VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu May 04 2006 - 16:58:04 CDT

Shirley,
  I don't have such a script written yet, but it'd probably be a
straightforward thing to write so long as the structures have identical
topology, sequence (e.g. the easy case...). The existing VMD scripts that do
this sort of thing work well for MD trajectories because they match this
criteria. If you have structures that aren't so nicely related, you may
have to resort to other approaches. The multiple alignement extension in
VMD will deal with alignment of structures that aren't so nicely similar,
but has no scriptable text-only interface presently. If your structures
meet the "easy" criteria I described up top, then you could probably just
adapt one of the alignment scripts others have already written for your
purpose. These two scripts are good starting points for your reference:
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/fitframes/
  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/frame_rmsd/

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, May 04, 2006 at 12:16:19PM -0700, Shirley Li wrote:
> Hello John,
>
> I have a question about multiple structure superimposition. I have thousands of structures, and need to superimpose them n BATCH mode, without the need to open VMD graphic interface. I would like the output of both the RMSDs and the coordinates after superimposition. In the superimposition, I want to exclude all hydrogen atoms.
>
> I saw your comments by using "vmd -dispdev text -eofexit < input.tcl > output.log". I wonder if you have a sample "input.tcl" script.
>
> Your help will be greatly appreciated.
>
> Sincerely,
>
> Shirley
>
>
> ---------------------------------
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-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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