VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Thu Jul 29 2010 - 10:33:26 CDT

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

Works fine on 1.8.7 for me as well.

>
> 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
> 

-- 
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