[Chimera-users] colour by attributes is only colouring one chain of the dimer, how to make the colouring apply to both chains of homodimer

Elaine Meng meng at cgl.ucsf.edu
Fri Jun 28 10:55:21 PDT 2013

Dear Anne-Frances,
We're glad you like Chimera!

Probably the issue is not the coloring step, but that only one monomer has the conservation attribute.  In other words, only one chain of the structure is associated with the sequence alignment.  If both chains were associated with the sequence alignment, then I believe the coloring-by-conservation would work as intended.

The limitation is that multiple chains in the same model cannot be associated with the same alignment.  Not to worry, however, there are at least two different workarounds: opening another copy of the same alignment or splitting the model.  Details:

(1) Open another copy of the same sequence alignment.  If you don't already have it as a file, you can save with  "File… Save As" in the Multalign Viewer (sequence window) menu.  Then open the file you just saved (e.g. with main menu File… Open).  You will then have two sequence windows with the same alignment.  In the second sequence window, choose "Structure… Associations" and associate the sequence with the chain that wasn't colored, i.e. the chain that's not associated with the first alignment.  Then coloring by conservation will color both chains.  Just make sure you are using the same method to calculate conservation in the two copies of the alignment (controlled with "Preferences… Headers" in the Multalign Viewer menu, Conservation style; if you choose AL2CO you get all kinds of additional choices including entropy and variability methods).

(2) Split the model so that each chain is a separate model, i.e. use command "split".  If the model was #0, this will create a model #0.1 with chain A and #0.2 with chain B (etc. if there are more chains).  Then use "Structure… Associations" in the Multalign Viewer menu to associate both models with the same sequence.

I hope this helps,
Elaine C. Meng, Ph.D. 
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jun 27, 2013, at 6:17 AM, Anne-Frances Miller <afm at uky.edu> wrote:

> Dear team Chimers
> 1-  Thank you for GREAT software !
> 2- How to make the colouring apply to both chains of homodimer ?  I have a homodimer in which features of the active site derive from both monomers so the degree of active site conservation will only show up if I can apply colour by attributes to both monomers (attribute will be conservation)  Right now, colour by attributes is only colouring one chain of the dimer, chain A.
> Anne-Frances
> Anne-Frances Miller
> Professor of Chemistry
> Director, Magnetic Resonance Centre
> University of Kentucky
> Dept. Chemistry, 505 Rose Street
> Lexington KY 40506-0055

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