VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Aug 22 2007 - 15:04:15 CDT

Hi,
  Please make a selection on "resid 247" and verify you don't
have duplicate resids. In general, don't use selections based only on
"resid" if you need to get a unique residue, as some structure file
formats (e.g. PDB) don't gaurantee uniqueness.
Use "residue" instead, which is the VMD-internal guaranteed unique
numbering, and adjust your selection accordingly.

For trajectory animations, you may wish to enable the "update selection"
checkbox in the trajectory tab, and it will re-evaluate the selection
based on the new atom positions, which will allow you to focus on a
region of interest.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Aug 22, 2007 at 03:28:53PM -0400, Mark Zottola wrote:
> I have two questions concerning VMD.
>
> After loading a GROMACS-generated pdb file and trajectory into VMD I issue
> the command "all within 10 of resid 247". This results in a "ball" of
> protein atoms and water molecules - all well and good. However, I also get
> a "ball" of waters (only water) separate and distinct from the expected and
> desired selection. Unless this is a bug, I am obviously missing something.
>
>
> Second, I would like to watch the dynamics of that previous
> selection. Since the ball of unwanted waters is far from the
> protein/solvent of interest, I figured I would let the simulation run.
> However, What I apparently observe is the motion of all the waters slowly
> diffusing away from their original position. Is there any way of simply
> focusing in on a region of the ensemble and simply watching the atoms that
> exist *within that region*?
>
> Thanks!
>
>
> Mark 

-- 
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