VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Aug 24 2004 - 09:33:01 CDT

Hi,
  It sounds like you're getting something wrong in the atom selections
you're passing into 'measure fit', as you shouldn't be getting an identity
matrix if they aren't exact copies in the same position in space.
One way to visually check all this is to use the same atom selections to
highlight the two segments in different colors on the display. If you're
still unable to solve the problem, it'd be easier to help you if we saw
the structure file and the sequence of commands you're running that yields
the identity matrix.

  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 24, 2004 at 04:46:56PM +0300, vivek sharma wrote:
>
> Sir,
>
> I have a problem.
>
> I am trying to superimpose two same segments but with different pdb files
> i.e. different coordinates using 'measure fit' and 'move' commands but
> 'measure fit' command produces the identity transformation matrix (as these
> two pdbs are similar in 3D-arrangement but with different coordinates) and
> as this is a identity transformation matrix no change takes place by 'move'
> command.
>
> How to deal with such problem? say, I want to move third fragment using this
> transformation matrix.
>
> please suggest some solution.
>
> thanks in advance,
>
> sincerely,
>
> --
> VIVEK SHARMA
> HBG BI 

-- 
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