VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Nov 19 2004 - 10:24:35 CST

There was a bug in the measure fit implementation in VMD 1.8.2, can you
try the most recent VMD 1.8.3 test version and see if that cures your problem:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Nov 18, 2004 at 08:37:35PM -0800, Gavin Murphy wrote:
> Hello,
> I am working on the cubic core of pyruvate dehydrogenase. It has 8
> corners, each made of 3 monomers. I am trying to align 7 of the 8
> corners to one particular corner. I get bad alignments with three of
> the corners, and I believe that it has to do with symmetry. They are
> the corners that are diagnolly opposite one another on any given face.
> All the other corners align well. I am using the
> measure fit command. Is there a bug in the software, or am I missing
> something? I could give out the pdb files to anyone who wants to
> reproduce it.
>
> Thank you,
> Gavin Murphy
> 

-- 
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