AMBER Archive (2001)

Subject: RE: movie for subset of atoms

From: DeLano, Warren (warren_at_sunesis.com)
Date: Thu Aug 30 2001 - 16:32:53 CDT

You would have to save the entire trajectory in PDB format, but if you
then load it into PyMOL, it can do this on-the-fly with a command like:

show (resi 1:5 or (byres (resn WAT and (resi 1:5 around 6))))

Assuming you want to see waters within 6 A of residues 1:5.

If you trajectory is huge, the it would make sense to first run PyMOL in
batch/command mode in order to generate the subset, and then load the
result into interactive PyMOL.

http://pymol.sourceforge.net

Cheers,
Warren 

--
mailto:warren_at_sunesis.com
Warren L. DeLano, Ph.D.
Informatics Scientist
Sunesis Pharmaceuticals, Inc.
341 Oyster Point Blvd.
S. San Francisco, CA 94080
(650)-266-3606 fax: (650)-266-3501

> -----Original Message-----
> From: Anton B. Guliaev [mailto:anton_at_vostok.lbl.gov]
> Sent: Thursday, August 30, 2001 1:42 PM
> To: amber_at_heimdal.compchem.ucsf.edu
> Subject: movie for subset of atoms
> 
> 
> Dear Amber Users,
> 
> I would like to create a movie based on MD trajectory for only a 
> subset of atoms. Let say RES 1-5 and a couple of solvent molecules 
> out of system with 240 residues in a water box. The programs i used 
> so far let me do it only if I recreate the new topology (or 
> .parm in case 
> of VMD) file and load it together with the new (modified) coordinate 
> stream.
> Is there any way to do it without creating a new .top file? 
> 
> Thanks a lot,
> 
> Anton
>         *******************************
>         *   Anton B. Guliaev, Ph.D    *
>         *   Life Sciences Division    *
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