I tried to use graph button on label form, I had the error message:
> ERROR) label graph must specify a filename
>
> Should I specify a filename in 'Graph Command' or how?
> I used 'xmgr %s' in 'Graph Command', and got another error message: Bad
> command or file name
>
> So, actually how can I use the 'Graph' button correctly?
>
> Yufang
>
>
>
> _________________________________________________________________
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349              
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078