VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 18 2006 - 12:58:30 CDT

Vlad,
  You need to fix a couple of problems with that script.

The version you posted creates a new selection at each frame, which is
very slow, and unnecessary unless you're fundamentally changing what
is selected for each frame. In general, you want to use '$sel update'
for position-based selections (faster than re-creating from scratch), or
'$sel frame' for the simplest case (the one below) where the selected atoms
remain constant, and you're just stepping through frames.

Your original script also leaked selections, since they were not being
deleted within the loop. I wasn't sure why you placed the extra braces
around your variables, as that shouldn't be necessary, but I've left those
parts as you wrote them.

Try this version instead (or something like it):

 set numframes [molinfo 0 get numframes]
 set ref [atomselect 0 "resid ${resid_ref}"]

 for {set frame 0} {${frame} < ${numframes}} {incr frame} {
    $ref frame $frame
    set com_ref [measure center ${ref} weight mass]
 }
 $ref delete

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 18, 2006 at 07:35:14PM +0200, Vlad Cojocaru wrote:
> Dear vmd users,
>
> I am trying to retrieve the center of mass of a residue during a
> trajectory. However, the script below will give me only the CoM for the
> last frame. Is there a way to modify this script such as to retrieve the
> CoM for each frame?
>
> Thanks
>
> Best
> vlad
>
> set numframes [molinfo 0 get numframes]
> for {set frame 0} {${frame} < ${numframes}} {incr frame} {
> set ref [atomselect 0 "resid ${resid_ref}" frame ${frame}]
> set com_ref [measure center ${ref} weight mass]
> }
>
> --
> Dr. Vlad Cojocaru
> EML Research gGmbH
> Molecular and Cellular Modeling Group
> Schloss-Wolfsbrunnenweg 33
> 69118 Heidelberg, Germany
> Phone: +49-6221-533266
> Fax: +49-6221-533298
> e-mail: Vlad.Cojocaru_at_eml-r.villa-bosch.de
> http://projects.villa-bosch.de/mcm/people/cojocaru/
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078