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) 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