VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Mar 18 2012 - 12:26:39 CDT

Hi,
  I think you're going to want to compute the RMSD in a residue-by-residue
manner, assigning the resulting RMSD values to one of the per-atom fields,
such as beta, and then coloring by the field you stored the RMSD into.
I believe there's a simple residue-by-residue RMSD example script included
in the NAMD tutorial that can be made to do what you want:
  http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/index.html
  http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-unix-html/node13.html

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Mar 18, 2012 at 12:47:36PM +0100, George Tzotzos wrote:
> I'm a novice to VMD and would be most grateful for any guidance.
>
> I'm trying to work out the parts of a structure that shows the greatest rms deviation during a trajectory as compared to the crystallographic structure. I couldn't see how this could be done by means of the RMSD trajectory tool. Probably it cannot.
>
> Is there a script available that can handle this? Or an alternative plug in?
>
> Thank you in advance for any help
>
> George 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078