Using APBS with other programs
APBS was designed to facilitate use with other programs. This section outlines some of the programs with which APBS is known to work. However, it is likely that applications which use APBS have been inadvertantly omitted from this list. If you know of software that uses APBS and is not listed here, please contact Nathan Baker <baker@biochem.wustl.edu>.
Graphical user interfaces
PMV
PMV (http://www.scripps.edu/~sanner/python) is a Python-based molecular visualization package which provides an interface to APBS. It not only permits visualization of APBS results but it also integrates setup and executation of APBS calculations. The PMV/APBS interface (http://mccammon.ucsd.edu/pmv_apbs/) is under active development and future versions will offer even more setup, visualization, and analysis functionality.
The APBS interface is distributed with recent beta versions of PMV, avalaible from http://www.scripps.edu/~sanner/python. Additional documention for using APBS with PMV is provided at http://mccammon.ucsd.edu/~jswanson/apbsDoc/command_doc2.html.
VMD
VMD (http://www.ks.uiuc.edu/Research/vmd/) is a molecular visualization and animation package which provides an interface to APBS. It permits isocontour-based visualization of APBS results and provides a Tcl plugin to setup APBS calculations for visualization.
The APBS interface is provided as a plugin to VMD and is available from http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/.
Visualization software
Electrostatic potentials are commonly visualized in the context of biomolecular structure to better understand functional aspects of biological systems. This section describes molecular graphics software which can display potentials and other data output from APBS.
PMV
PMV (http://www.scripps.edu/~sanner/python) is a Python-based molecular visualization package which provides an interface to APBS. It not only permits isocontour- and surface-based visualization of APBS results and it also integrates setup and executation of APBS calculations. The PMV/APBS interface is under active development and future versions will offer even more setup, visualization, and analysis functionality.
The APBS interface is distributed with recent beta versions of PMV, avalaible from http://www.scripps.edu/~sanner/python.
VMD
VMD (http://www.ks.uiuc.edu/Research/vmd/) is a molecular visualization and animation package which provides an interface to APBS. It permits isocontour-based visualization of APBS results and provides a Tcl plugin to setup APBS calculations for visualization.
The APBS interface is provided as a plugin to VMD and is available from http://www.ks.uiuc.edu/Research/vmd/plugins/apbsrun/.
Additionally, APBS includes simple visualization-only Tcl scripts for VMD in the tools/visualization/vmd (see the discussion of Data visualization tools in this manual).
PyMOL
PyMOL (http://pymol.org/) Python-based a molecular graphics program. Upcoming versions of PyMOL may directly support APBS integration. In the meantime, Michael Lerner <mlerner@umich.edu> has written a module to read APBS electrostatics output into PyMOL; this module is available from http://www.umich.edu/~mlerner/PyMOL/.
Dino3D
Dino3D (http://www.dino3d.org/ is a molecular graphics program which can read UHBD-format electrostatic data. APBS can write multigrid results in UHBD format (see the write ELEC command) and therefore can be used with Dino3D.
MOLMOL
MOLMOL (http://www.mol.biol.ethz.ch/wuthrich/software/molmol/) is a molecular graphics package with an emphasis on NMR-generated structural data. A program is provided with APBS (see tools/mesh and the Data conversion tools in this manual) which converts OpenDX data to MOLMOL format.
OpenDX
OpenDX (http://www.opendx.org) is a general data visualization package which can read APBS output using the scripts provided in tools/visualization/opendx (see the discussion of Data visualization tools in this manual). However, as there is no straightforward way to visualizate the potential in the context of the atomic structure, OpenDX should not a first choice for APBS visualization.