Conda installation

The simplest and recommended way to install Ammolite along with open-source PyMOL is via the Conda package manager:

$ conda install -c conda-forge ammolite

If you prefer the proprietary version of PyMOL, you can install PyMOL via Conda and Ammolite via pip.

$ conda install -c schrodinger pymol-bundle
$ pip install ammolite

PyMOL installation from

Otherwise, if you have downloaded the PyMOL binary from, add the install location the $PYTHONPATH path variable:

$ export PATH="/path/to/pymol/lib/python3.7/site-packages:$PATH"

or add the path directly in your Python script.

import sys
sys.path.insert(0, "/path/to/pymol/lib/python3.x/site-packages")

Note that this only works, if the Python version of your PyMOL installation matches the version of your Python interpreter.

The correct installation of PyMOL can be checked by opening your Python interpreter in interactive mode and typing

import pymol
pymol.finish_launching(["pymol", "-qk"])

If no error shows up, the installation is correct.