[Chimera-users] multialign

Tom Goddard goddard at sonic.net
Wed Oct 17 13:08:09 PDT 2012

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."


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.


> 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

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