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Pymol on Biowulf

PyMOL ( is a powerful and comprehensive molecular visualization product for rendering and animating 3D molecular structures. Pymol is a user-sponsored molecular visualization system on an open-source foundation.

Pymol is a graphics-intensive program that is not well suited to running over a network. The best way to run Pymol is via Sciware. However, some users may want to use Pymol to view molecular structures that were generated on Biowulf. Here are some ways to accomplish this:

  1. Mount your Biowulf /data directory on your desktop system, and run Pymol via Sciware locally on your desktop against that data. In most cases, this will be the most efficient way to use Pymol if your Mac, PC or Linux system has sufficient memory resources. Instructions for running Sciware programs on your desktop system are at the Sciware site.

  2. Run Pymol on Helix and access your files in your /data directories. Helix has greater memory resources than the Biowulf head node, but like the head node you will not get very good visualization performance since the graphics need to be displayed across the network rather than on your local machine.
    • From your desktop, make sure you have Xwindows running, and then connect to using 'ssh -X'.
    • You can now type 'pymol' and access your files in /home/user, or /data/user.
  3. Run Pymol on the Biowulf head node. This is ONLY to be done if you are using very little cpu or memory, as otherwise you could impact other users and the stability of the system.
    • From your desktop, make sure you have Xwindows running, and then connect to using 'ssh -X'.
    • On the Biowulf head node, type 'pymol'.
Useful tip: The entire PDB structural data archive is mirrored on all the systems in the area /pdb/pdb. Corresponding sequences are in /pdb/sequences/. The structural data is divided into directories named with the middle two letters of the PDB code. Thus, the data for 1crn is in /pdb/pdb/cr/pdb1crn.ent.gz