VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri May 28 2010 - 13:32:38 CDT

Hi,
  I don't have any knowledge of the details of how Desmond files
are organized, but my suspicion is that they do not maintain original
residue sequence, or that the maeffplugin or dtrplugin code may not
communicate the structure into VMD with the residues organized
in the same sequence they should be. VMD itself doesn't do anything
unusual with the sequence or ordering of residues, so in any normal
circumstance I would expect them to be listed in the correct order.
If the ordering you see is different than you expect, it may be worth
delving into the details of how this information is stored in the
Desmond file formats and whether or not the existing VMD plugins are
correctly interpreting this information when it is read in. We didn't
develop the Demond related plugins, they were a kind donation by the
folks at D. E. Shaw Research. I could ask them about this but without
example files to provide them for testing, I'm afraid they will have all
of the same questions I do about what might be going on here. Perhaps
the best thing would be for you to provide an example structure that
illustrates your problem, and then provide the expected residue sequence
and the actual residue sequence you see in the VMD plugins. With this
information, someone might actually be able to help track down what is
happening with your files.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, May 28, 2010 at 08:29:55AM -0400, Sally Fisher wrote:
> Hi all,
>
> This is a follow-up on a question I asked earlier. VMD does not seem to be
> assigning the residue numbers properly for my desmond files upon import,
> causing the sequence to be displayed completely out of order in Multiseq
> and Sequence Viewer. Should I be concerned about my structure files? Is
> there anyway to correct this issue?
>
> Thanks,
> Sally Fisher
> Department of Chemistry
> University of Richmond, VA 23173 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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