VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 22 2005 - 11:11:44 CDT

Hi,
  You can do RMS alignments in VMD with one of several methods.
The VMD molecular graphics tutorial includes basic instructions for
doing this with text commands (see "aligning two molecules"):
  http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node3.html

You can also do this with the Analysis->Multiple Alignment
or Analysis->RMSD Calculator extensions included in VMD 1.8.3,
or with the RMSDTT extension here:
  http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/

  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Aug 19, 2005 at 02:26:32PM -0700, Kara Di Giorgio wrote:
> I'm trying to overlay two drug molecules in a binding site of a DNA
> strand from a pdb file. I've read in the manual that you can overlay
> structures in VMD, but I've never been able to understand how to get it
> to work. I've been getting help with this from a friend who knows
> MIDAS. In MIDAS it's relatively easy, you give it the match command
> and then pick the four atoms of each structure you want to match.
> However, the computer that has MIDAS is not convenient to access ( a
> VERY old SGI) and I'd like to be able to do something similar on my
> Mac. Has anyone done this before and would someone be willing to talk
> me through it?
>
> Thank you in advance,
>
> Kara Di Giorgio
> University of the Pacific 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078