VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Apr 01 2007 - 23:07:46 CDT

Hi,
  Do I understand you correctly that you have identical copies of
the same nucleotide in both structures? Or, are you saying you need
to dock the two structures (with no corresponding identical
nucleotide structure to use for alignment)? In the first case, you could
use the 'measure fit' command to compute an alignment transformation matrix.
You can read the various VMD tutorials and the VMD User's Guide to learn how
to do this type of alignment.

In the second case, I'm afraid VMD doesn't really contain any
built-in functionality for that purpose, and you'll have to consult other
software packages or databases to perform that kind of alignment.

  John Stone
  vmd_at_ks.uiuc.edu

On Sat, Mar 31, 2007 at 09:43:07AM -0400, zhangh1_at_umbc.edu wrote:
> Hi all:
> I have one protein with a single nucletide in the active side. I have
> another whole sequence nucleic acid which is supposed to bind protein with
> the specific nucletide. Two molecules are far away, and sequentially
> irrelavent. How do I overlap that specific nucletide between them in VMD?
> Thanks. 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
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