VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 27 2007 - 14:25:01 CDT

Fred,
  The B and C representations you're describing appear to have
the same selection text from your note below. That being the case,
if they reference the same frame of the same molecule, then I
would expect them to select exactly the same atoms.
If you have enabled "update selection every frame" in the Trajectory
tab of the graphical representations window, this will no longer
be true however, since your Z coordinate selection criteria might
not be the same for both representations. I suggest you look at
your representation settings carefully and make sure that you don't
have one set to update dynamically while the other is not, or some
other similar variation. Another way this could conceivably happen would
be by (re)loading the same PDB into separate molecules, and toggle
one of them "inactive" (the "A" in the main molecule menu status line)
and and have dynamically updating atom selections enabled, causing
them to get out of sync. Let us know if you need more help with this.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 27, 2007 at 12:06:21PM -0700, Fred Moore wrote:
> 2nd posting from a newbie to VMD.
>
> I'm running the latest version on a macintosh pb 12" powerpc with the
> latest osx.
>
> I'm trying to view and animate a .pdb file full of chloroform
> molecules. 475 molecules per frame, 2500 frames. The .pdb file names
> the atoms in each molecule:
>
> C1, CL1, CL2, CL3, H
>
> Those names show up properly when I go to Graphics->Representations
> and look under "keyword".
>
> In trying to view and represent these critters I've used different
> representations.
>
> A: style: CPK, color:Element, Selection: all
> B: A: style: CPK, color:Element, Selection: { same residue as (name
> C1 and z>19 and z<61)}
> C: A: style: licorice, color:Name, Selection: { same residue as (name
> C1 and z>19 and z<61)}
>
> I have turned off the display of representation "A" by double
> clicking on it. B and C are turned on.
>
> Here's the newbie question: Should those two representations be
> showing the same molecules? I must be missing something because
> they're not.
>
> It's not the coloring or drawing method either, as I can make them
> identical and the two representations still show different molecules.
>
> What am I missing?
>
> Thanks in advance,
>
> Fred M. 

-- 
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