VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Jan 30 2007 - 11:13:14 CST

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> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.