VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Jun 05 2006 - 10:34:29 CDT

Hi,
  Alignment of large and small structures is done in exactly the same way.
Which method did you use previously? If you're using one of the graphical
alignment tools, it would help to know which one you're using.
(e.g. RMSD, RMSDTT, Multiple Alignment, or scripts...)

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Jun 05, 2006 at 02:16:47PM +1000, Alexe Bojovschi wrote:
> Hi All,
>
> Can you please let me know how can I align small molecules using VMD?
> I did some alignments of proteins, but I can't figure out how to align
> small molecules as Adenosine.
>
> Thank You!
> Alex
> Small molecules alignment with VMD
>
> >******************************************************************
> >* Alexe Bojovschi - PhD student
> >* Centre for Molecular Simulation
> >* Swinburne University of Technology
> >* P.O. Box 218 Hawthorn
> >* Victoria 3122 Australia
> >* Tel: +61 3 9214 4892
> >* Fax: +61 3 9214 5075
> >* http://www.it.swin.edu.au/centres/cms/
> >* www.geneyas.com
> >* Beauty in things lies in the mind which contemplates them.
> >****************************************************************** 

-- 
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