PyMOL

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PyMOL is a stand-alone molecular visualization program that is very popular with protein crystallographers because of the high quality of its rendering, its speed and versatility. A large percentage of the figures in journal publications reporting new macromolecular structures are created using PyMOL. PyMOL is the creation of Warren DeLano. Effective use of PyMOL requires that you become familiar with highly abbreviated menus, and/or a command scripting language.

Molecular scenes prepared in PyMOL can be imported into Protoepedia scenes. Jmol which Proteopedia, uses for displaying molecular scenes can read a PyMOL session files (.pse file) that you have saved on your computer and convert it directly into a Jmol scene to be saved and displayed in Proteopedia. Specifically, if you open Proteopedia's Scene Authoring Tool, you can click-and-drag the PyMOL session file from your computer's file browser interface into the structure window of the Scene Authoring Tool (on the right). Jmol will then make its best attempt at reproducing the scene. (Be aware there a few features of PyMOL that are not supported by Jmol. Also, as PyMOL continues to be developed, new fixes in Jmol will likely be needed.) You can then use the Scene Authoring Tool interface to save that scene to Proteopedia in the typical way.

PyMOL has an innovative license: it is open source, but not free in all forms: the author's current ready-to-run downloads (binaries) and up-to-date documentation require payment of modest annual subscription fees. However, a current free version is available to students and educators for classroom use, old out-of-date binary builds can be freely downloaded by anyone, and some Linux distributions provide PyMOL packages compiled from the open-source code.

PyMOL has a strong user community which interacts via the PyMOL-Users mailing list and operates the PyMOL Wiki documentation site. The "Py" in PyMOL refers to the Python language, an integral part of the package. Python enables users to automate PyMOL with simple command scripts and to develop plugins with their own custom user interfaces.

Warren Lyford DeLano passed away suddenly on November 3, 2009, at the age of 37[1]. DeLano Scientific LLC has announced that PyMOL remains available for download, and that support for PyMOL is continuing. A statement similar to the following was displayed on the Main Page of Proteopedia during the month following Dr. DeLano's passing:

It is with great sadness that we learn of the passing on November 3rd, 2009, of Dr. Warren Lyford DeLano. Dr. DeLano was the brilliant software innovator who created PyMOL, widely used by structural biologists, and for creating images of macromolecular structures displayed in scientific journals. Through his software, and his engaging, supportive, and accessible personality, he forged a bond even with people across the world whom he had never met. His presence will be sorely missed by his friends and family and the crystallographic and molecular visualization communities.

Schrödinger took over development of PyMol after Warren DeLano's passing.

See Also

References and Notes

  1. Obituary for Warren L. DeLano (open access at Nature Structure and Molecular Biology).

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Wayne Decatur, Warren DeLano, Eran Hodis

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