APBSCommand
A graphical user interface for APBS (Adaptive Poisson-Boltzmann Solver) in PMV (Python Molecule Viewer)
Version 2.2.0
Authors: Hovig Bayandorian, Jessica Swanson, Sophie Coon, Michel F. Sanner
APBS (Adaptive Poisson-Boltzmann Solver) is software for the numerical solution of the Poisson-Boltzmann partial
differential equation, which models the electrostatic potential of
charges in an ionic solution at equilibrium. PMV (Python Molecule Viewer) is a molecule visualization suite. APBSCommand is a GUI that runs on top of PMV allowing users to prepare configuration files for APBS while visualizing their input grids. It minimizes text editing and provides default parameters based on the loaded molecule. Finally, it allows users to save their grid and system setup for future use or alteration.
The current APBSCommand is in testing and is not considered complete.
Future versions of the APBSCommand will include electrostatic potential
visualization, PDB to PQR conversion, and APBS run progress reporting.
APBSCommand is currently distributed with MGLTools so no new installation is neeeded.
If you wish APBSCommand to load every time PMV loads:
In UNIX:
1. Copy the $PMV_HOME/share/lib/python2.3/site-packages/Pmv/_pmvrc file to your home directory or change its permissions:
chmod 664 _pmvrc
2. Open the _pmvrc in a text editing program (such as emacs or vi), and
add the line (preferably immediately above the line reading "# load
the DejaVu Macros":
self.browseCommands("APBSCommand")
In Windows:
1. In the Pmv subdirectory of site-packages (likely being
C:\Python23\Lib\site-packages\Pmv), right click on _pmvrc, click Open,
then Select the program from a list, and select Wordpad.
2. Immediately above the line reading "# load the DejaVu Macros", add
the following (and save the file):
self.browseCommands("APBSCommand")
If you want to load APBSCommand for a single session of PMV:
In PMV, click File, then Browse Commands, then select the PMV package,
and then the APBSCommand Module. Click Load Module, and then Dismiss.