[Chimera-users] Map conservation of my sequence compared to sequence alignment

[Elaine Meng]

Hello Matthias,
The conservation values automatically calculated by Chimera are based on the corresponding column in the sequence alignment.  As you have found, it does not matter which residue type is actually in your structure.  It might be that associated column in the sequence alignment does not even have any residues of the same type as the structure, since a structure can associate with a sequence that is not exactly the same as the structure’s sequence.

The default “percent conserved” measure does show % that is the consensus residue.  Some of the other built-in measures from AL2CO (entropy, variability, or sum-of-pairs) do not use the consensus residue at all, but they are still only calculated from the sequence alignment column.  So you might want to choose one of the AL2CO measures to be less tied to the “consensus” residue.  Still, however, to show something like the % of the column that has the same residue as the structure, you would have to use some python code since none of the measures available in the user interface involve the associated structure’s residue type.

These tutorials mention using AL2CO conservation measures:
<https://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
<https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>

I can’t advise on the potential Python code (beyond my skill set, sorry), so I don’t know how difficult that approach would be.
Best,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Jan 5, 2017, at 9:37 AM, mfellner at msu.edu wrote:

> Good day
> 
> I like the mapping sequence conservation tool in chimera, however I ran into a problem that IÂ could not overcome with anything IÂ found online.
> 
> I have the consensus mapped onto my protein but that is not what IÂ want. IÂ want to show how the residues of my protein are conserved. For example at a particular residue the consensus is a C but in my structure its a W. at the moment the W is colored to be highly conserved based on the consenus of the C. The W is maybe 15% conserved, how can IÂ map the conservation of my sequence compared to all the other sequences.
> 
> IÂ hope IÂ explained what my issue is
> Thank you for this great tool
> Matthias Fellner