[Chimera-users] match-align using just selected protein areas ?

Marek Maly marek.maly at ujep.cz
Wed Mar 12 11:44:27 PDT 2014


Dear Elaine,
thank you very much for your help !

   Best wishes,

     Marek

Dne Wed, 12 Mar 2014 17:35:39 +0100 Elaine Meng <meng at cgl.ucsf.edu>  
napsal/-a:

> Hi Marek,
> Yes, if you mean MatchMaker (Match->Align does not align the structures,  
> it just makes a sequence alignment from a structural alignment you  
> already made).
>
> In the MatchMaker GUI, there is a "Further restrict matching to current  
> selection" setting:
> <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/matchmaker/matchmaker.html>
>
> In the matchmaker (mmaker) command,
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html>
> ... it is similar but you instead specify the residues directly instead  
> of selecting them:
> <http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/midas/mmaker.html#restrict>
>
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
>
> On Mar 11, 2014, at 6:53 PM, Marek Maly wrote:
>
>> Hello,
>> I would like to know if it is possible in Chimera
>> align two proteins let say protein A and protein B,
>> but just using selected subsequences A_sel, B_sel
>> (i.e. just the selected subsequences are going to be
>> optimally matched and the rest of both proteins is not involved
>> in the matching process/calculation) ?
>>   Thank you in advance !
>>       Best wishes,
>>          Marek
>
>
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