I've been working with Jason Vertrees on a new version of the PyMOL-APBS
plugin and it's now ready for pre-release. There are three big advantages of
the new version:
* It's been tested modern OS X, Windows and Linux systems and fixes several
* It allows you to call through to PDB2PQR directly.
* It has two visualization panels to aid in showing multiple potential
surfaces at once.
I've also upped the default maximum allowed memory since typical users have
bigger and faster computers these days.
The main reason that I'm sending this out now is to get bug reports. I think
it runs everywhere, but *please* let me know if you have problems with it.
Once it's shown to be stable, it'll be included in the next PyMOL release.
A slightly longer list of changes is included below.
== How to get it ==
There are two ways to get the new plugin
* If you have subversion installed, you can always get the latest version
* You can download the it from
That should give you a file called apbsplugin.py
Once you have the plugin, you can install it via PyMOL's plugin installer:
Plugin --> Manage Plugins --> Install
Note that the plugin will be installed as "APBS Tools2" so that you can
continue to use your old version.
== Longer feature list ==
* The ability to call through directly to PDB2PQR
* More modern apbs input files
* Two visualization panels. It's often quite useful to look at two different
electrostatic potentials at once. It's also quite useful to look at
electrostatic potentials mapped onto two different surfaces at once.
Multiple visualization panels makes this a snap: just set up one surface on
panel 1 and another surface on panel 2.
* Fixes several bugs that caused crashes on both OS X and Linux systems
* Increased maximum allowed memory
* Switch from os.system to subprocess for running external programs
* Deals with paths on Windows properly
* Gives better diagnostic information so that PyMOL/APBS developers can find
bugs more easily
* Lots of internal code cleanup
You can find this same information on the PyMOL wiki:
Michael Lerner, Ph.D.
IRTA Postdoctoral Fellow
Laboratory of Computational Biology NIH/NHLBI
5635 Fishers Lane, Room T909, MSC 9314
Rockville, MD 20852 (UPS/FedEx/Reality)
Bethesda MD 20892-9314 (USPS)