A molecular visualization system on an open-source Python foundation


PyMOL is an open-source molecular visualization tool written in Python. The program has a number of different visualization options and presentation settings. The program also has the ability to create animations of molecular visualizations in 3D.

Using PyMOL on RCC Resources

PyMOL is installed in the Spear cluster path. To execute it, connect to Spear with graphical forwarding enabled:

ssh -X

PyMOL is installed in the Spear path

$ pymol

Testing PyMOL with Sample Data

  1. Upload the sample data package to Spear.
  2. Untar the sample data: tar -xvf Data.tar
  3. Run PyMOL with the sample data: pymol il2.pdb

To learn more, refer to the official PyMol Wiki.