VMD-L Mailing List

From: Ian Stokes-Rees (ijstokes_at_hkl.hms.harvard.edu)
Date: Tue Jul 27 2010 - 16:54:53 CDT

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