VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Oct 12 2005 - 17:54:13 CDT

Hi,
  If these molecules share significant structure, you could probably
use RMS fitting to align them reasonably closely. Have you tried doing
this yet? It's described in the VMD tutorials on the web site if you
need examples. If that isn't possible, you could do some rough alignments
by using this command to get the COM for a selection:
  set sel [atomselect top all]
  set com [measure center $sel weight [$sel get mass]]

>From there you could use this to move it's COM to the origin:
  $sel moveby [vecscale -1.0 $com]

Once you've got the COM's roughly aligned, you can force VMD
to recalculate the view with the new coordinates:
  display resetview
  display update ui

>From there, you should be in a better position if it has to be
done by hand and can't be done with RMS fitting for some reason.

  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Oct 05, 2005 at 07:13:53PM +0200, pascal.baillod_at_epfl.ch wrote:
> Dear community,
>
> In my tcl script, I translate molecules in order to carry out a superposition,
> so that
>
> 1) my collection of molecules first has to be dragged back to the middle (they
> are not at all visible on the display after I run my script).
>
> 2) I then have to center the rotation on an atom of a molecule, in order study
> the molecule by rotating it uppon itself. I also carry out this second step
> with the mouse, "mouse" menu, "center".
>
> Is it possible to automate these two steps with some tcl command to add to my
> script?
>
> Thank you very much for any help!
>
> Pascal
>
>
>
> *******************************************************************************
> Pascal Baillod (PhD student)
> *******************************************************************************
> Swiss Federal Institute of Technology EPFL Tel: +41-(0)21-693-0322
> Institute of Chemical Sciences and Engineering , Fax: +41-(0)21-693-0320
> Laboratory of Computational Chemistry and Biochemistry pascal.baillod_at_epfl.ch
> Room BCH 4121, Avenue Forel, http://lcbcpc21.epfl.ch
> CH-1015 Lausanne
> *******************************************************************************
> 

-- 
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