PyMOL Commands

This library includes two commands for visualizing 3D macromolecular images in PyMOL:

voxelize	Generate a 3D image of a macromolecule in PyMOL.
load_voxels	Load a 3D image of a macromolecule into PyMOL.

In order to use these commands, the macromol_voxelize package must be installed into the same version of python used by PyMOL. The details of how to do this depend on how PyMOL was installed. You can always find the path to the relevant python installation by running the following command in PyMOL:

PyMOL> import sys; print(sys.exec_prefix)

However, be aware that if the resulting path is managed by the operating system (i.e. if it starts with /usr or something similar), then you will need root access to install macromol_voxelize. Even if you have root access, you should probably not do this. Manually installing packages into OS-managed python installations can cause dependency conflicts in other packages installed by the OS. Instead, you should make a virtual environment, then install both PyMOL and macromol_voxelize into that environment. Note that installing PyMOL into a virtual environment will require compiling it from source. The details of how to do that will depend on whether you’re using open-source or incentive PyMOL, and are unfortunately beyond the scope of this documentation.