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PyMOL for Molecular Visualization

This tutorial shows how to effectively use the program PyMOL for visualizing biological macromolecules. You will learn about the layout and functionality of the program through a set of guided tasks. According to the program's author, Dr. Warren DeLano, PyMOL is a molecular graphics system with an embedded Python interpreter designed for real-time visualization and rapid generation of high-quality molecular graphics images and animations. It can also perform many other valuable tasks (such as editing PDB files) that assist you in your research.

The strengths of PyMOL arise from the emphasis on high-quality graphics, the use of the powerful programming language (Python), and the extendability with Plugins. During the early development, emphasis was placed on providing functionality, and not on intuitive user interface. As a result, it takes some time to learn the program. The PyMOL commands are explained in the PyMOL Wiki. Examples of PyMOL images with commands used to generate these views are available in the Biomolecular Images and Movies for Teaching page. In more difficult cases you can ask help from PyMOL users via the PyMOL forum. PyMOL is available for many computer platforms either as a pre-compiled binary or in the free source code form. As of early 2010, development of PyMOL is continued by Schrodinger, LLC.

You can interact with the program via four complimentary ways:

So, lets get started. Open the PyMOL program either by clicking on its icon or by typing pymol in Terminal. Load a structure of a protein-DNA complex (PDB code 1B01 (this is one-b-zero-one)). You can load the structures via the PDB Loader Service from the Plugin menu.

One of the strengths of PyMOL lies in the ability to create intricate and beautiful graphical representations of complex objects. The program comes with several presets that can be accessed from the Actions menu. Try some of these.

PyMOL Preset

Enough of the easy stuff! You can interact with the program via several complimentary ways:

Play few minutes with this structure until you feel comfortable with the basic selection and rendering options.


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Tutorial by Dr. Kalju Kahn, Department of Chemistry and Biochemistry, UC Santa Barbara. ©2007.