VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Mar 21 2006 - 10:16:00 CST

Hi,
  You can transform an atom selection by a 4x4 matrix with the
the "atomselect move" command:
  http://www.ks.uiuc.edu/Research/vmd/current/ug/node177.html#13498

Once transformed, you can write out the piece of structure with
$sel writepdb, load it into psfgen, etc...

If you feel enterprising, this could potentially be entirely automated
with scripts, as the test versions of VMD 1.8.4 retain PDB REMARK lines
which typically contain the necessary transformation matrices, which
can be queried (one huge string) with 'molinfo top get remarks',
for example.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Mar 21, 2006 at 08:39:31AM -0400, Osmany guirola Cruz wrote:
> Hi
> I have a pdb file(single unit of a viral capside) that have some matrix
> inside....how can i generate the complete structure of the capside using
> that matrix.?
> Thanks
>
> Osmany
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
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