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.