[chimerax-users] Automate calculation and saving of residues' structural attributes

[André]

Hello!

I'm working on an automated pipeline (in Python) for the structural
analysis of proteins. In particular, I'm using Chimera to calculate and
save to .txt files some structural properties of residues (namely: areaSAS,
areaSES, relSESA, bfactor, kdhydro, phi, psi). These files are the inputs
of the pipeline.
However, currently the files are exported manually, and, for the purpose of
building a fully automated pipeline, it would be great to also automate
this step of calculating the attributes and exporting their respective
files.

I searched a lot, and tried some ways to achieve such an automation (using
Chimera), but nothing worked.
And I also considered using ChimeraX. In particular, I went through
ChimeraX Programming Manual (
https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html#), but, if I
understood correctly, I'd only be able to import chimerax and use its
functions in the Python interpreter within ChimeraX (Tools >> General >>
Shell).
At first, I'd like to import chimerax as a module in a Python interpreter
outside of ChimeraX, so that manually opening ChimeraX wouldn't be
necessary in order to save the files with the residues' attributes. But,
from some other threads in the mailing list, I found that it wouldn't be
possible (right?)

But I also found out that I could write a .py script which calculates and
exports the files with the residues' properties, and then run it with
ChimeraX application from the command-line, something like: *chimerax
--nogui myscript.py*
If that works, I think that my automation problem would be solved! The only
problem is that I really couldn't figure out the Python code to calculate
and export the aforementioned residues' properties (I took a look in
ChimeraX Recipes (https://rbvi.github.io/chimerax-recipes/), but I couldn't
find what I need, nor more detailed documentation).

Given that, I'd like to know if anyone has done something like this, and/or
have any guidance on how I could proceed.

I really appreciate any help you can provide!
(And thanks to Tom Goddard for suggesting moving the discussion here to the
ChimeraX mailing list).

Thank you so much,
André.
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