Hi André, i am pretty sure, that my solution is very crude and that there are better ways of doing it (like importing chimerax in the python code directly). I guess, you'll get more anwsers soon. I quickly wrote a script, which performs a chimerax task independently, by just running python code. First: a chimerax script file with the desired commands: script.cxc: open 7ott surface #1 mearuse area #1 exit Note: the exit command is needed, otherwise the subprocress will idle in the chimerax cmd line. Second: a python script, which execute this script in chimerax and fetches the output: test.py: import subprocess import os cwd = os.getcwd() chimerax = "/Applications/ChimeraX_Daily.app/Contents/MacOS/ChimeraX" scriptfile = f"{cwd}/script.cxc" cmd = [chimerax, "--nogui",scriptfile] p = subprocess.run(" ".join(cmd),shell = True,capture_output=True) stdout_as_str = p.stdout.decode("utf-8") print(stdout_as_str) This just runs a subprocess and fetches the output to a string, which you can than further analyse. Best Christian Dr. rer. nat. Christian Tüting Kastritis Laboratory for Biomolecular Research Cryo-Electron Microscopy & Computational Structural Biology ________________________________________________ Martin-Luther-Universität Halle-Wittenberg Biozentrum, Room A.2.19 IWE ZIK HALOmem NWG III "Kryo-Elektronenmikroskopie an Membranproteinkomplexen" Weinbergweg 22, 06120 Halle tel: +49 345 5524985 web (Lab): https://blogs.urz.uni-halle.de/kastritislab/ web (HALOmem): https://www.halomem.de/en/
André via ChimeraX-users <chimerax-users@cgl.ucsf.edu> 01/21/22 1:29 PM >>> 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.