From: Ran Friedman (r.friedman_at_bioc.unizh.ch)
Date: Wed Jan 31 2007 - 03:33:36 CST

Thanks everybody.'animate delete all' did the work.

Ran.

Axel Kohlmeyer wrote:
> On Tue, 30 Jan 2007, Ana Celia Araujo Vila Verde wrote:
>
> ACAVV> I'm not sure I understand what you mean (for most NAMD and VMD
> ACAVV> users, the structure file is the psf file, which contains
> ACAVV> connectivity but not coordinates; the pdb is the coordinate
> ACAVV> file).
>
> ana,
>
> please note, that indeed the .psf file contains the structure
> information but no coordinates. however many other packages have
> the equivalent information in a format that VMD does not support,
> but do support .pdb or .gro or .xyz files. you can still extract
> or guess the essential information (atom and residue name, bonding)
> for those files, but VMD also reads the coordinates that do not
> correspond to what the trajectory is about.
>
> now to alleviate that situation in a convenient fashion, there
> is a number of options.
>
> a) you can read the .gro, .pdb, .xyz file first and then just
> do an 'animate delete all' (in the VMD console) and then read
> the rest of the trajectory.
> b) you read the .gro, .pdb, .xyz file once and then just save
> a (minimal) .psf file. this file will not be suitable for simulations,
> but will contain all information needed for visualization and
> not coordinates. so for all future uses it can replace the
> coordinate containing file with the structure information.
> c) you read everything in, right click on the molecule in
> the vmd main menu and delete the frame 0.
>
> a) is easiest for scripting
> b) is cleaner, if you can re-use the structure
> information frequently.
> c) is the GUI solution.
>
>
> cheers,
> axel.
>
> ACAVV>
> ACAVV> In any case, in the "molecule file browser" window you can choose
> ACAVV> to load only the first frame of a dcd (just choose " first 1" and
> ACAVV> "last 1")
> ACAVV>
> ACAVV> Also, have a look at the information on the "mol new" command in
> ACAVV> the VMD manual. And, if you haven't yet done the VMD tutorial,
> ACAVV> you should definitely do it. It will save you time in the long
> ACAVV> run.
> ACAVV>
> ACAVV> Ana
> ACAVV>
> ACAVV> _________________________________
> ACAVV> Ana Célia Araújo Vila Verde
> ACAVV> Penn State University
> ACAVV> Department of Chemical Engineering
> ACAVV> Fenske Laboratory
> ACAVV> University Park, PA 16802
> ACAVV> USA
> ACAVV>
> ACAVV>
> ACAVV> Phone: +(1) (814) 863-2879
> ACAVV> Fax: +(1) (814) 865-7846
> ACAVV> avilaverde_at_engr.psu.edu
> ACAVV> http://www.che.psu.edu/Faculty/JMaranas/group/avv.html
> ACAVV> http://www.gfct.fisica.uminho.pt/Members/acvv
> ACAVV> _________________________________
> ACAVV>
> ACAVV>
> ACAVV>
> ACAVV> -----Original Message-----
> ACAVV> From: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] On Behalf Of Ran Friedman
> ACAVV> Sent: Tuesday, January 30, 2007 7:12 AM
> ACAVV> To: vmd-l_at_ks.uiuc.edu
> ACAVV> Subject: vmd-l: Delete frames in a script
> ACAVV>
> ACAVV>
> ACAVV> Dear VMD users/developers,
> ACAVV>
> ACAVV> 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.
> ACAVV>
> ACAVV> Thanks,
> ACAVV> Ran.
> ACAVV>
> ACAVV>
>
>

-- 
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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
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