VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri Jan 08 2010 - 08:49:01 CST

On Fri, 2010-01-08 at 14:56 +0100, Vlad Cojocaru wrote:
> Dear VMD developers,

dear vlad,

> Is it possible to change the VMD code such as to allow negative numbers
> in selection strings using the keyword 'resid' ?
> In many PDB files, residues that were added at the N-terminus of a
> protein for the purification are labeled with negative resids. Currently
> VMD does not allow negative 'resids' in selection strings. However the

correction. VMD _does_ allow it. at least the version i have on
my desktop. try 'resid "-1"' or "resid < 0".

> command "[ atomselect $molid "$string" ] get resid" outputs a list which
> contains the negative 'resids'. This creates a bit of confusion in
> scripts that process pdb files with negative 'resids'

well, this is indeed a bit of a problem. the scripts will have to be
"fixed up" to be safe to use with negative resids. there are other
issues, many more severe than what you are reporting, with many
scripts that make assumptions about the kind of information they
get from a molecule. please see it as a motivation to produce
examples documenting the problems and upload them to the VMD biocore
biofs with a note to vmd_at_ks.uiuc.edu or even better consider fixing
the scripts by yourself and hand in the resulting changes.

a _lot_ of the existing plugins are not perfect and barf on unusal
or unexpected input. no developer can take care of that, since for
the most part one cannot imagine what other people might want to do.
this is a task for the VMD user community to step up and contribute.

cheers,
   axel.

cheers,
    axel.

> Best wishes
> Vlad
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.