[chimerax-users] User defined color values for each residue/position

[Niccolò Arecco]

Hi, 

I’m using ChimeraX to visualise the structure of a complex of 4 proteins. 
I generated a sequence alignment of protein sequences of 1 of the 4 proteins and at each column (amino acid) of the multi protein alignment I assign a score from 0 to 1, where 0 represents no sequence conservation and 1 represent perfect sequence conservation. 

I’d like to colour-code these values on a publicly available structure. Can I do it with ChimeraX? I tried to google a bit and read the docs but couldn’t fine a way. 

The input “colouring” file could be something like this tab delimited file:

#POS AA 	SCORE
1	  M 		0.2
2 	  V		0.5
….
n       N 		0.8

But I can reshape it in a better format if necessary.

If this is not possible to do it with ChimeraX are you aware of any other tool / software that would allow me to do this?

In the end I’d like to be able to do something like ConSurf (https://consurf.tau.ac.il <https://consurf.tau.ac.il/>) does but I’d like to avoid if possible always having to use the web interface as I’d like to semi-automatise this process for every protein in the complex at least.

Thanks a lot!
Best wishes
Nicco
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