VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed Aug 17 2011 - 10:13:09 CDT

maria,

On Wed, Aug 17, 2011 at 5:05 AM, maria goranovic
<mariagoranovic_at_gmail.com> wrote:
> Dear List,
> I am labeling aa residues in my pdb file in VMD. Is it possible for me to
> modify the %R%d label, such that I can do some arithmetic on the residue
> number? For example, I want ARG220 to be shown as ARG228 by using something
> like %R%(d+8). To make the problem simpler, can I add 8 to all my residue
> numbers in the labels without modifying the original pdb file or the

you cannot do this with a label command, but you can
do this with tcl scripting.

> trajectory? This is useful because in a simulation, residue numbering may
> start from 1 even though  the residue numbering does not start from 1 in the
> original pdb

a program that requires this numbering is a broken program.
the residue id is just a label and there is no requirement in
the pdb standard that it has to start from 1 or be consecutive.
it only has to match the sequence (which may be incomplete
in the crystal structure). in VMD you have to be very careful
to not mix up the "residue" property with the "resid" property.
the former is generated by VMD, cannot be changed and is
consecutive and starts at 0, while the latter is literally imported
from a .pdb file and can be reset at any time.

axel.

> I could not find any previous posts on the list about this,
> Thank you
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.