VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon May 08 2006 - 18:21:19 CDT

Yes, if you do the $sel move steps etc in the correct order, you can then
immediately use the updated coordinates in a subsequent rmsd calculation.

  John Stone
  vmd_at_ks.uiuc.edu

On Mon, May 08, 2006 at 02:50:55PM +0000, ziemys_at_ecr6.ohio-state.edu wrote:
> Hi,
>
> I want to calculate RMSD of subset AFTER I "fit" and "move" ? Say, I fit the protein in each frame and move the whole system :
>
> $p_mov frame $i
> $p_ref frame [expr $i - 1]
> $sys_m frame $i
> $sys_r frame [expr $i - 1]
> $sys_m move [measure fit $p_mov $p_ref]
>
> Will I get the new coordinate values for RMSD calculation of subset in system, if i will try something like:
>
> set x [atomselect top "index 1" frame $i]
> set y [atomselect top "index 1" frame [expr $i - 1]]
> puts "[measure rmsd $x $y]"
>
> If not, then how to access the coordinates of moved selections ?
>
> Arturas
>
> 

-- 
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