VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sat Nov 03 2007 - 23:30:57 CDT

Hi,
  Luis' RMSDTT plugin can do the both of the alignments you're asking about
without having to write scripts etc. Please see the documentation for
it here:
  http://www.ks.uiuc.edu/Research/vmd/plugins/rmsdtt/

Read the section "calculation type", and "reference molecule" in particular.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 01, 2007 at 03:52:12PM -0600, Zhaochuan Shen wrote:
> Hi all,
>
> I have two quesiotns:
>
> 1) For all the scripts posted on the website and plugins about RMSD, there
> are feature about alignment. Why people want to do alignment? How people do
> this? The scripts are not very clear. Just "measure fit" and then "move".
> 2) I have a long trajectory (100000 frames) and want to find out RMSD
> for some alpha carbons. The reference is average coordinate. Is there any
> standard process? What I did is exprot the trajectory and then use RMSDTT
> plugin directly. Do I need to do the alignment? Or anyone can give a
> standard process? Thanks!
>
> Wishes,
> Zhaochuan 

-- 
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