[chimerax-users] color by conservation

[Elaine Meng]

Hi George,
Currently we would still recommend using Chimera for this purpose… in ChimeraX it is “coming soon” since it’s being worked on now, but not quite there yet.

Tutorials for doing it in Chimera:
… this one is more basic, includes intro to sequence viewer, coloring by conservation is at the end:
<http://www.rbvi.ucsf.edu/chimera/docs/UsersGuide/tutorials/super.html>
… this one is more comprehensive and focuses more exclusively on coloring by conservation:
<https://www.rbvi.ucsf.edu/chimera/data/tutorials/systems/outline.html>

You could do the final rendering in ChimeraX if you did most of it in Chimera.  After calculating conservation in Chimera using the desired sequence alignment and calculation method as covered in the tutorials above, then you would use Chimera's “Attribute Calculator” (in menu under Tools.. Structure Analysis) to change the bfactor values to the conservation values, i.e. calculate attribute "bfactor" for "atoms" using the formula:

residue.mavConservation

…then write a PDB file, which would now have residue conservation in the bfactor column. (This column is not that wide, so you would lose some information to rounding.)
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#mavAttributes>
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/calculator/calculator.html>

Then you could read the PDB file into ChimeraX and use the “color bfactor” command:
<http://rbvi.ucsf.edu/chimerax/docs/user/commands/color.html#attribute>

I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco




> On Jan 16, 2019, at 4:07 PM, George Ghanim <gghanim at berkeley.edu> wrote:
> 
> Hello, 
> 
>  Is it possible to color amino acids by conservation from an alignment file?
> 
> Thanks,
> George Ghanim
> 
> ——
> PhD Student Rio Lab
> Molecular and Cellular Biology,
> University of California Berkeley
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