Hi! Such an honor to see my name listed here! Yes, with pychimera you should be able to do it! All you need to do is to patch the environment so that Chimera can find its libraries and dependencies, and then initialize it. In practice, this means importing pychimera and calling pychimera.patch_environ() and pychimera.load_chimera() at module level. Then you can proceed as you'd do with a standard Python distribution. If you don't want (or are not able) to modify the script, pychimera also installs a binary that will patch and load Chimera for you, so you can just do "pychimera myscript.py" However, it's a bit buggy when it comes to parsing additional arguments for your script. That said, the binary is very useful to fiddle with Chimera internals from the command line, since it provides a patched python in which you can import chimera, and also hooks for ipython and jupyter notebook (with magic calls to render inline!). pychimera will do its best to locate your Chimera installation, but if it doesn't succeed, you can always provide it manually with the envvar CHIMERADIR, which is what you would probably need to load the headless edition of Chimera. Additionally, it will load your current Python distribution sys.path, which means it will be able to import already installed packages in such distribution. As a result, you don't need to install the packages again for Chimera. This is particularly useful if you are using virtual envs or conda envs! I think that's all. If further questions arise or something is not working as you'd expect, please report that in the issues page of GH ( https://github.com/insilichem/pychimera), or write to me directly. Cheers, Jaime.