VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jun 11 2004 - 10:16:03 CDT

Hi,
  The new code may not completely solve this problem, as I've
still seen some cases where the alignment didn't work as well as one
would hope. But yes, I can certainly make test versions available.

  John

On Fri, Jun 11, 2004 at 08:07:54AM -0700, Justin Gullingsrud wrote:
> Hi,
>
> Yes, this is a recently corrected bug in the fitting algorithm,
> affecting VMD 1.8.2. There should be beta versions of VMD available
> upon request that do not have this problem.
>
> As a workaround, I think you can avoid the bug by moving the reference
> system so that it's center is at the origin. Best of course would be
> to use a newer VMD version.
>
> Cheers,
> Justin
>
> On Jun 11, 2004, at 12:48 AM, Jérôme Hénin wrote:
>
> >Hi all,
> >
> >I have met an unexpected behaviour using the "measure fit" command,
> >and I'd
> >like to know if anyone has had a similar experience.
> >
> >When computing the rmsd along a trajectory, some frames were not
> >properly
> >aligned with the reference system, which resulted in jumps in the
> >measured
> >rmsd. By repeating the fitting procedure, the alignement problem was
> >eventually corrected.
> >
> >Is this to be considered a bug of the alignement algorithm?
> >
> >Jerome
> >
> --
>
> My kung-fu incorporates office supplies. -- Herbert Kornfeld
> 

-- 
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