VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 05 2003 - 23:00:52 CDT

Ioana,
  What I was trying to suggest in my previous email, is that
you're having problems _because_ you're forwarding your
display to a different machine. Try running it on the console
of the machine and you'll probably be ok. I believe the 'dgl'
error you got is caused by forwarding the display connection.

Regarding getting Z coords, you can use the 'atomselect' command
in VMD to retrieve coordinates as in an example along these lines:
  set sel [atomselect top "all"]
  $sel get z

You may also wish to set the active frame and other things but
the concept is similar. This is all documented in the VMD
User's Guide.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 05, 2003 at 08:32:21PM -0700, Ioana Cozmuta wrote:
> Hi John,
>
> I am running the vmd on another machine by forwarding the graphical
> display on my station. Moreover I understood that the machine (it is a
> mass storage) moves files biger than a certain size on tape automatically
> so when the files are used they are read from the tape. Do you think that
> this delay causes the trouble I've got?
>
> I am using this opportunity to ask another question:
> I want to retrieve the z coordinate of a couple of atoms from the NAMD
> generated dcd (trajectory) file. What is the way to do this (I wrote out
> the trajectory in binary format)?
>
> Thank you,
> Ioana
>
>
>
> On Tue, 5 Aug 2003, John Stone wrote:
>
> >
> > Ioana,
> > That looks like a low level error in dmconvert. The "dgl" error
> > sounds like it may require that you be running it locally on the
> > console of the SGI, since "dgl" is the SGI way of doing their
> > proprietary graphics stuff, potentially employing hardware
> > video codecs etc. Did you run all this on the console of
> > your SGI?
> >
> > Thanks,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> > On Tue, Aug 05, 2003 at 04:04:15PM -0700, Ioana Cozmuta wrote:
> > > Hi,
> > >
> > > I am trying to make an mpeg (dmconvert) movie using the vmdmovie menue but
> > > I get the following error.
> > >
> > > Converting frames from rgb format to ppm... Converting frames to SGI
> > > MPEG-1 video format dmconvert -v -f mpeg1v -p video,rate=24 -n
> > > /u2/ioana/calibr_meas/1K/diff_1K/movieK.####.ppm,start=0,end=9,step=1
> > > /u2/ioana/calibr_meas/1K/diff_1K/movieK.####.ppm
> > > /u2/ioana/calibr_meas/1K/diff_1K/movieK.mpg
> > > bgerror failed to handle background error.
> > > Original error: -------- Scanning input ... dgl error (read): <bad
> > > errno = 0>
> > > Error in bgerror: invoked "break" outside of a loop
> > >
> > > Does anyone have any idea what is causing this error?
> > >
> > > Thank you,
> > > Ioana
> >
> > --
> > 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
> > 

-- 
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