VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Mar 08 2004 - 17:31:26 CST

Hi,
  The current implementation of the "RMSD Tool" extension only works
with a single selection on multiple structures, which must yield the same
number of atoms. If they do not, it will give an error as you've seen.
If you want to do comparisons/alignments of structures with differing numbers
of atoms, you'll have to do it via Tcl commands at this point. I believe
we have some examples of this in the User's guide and/or VMD tutorials.

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Mon, Mar 08, 2004 at 04:20:56PM +0100, Maik Götte wrote:
> I'm trying to fit the alignment of two C-subunits of PKA, which have different
> conformational states (btw. they differ in aminoacid counts).
> Now, if I'm telling the RMSD-tool to fit 13 residues from the A-Helix with
> "top"-option (which are the same aminoacids in each molecule), and just fit
> the backbone, the result is junk (the molecules obviously doesn't fit). If I
> try to fit all atoms of the residues (that should fit much better), the
> following message is displayed: measure fit: selections must have the same
> number of atoms (while using "align". "RMSD" worked
> When I use the "average" or "selected" option the error sounds:
> vecsub: two vectors don't have the same size.
>
> What did I do wrong?
> --
> Maik Götte
> University of Kassel, Germany
> Student, Dipl. Biology
>
> Email: maik.goette_at_uni-kassel.de
> Webpage: http://http://www.biologie.uni-kassel.de/
> 

-- 
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