VMD-L Mailing List

From: J. Nathan Scott (scottjn_at_chemistry.montana.edu)
Date: Thu Oct 27 2011 - 13:13:09 CDT

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