VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jan 30 2007 - 11:00:41 CST

What about using the "animate" command?

2007/1/30, Ran Friedman <r.friedman_at_bioc.unizh.ch>:
> Dear Ana, VMD users,
>
> I'm trying to do this automatically, in a script, and delete the first
> frame after everything was loaded:
>
> 1. Read the coordinates (pdb, gro or cor)
> 2. Read a trajectory (xtc or dcd)
> 3. Delete only frame zero, which corresponds to the structure file
>
> Therefore, the molecular file browser won't help me, as far as I
> understand. I checked the "mol" command but didn't find any help there.
> Sorry if I wasn't clear.
>
> Ran.
>
> Ana Celia Araujo Vila Verde wrote:
> > I'm not sure I understand what you mean (for most NAMD and VMD users, the structure file is the psf file, which contains connectivity but not coordinates; the pdb is the coordinate file).
> >
> > In any case, in the "molecule file browser" window you can choose to load only the first frame of a dcd (just choose " first 1" and "last 1")
> >
> > Also, have a look at the information on the "mol new" command in the VMD manual. And, if you haven't yet done the VMD tutorial, you should definitely do it. It will save you time in the long run.
> >
> > Ana
> >
> > _________________________________
> > Ana Célia Araújo Vila Verde
> > Penn State University
> > Department of Chemical Engineering
> > Fenske Laboratory
> > University Park, PA 16802
> > USA
> >
> >
> > Phone: +(1) (814) 863-2879
> > Fax: +(1) (814) 865-7846
> > avilaverde_at_engr.psu.edu
> > http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
> > http://www.gfct.fisica.uminho.pt/Members/acvv
> > _________________________________
> >
> >
> >
> > -----Original Message-----
> > From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Ran Friedman
> > Sent: Tuesday, January 30, 2007 7:12 AM
> > To: vmd-l_at_ks.uiuc.edu
> > Subject: vmd-l: Delete frames in a script
> >
> >
> > Dear VMD users/developers,
> >
> > How can I delete frames from a trajectory in a script after these have been loaded? For example, if I want to load a .xtc or .dcd file, I should first upload a .gro, .pdb or .cor file and then the xtc or dcd. I want to get read of the first frame which corresponds with the structure file.
> >
> > Thanks,
> > Ran.
> >
> >
>
>
> --
> ------------------------------------------------------
> Ran Friedman
> Postdoctoral Fellow
> Computational Structural Biology Group (A. Caflisch)
> Department of Biochemistry
> University of Zurich
> Winterthurerstrasse 190
> CH-8057 Zurich, Switzerland
> Tel. +41-44-6355593
> Email: r.friedman_at_bioc.unizh.ch
> Skype: ran.friedman
> ------------------------------------------------------
>