VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Oct 28 2008 - 09:17:03 CDT

On Mon, 27 Oct 2008, Brian Kidd wrote:

BK> hello,
BK> i have a number of pdb files that make up a trajectory and i wanted to use
BK> the beta and occupancy columns as variables that contain information about
BK> the state of particular atoms. in principle, i should then be able to use
BK> the beta or occupancy coloring method and the atoms ought to change color
BK> during the trajectory in correspondence with their beta or occupancy values.
BK> however, when i load a set of pdb files and a psf file into vmd, the beta
BK> and occupancy values match the numbers in the last pdb file and are constant

brian,

this is a known and frequently discussed property of VMD.
data fields like mass, charge, beta, occupancy are stored
once per molecule. the only data fields that are once per
time step are x, y, z, and user. only the latest alpha test
versions add to this (e.g. multiple user files and velocities).

all you'd have to do is to load your pdb files one by one
and then copy the beta/occupancy into user.
set sel [atomselect top all]
$sel set user [$sel get beta]

or with the alpha version even:

$sel set {user user2} [$sel get {beta occupancy}]

for other methods and examples of how to use "user"
please have a look at, e.g., the following pages.

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part3.html#chap5_sect3

http://www.theochem.ruhr-uni-bochum.de/~axel.kohlmeyer/cpmd-vmd/part4.html#chap6_sect4

cheers,
    axel.

BK> throughout the entire trajectory. this statement has been verified by
BK> querying the beta and occupancy values for various frames in the trajectory.
BK> is there a way to use the information in these columns as i've outlined?
BK> does vmd simply discard this information for all the other frames?
BK>
BK> thanks,
BK> -brian
BK> 

-- 
=======================================================================
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
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