VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 23 2006 - 11:13:26 CDT

Hi,
  Yes, the order of atoms matters. The order of the atoms in your two
selections must be the same in order for any of measure commands that
do things like rmsd, rmsd, rms fitting, etc. If the order of the atoms
isn't consistent, you'll get nonsense results. You can give VMD an
extra "order" parameter which reorders the second selection if you
need to match up atom selections from fairly dissimilar structures.

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jun 22, 2006 at 09:36:59PM -0400, dwang_at_cs.kent.edu wrote:
> Hi,
>
> Currently I am working on a project involve superimposing two sets of
> atoms from two proteins. I just wonder when we do the "measure fit", does
> the order of the atoms within the same set matters? I noticed that when I
> use the "list" option, the atoms are ordered in the increasing order. So
> the correspondence between two lists seems lost. I suppose the algorithm
> will treat all the atoms within one set equally, and try to minimize the
> RMSD between the two atom sets.
>
> thanks a lot
>
> Dong Wang 

-- 
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