[Chimera-users] multialign

[Edward Egelman]

Yes, the only way that I found was to do the association one chain at a 
time - pretty tedious.
Thanks,
Ed

On 10/17/2012 4:08 PM, Tom Goddard wrote:
> Hi Ed,
>
>   I don't know if more than one chain can be associated with a 
> sequence in Multalign Viewer.  The documentation says
>
> " A structure (even if it has multiple chains) cannot be associated 
> with more than one sequence, but a single sequence can be associated 
> with more than one structure."
>
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association
>
> That doesn't really say whether multiple chains of a single structure 
> can associate with a sequence, only that multiple structures 
> (different PDB models) can associate with the same sequence.  So I 
> tried it as I'm sure you did and I was not able to make it associate 
> more than one chain (I used groel 1grl) with the same sequence in a 
> multiple alignment.  When I load the structure it associates chain A 
> but not any of the other chains.  Then if I use MultAlign Viewer menu 
> Structure / Associations... to associate chain B with the same 
> sequence then it seems to lose the association of chain A.  At least 
> when I select residues on the sequence, only chain B on the structure 
> has residues selected.
>
>   I'm forwarding this to the Chimera list since Elaine Meng or Eric 
> Pettersen will have a better answer.
>
>     Tom
>
>> Hi,
>>   I am wondering if this is a bug or limitation in Chimera, or if I 
>> am missing something. I have a molecular model of F-actin, with many 
>> identical chains. Using the Multialign Viewer, it appears that I can 
>> only do a 1 to 1 mapping of a single chain to a single sequence. How 
>> can I map 10 identical chains to one sequence?
>> Regards,
>> Ed
>> -- 
>>
>> <imap://goddard@imap.sonic.net:993/fetch%3EUID%3E.INBOX%3E23891?header=quotebody&part=1.2.3&filename=signature.html>
>>
>> Edward H. Egelman, Ph.D.
>>
>> Professor
>>
>> Dept. of Biochemistry and Molecular Genetics
>> University of Virginia
>>
>

-- 

<cid:part5.09080804.09060606 at virginia.edu>

Edward H. Egelman, Ph.D.

Professor

Dept. of Biochemistry and Molecular Genetics
University of Virginia

phone: 434-924-8210
fax: 434-924-5069
egelman at virginia.edu <mailto:egelman at virginia.edu>
http://www.people.virginia.edu/~ehe2n 
<http://www.people.virginia.edu/%7Eehe2n>


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