VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Jul 28 2010 - 16:23:51 CDT

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 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
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