VMD-L Mailing List

From: Kirby Vandivort (kvandivo_at_ks.uiuc.edu)
Date: Tue Aug 13 2013 - 12:03:49 CDT

On 08/13/2013 11:40 AM, Eli Alster wrote:
> Hi,
>
> I am experiencing an error when using the STAMP structural alignment feature of
> Multiseq. I have two protein segments: a complete g-actin protein and a fragment
> of the Arp2 protein. I want to align the structurally homologous region of
> g-actin to the Arp2 fragment. If I put the Arp2 fragment on top of the alignment
> list, and g-actin on the bottom (so that the g-actin moves upon alignment),
> everything works. However, if I reverse the order of the list because I would
> like the Arp2 fragment to move to g-actin's location, the program fails with the
> error message "STAMP alignment failed." This is followed by a 756 line error
> message.
>
> Thanks,
> Eli Alster
> Caltech '14

What error is it giving you? 

-- 
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) 244-5711                405 N. Mathews Ave
Fax  : (217) 244-6078                Urbana, IL  61801, USA