PyMOL (www.pymol.org) 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:
- 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.
- 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
- From your desktop, make sure you have Xwindows running, and then connect to helix.nih.gov using 'ssh -X helix.nih.gov'.
- You can now type 'pymol' and access your files in /home/user, or /data/user.
- 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 biowulf.nih.gov using 'ssh -X biowulf.nih.gov'.
- On the Biowulf head node, type 'pymol'.