VMD-L Mailing List

From: Anurag Sethi (anurag.sethi_at_gmail.com)
Date: Tue Aug 13 2013 - 13:46:42 CDT

Eli,

When you align a smaller protein (for example, a single domain) to a
larger protein (typically with multiple domains), the structural similarity
score is high and STAMP can align the two structures. However, the
converse is not necessarily true (i.e., the structural similarity score
when you try to align a large protein with multiple domains to a smaller
protein might be much lower and STAMP cannot produce a reliable alignment
in such a case).

I think you should be able to solve your problem by
1) Choosing Selected Regions option within the Stamp Alignment Options
window.
2) selecting all the residues in the Arp2 fragment and the corresponding
region of g-actin that they should align to.

If you do this, the alignment should work irrespective of which protein is
placed on top in the list.

I hope this works,
-Anurag

Genius is nothing more or less than doing well what anybody can do badly. -
Amelia Barr

On Tue, Aug 13, 2013 at 1:03 PM, Kirby Vandivort <kvandivo_at_ks.uiuc.edu>wrote:

> 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/ <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
>