Scripts for performing useful tasks within PyMOL

Assuming this repo is located in your home directory, add the following to your ~/.pymolrc file:

python

import os
import glob

script_repo_path = os.path.join(os.path.expanduser("~"), "pymol_scripts")
scripts = glob.glob(script_repo_path+"/*.py")
for script in scripts:
    cmd.run(script)

python end

When PyMOL starts up, all of these scripts should be available in PyMOL.

• align_to_axis
  • Transform protein so that an atom selection (default N-terminal nitrogen) is located at the origin and the center of mass is located along a provided axis (default y-axis).

Note: These scripts require that the RDKit distribution be in your $PYTHONPATH and compiled for the same version of Python as PyMOL.

• rdkitalign
  • Align molecules using RDKit's 3D molecular alignment. See documentation.
• open3dalign
  • Align molecules using RDKit's interface to Open3DAlign. See documentation.