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