VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 11 2011 - 12:24:10 CST

Hi,
  The structure analysis and residue/fragment classivication done by
VMD is in the hard-coded C/C++ portion of the code, and cannot be changed
without recompiling the program presently. You might be able to get around
this problem in various ways without changing the VMD source code,
but I'd have to know much more about your structure and the unusual residue
to be able to provide any useful suggestions.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Oct 27, 2011 at 12:13:09PM -0600, J. Nathan Scott wrote:
> Hello all,
>
> I know this must have been asked before, but my Google-fu has alas failed
> me repeatedly. Is there a way to add a new three letter residue name to
> VMD such that it will recognize that residue as protein? The issue I've
> run into is that I have a Tcl script which works it way through each
> protein residue and water molecule and ion assigning a value to User
> (based on external data that I load) which I then use to color each
> residue/molecule. However, it appears that my new residue is not
> recognized as protein and so I end up with a mismatch when I try to assign
> the user list I've put together to my $prot selection.
>
> I noticed these warnings involving my new residue when I closed VMD, I'm
> not sure how important they are (the bonds between my new residue and its
> 2 neighbors look perfectly fine in VMD):
>
> Warning) Unusual bond between residues: 65 (protein) and 68 (none)
> Warning) Unusual bond between residues: 68 (none) and 69 (protein)
>
> Can someone suggest a fix for this? Is there a simple file somewhere that
> I can my three letter residue name to? Thanks in advance for any help,
> this is the last issue holding me up on this reworked Tcl script.
>
> --
> ----------
> J. Nathan Scott, Ph.D.
> Postdoctoral Fellow
> Department of Chemistry and Biochemistry
> Montana State University 

-- 
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