VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Fri May 28 2010 - 08:24:45 CDT

On Fri, 2010-05-28 at 08:29 -0400, Sally Fisher wrote:
> Hi all,

dear sally,

> 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?

at the moment, it is not even clear that there is
an issue. you'll first have to provide some examples
and explanations that document the difference between
what you see and what you expect.

in my experience, a lot of the confusion about residue
numbering goes back to people not understanding correctly
what VMD shows them where. every once in a while a legitimate
problem shows up and then this can be fixed, if there is
a way to reproduce it.

sequence numbers are typically ignored in simulations
(unless you use them for special purposes).

cheers,
   axel.

>
> Thanks,
> Sally Fisher
> Department of Chemistry
> University of Richmond, VA 23173 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com
http://sites.google.com/site/akohlmey/
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.