VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jul 29 2010 - 10:21:11 CDT

Kirby,
  Can you also check how it behaves for VMD 1.8.7? I'm assuming
that's the version that Ian was running.

Ian, if the problem doesn't occur with the VMD 1.8.8 alpha versions
based on Kirby's comment, then you may want to try one of the
alpha builds and let us know if you still encounter any trouble:
  http://www.ks.uiuc.edu/Research/vmd/alpha/

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Jul 28, 2010 at 04:36:10PM -0500, Kirby Vandivort wrote:
> Ian,
>
> I have downloaded the zip file you specified, loaded all the PDB files into
> the latest CVS version of VMD, loaded Multiseq, aligned with Stamp (via the
> menus) and then changed the coloring (View|Coloring) to Qres.
>
> This seems to have worked for me. How is it failing for you?
>
> Kirby
>
>
> John Stone wrote:
> >Ian,
> > Thanks, we will let the multiseq developers know about the problem
> >you have encountered and pass along any workarounds or suggestions
> >they may have.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Jul 27, 2010 at 05:54:53PM -0400, Ian Stokes-Rees wrote:
> >>
> >>On 7/27/10 3:37 PM, Ian Stokes-Rees wrote:
> >>> I'm trying to do two things with the pair of structures: 3cex and
> >>>1iesa_ (SCOP code). I would like to use MultiSeq to try and align
> >>>1iesa_ with 3cex using STAMP. I am failing to do this, and am having
> >>>trouble interpreting the error message. To check that STAMP is working
> >>>properly I have also tried aligning the two identical domains of 3cex.
> >>>I cannot get this to work properly, which makes me think something else
> >>>may be going wrong.
> >>An even better example that also does not work comes from comparing the
> >>12 PDB files here:
> >>
> >>http://abitibi.sbgrid.org/~ijstokes/drop/2vzf-models.zip
> >>
> >>These all align with 2vzf (RCSB PDB code), and have already been
> >>"superposed" using COOT's built-in SSM function. I simply wanted
> >>VMD/MultiSeq/Stamp to align these again and provide me with Qres
> >>coloring. It does not work.
> >>
> >>Thanks in advance for any advice.
> >>
> >>Ian
> >
> >
> >
>
>
> --
>
> Kirby Vandivort Theoretical and
> Senior Research Programmer Computational Biophysics
> Email: kvandivo_at_ks.uiuc.edu 3061 Beckman Institute
> http://www.ks.uiuc.edu/~kvandivo/ University of Illinois
> Phone: (217) 244-1928 405 N. Mathews Ave
> Fax : (217) 244-6078 Urbana, IL 61801, USA 

-- 
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