VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 22 2010 - 11:05:53 CDT

Hi,
  You may find it easier to first write out the structure that you move
to a new file, and then simply use the "mergestructs" plugin, or merge them
then move and write a new file, whichever works best for your intended purpose:
  http://www.ks.uiuc.edu/Research/vmd/plugins/mergestructs/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Mar 19, 2010 at 09:29:56PM -0700, Bernardo Sosa Padilla Araujo wrote:
> Hi All,
>
> I have two pdb files:
>
> -one of them with an enzyme and its substrate
> -the second one only has a very similar substrate( no enzyme)
>
> I want to load both pdbs, align the substrate from the second pdb to the
> substrate in the first pdb, and finally write a pdb file containing the
> enzyme (from the first pdb) and the substrate from the second pdb but in
> the same position(with respect to the enzyme) as the substrate in the
> first pdb.
> I have in mind this script :
>
> #molecule 0 is the enzyme +substrate
> #molecule 1 is the other substrate
> #BAS is the resname of the substrate
>
> # Create a reference structure
> set ref [atomselect 0 "resname BAS"]
>
> # Create a selection to align
> set sel [atomselect 1 "resname BAS"]
>
> # Move molecule 1 onto molecule 0
> set all [atomselect 1 all]
> $all move [measure fit $sel $ref]
>
> In order to use writepdb I need to have everything in one selection, but I
> don't know how to put structures form different pdb in one vmd slection.
> Does anyone know how to do/circunvent this ?
> Thanks a lot in advance,
>
> Bernardo
>
> 

-- 
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
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078