PyMOL

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 and displaying maps).

To use in the Core on a Linux or SGI workstation, simply type:

setup pymol

If you get a library error when attempting to run pymol, try:

setup pymol-old

PyMOL is also available on the Core Macintosh in the "Applications" folder, and is installed on most of the Windows PCs. These versions are less likely to be up-to-date, however.

Some movie-making features are available via the eMovie plugin. Select the "Plugin" pulldown menu, select "eMovie", then "Open eMovie".

Luca Jovine has made available the program nuccyl, which allows PyMOL to display atomic models of nucleic acids in a highly simplified representation. Follow the above link for pictures, as well as a detailed tutorial on using the program. If you have set up PyMOL, you do not need to worry about finding and copying nuccyl.pl. Simply use the command "nuccyl" with the relevant arguments.

nuccyl relies on RNAView or 3DNA to prepare an RNA or DNA structure, respectively. Both are available in the Core, via

setup rnaview

setup 3dna

A customized version of PyMOL that supports electrostatic potential calculation and display is also available. Details are here.

The PyMOL home page has additional information.

In particular, the User Manual is available. PDF versions of the new and old manuals are available locally. The old manual has more detail, but is obviously not up-to-date on newer features. Additionally, there is a PDF reference manual.

A few example scripts are locally available. These are also accessible from $PYMOLDIR/examples once PyMOL has been set up. See also the PyMOL script repository.

Of particular interest is the script fitting.py, which calculates the RMSD and fits one selection onto another within PyMOL without regard to matching residue names, etc. This script temporarily changes the selection2 to match selection1 so that the fit will work. This is usually easier than using PyMOL's built-in fit and pair_fit functions.

To use fitting.py:

• Copy /srv/local/pymol/current/examples/fitting.py to your working directory (or save from the above link)
• In PyMOL, type "run fitting.py" to define the function
• Invoke the fitting command:
  
  fitting object1, selection1, object2, selection2
  e.g. fitting 1xuu, c. a & (i. 296-309 or i. 335-340), 1ame, i. 8-21 or i. 47-52

Unfortunately, many variables that can be edited by the user are not in the current documentation. Some of these variables can be found in this script. For example, the bond radius in stick representations can be altered by typing "set stick_radius = [VALUE]"; e.g., "set stick_radius = 0.8". Obviously, some trial-and-error is required.

How does one cite PyMOL?

There are no peer reviewed publications on PyMOL yet. So, if your journal is hip enough to allow URL citations, please cite PyMOL as:

   DeLano, W.L. The PyMOL Molecular Graphics System (2002) on World Wide Web http://www.pymol.org

Otherwise, cite it as a program published by DeLano Scientific:

   DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA.

Or do both:

   DeLano, W.L. The PyMOL Molecular Graphics System (2002) DeLano Scientific, San Carlos, CA, USA. http://www.pymol.org

Failing that, cite the manual as a traditional book:

   DeLano, W.L. The PyMOL User's Manual (2002) DeLano Scientific, San Carlos, CA, USA.

You get the idea...and please don't forget to send Warren Delano the reference for your article when it comes out so that he can add it to the list of publications which used PyMOL. Contact him at warren(AT)delanoscientific.com.