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
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
--
Edward H. Egelman, Ph.D.
Professor
Dept. of Biochemistry and Molecular Genetics
University of Virginia