colour by attributes is only colouring one chain of the dimer, how to make the colouring apply to both chains of homodimer
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
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 ---------- 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@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
Dear Elaine,
I should have responded right away, because one of the wonderful things about your response was that it was prompt. Thank you very much for an informative response that got me to a good figure.
Anne-Frances
Anne-Frances Miller Professor of Chemistry Director, Magnetic Resonance Centre University of Kentucky Dept. Chemistry, 505 Rose Street Lexington KY 40506-0055
On 28 Jun 2013, at 13:55, Elaine Meng meng@cgl.ucsf.edu wrote:
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
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@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
participants (2)
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Anne-Frances Miller -
Elaine Meng