From: Michael George Lerner <mlerner@um...> - 2004-07-14 21:27:14
I've written a PyMOL (http://pymol.org) plugin that allows you to run APBS
and visualize the results very easily from within PyMOL (version 0.96 or
The plugin lets you configure all of the normal APBS parameters (whether
you want the full nonlinear Poisson-Boltzmann equation or not, what the
various dielectrics should be, ion concentrations, etc.) for calculation
of electrostatics potentials. If there are other things people would like
me to add to the plugin, just let me know .. it's should be pretty easy
for me to add new features.
Also, the plugin comes with a visualization tab that can be used to aid in
the visualization of any electrostatic potential.
It's quite easy to install, thanks to PyMOL's new plugin system.
Anyway, you can find the plugin on my webpage
or directly from
drop it into pymol/modules/pmg_tk/startup/ and you're ready to go.
Please let me know if you find this useful and/or have any questions or
Here are the directions, taken from http://www.umich.edu/~mlerner/PyMOL/
This is a PyMOL plugin which lets you run APBS from within PyMOL.
To install it,
1. Make sure you have PyMOL version 0.96 or higher.
2. Make sure you have APBS installed.
2. Download a copy of apbs_tools.py and place it in
Now, you'll see "APBS Tools..." under the Plugins menu. This plugin allows
fairly complete configuration of APBS, but it's very easy to set up a
standard electrostatic potential calculation:
1. Load your molecule into PyMOL
2. Load the plugin
3. Click on "Set grid"
4. Click on "Run APBS"
5. Use the plugin's "Visualization" tab to look at the results
This will use PyMOL's new ability to assign AMBER charges and radii. If
you wish to use your own externally-generated PQR file, you can set that
up on the plugin's main page.
The plugin should auto-detect the location of the APBS binary on your
system, but you can set it manually under the "APBS Location" tab.
My plugin can calculate appropriate grid lengths and spacings. It ensures
that the grid spacing is 0.5A or finer. If you have APBS's psize.py
installed and you wish to use it, you can set that up on the plugin's
"APBS Location" tab.
Finally, it's worth noting that the plugin's "Visualization" tab can be
used for easy visualization of any electrostatic potential, not just
things generated by APBS.
This isn't a democracy;| _ |Michael Lerner
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