VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 14 2000 - 18:58:34 CDT

Tim,
  As it turns out, this is in fact a bug in VMD 1.5. We also
discovered another problem with the RMSD code that has been plagueing
VMD since VMD 1.3, but we had not been able to debug until now.
We have already fixed the RMSD computation problem (sometimes crashed VMD,
particularly on Linux, and particularly noticable in VMD 1.3), and are
now working on fixing the GUI problem you have also discovered.

There might be a way for us to give a Tcl script to existing VMD 1.5
users that circumvents the GUI problem, but the sometimes-crash or
malfunction problem was in the measture_fit C++ code in VMD, and requires
updating to a new binary of VMD. We'll probably be releasing an "a1" version
of VMD 1.6 very shortly, and the RMSD fit problems will hopefully be
cured once and for all.

How are things going aside from RMSD fit? Any other comments/feedback?
Anyone? How was VMD 1.5 /wrt to other features, stability etc? Comments?

Thanks,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Aug 03, 2000 at 08:17:18PM +0200, Timm Essigke wrote:
> Hi,
>
> I really enjoyed the RMSD calculation/fitting feature in VMD 1.4 (Linux
> version), but I am not able to get it working with 1.5.
> I select e.g. Heavy (or whatever) and Molecule, click on Compute and get
>
> > RMSD of two molecules based on non-hydrogen atoms
> > Using the mouse, click on one atom of each of
> > the two molecules you wish to compare.
>
>
> in the log window and crosshairs. Clicking on atoms of two conformations
> of a molecule gives no reaction of VMD (label, output etc.)
>
> Am I doing something wrong or is it a bug in the new version?
>
> Thanks,
>
> Timm
> --
> Timm Essigke
> Freie Universitaet Berlin * Fachbereich Biologie, Chemie, Pharmazie *
> Institut fuer Chemie (Kristallographie) * Takustr. 6 * D-14195 Berlin *
> essigke_at_chemie.fu-berlin.de * http://www.chemie.fu-berlin.de/~essigke *
> Tel.: +49-30-838-54627 * Fax.: +49-30-838-53464 

-- 
Theoretical Biophysics Group   Email: johns_at_ks.uiuc.edu
Beckman Institute              http://www.ks.uiuc.edu/~johns/
University of Illinois         Phone:  (217) 244-3349
405 N. Mathews  Ave              FAX:  (217) 244-6078 
Urbana, IL 61801, USA          Unix Is Good For You!!!