[Chimera-users] multialign

[Eric Pettersen]

It was pretty much a design decision since the superposition functionality of MAV doesn't make any sense if you have multiple chains of the same structure associated with the alignment.  I can imagine some ways of dealing with the superposition issue, but at this stage of MAV's development I'd say the one-chain-per-structure association limitation is pretty much baked in and is unlikely to change.

You can work around the limitation by using the "split" command to break the chains into separate models, which can then all be associated with a single sequence of the alignment.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu

On Oct 17, 2012, at 1:08 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
>> -- 
>> 
>> <Mail Attachment.jpeg>
>> Edward H. Egelman, Ph.D.
>> Professor
>> Dept. of Biochemistry and Molecular Genetics 
>> University of Virginia
> 
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                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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