VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Wed Jul 28 2010 - 16:36:10 CDT

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