APBS APBS icon

** Requires installing APBS locally **

As of 4/30/2020, the APBS web service from the National Biomedical Computation Resource (NBCR) has been discontinued. This Chimera tool will no longer work unless you install APBS (available from GitHub) on your own computer and then in this tool, change the Executable location to Local and enter its location.

Alternatively, the APBS web service at server.poissonboltzmann.org can be run separately (not using this Chimera tool) and the resulting electrostatic potential map (.dx file) opened in Chimera.

The APBS tool is an interface for running APBS (Adaptive Poisson-Boltzmann Solver) electrostatics calculations. Users should cite:

Electrostatics of nanosystems: application to microtubules and the ribosome. Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Proc Natl Acad Sci USA. 2001 Aug 28;98(18):10037-41.
A structure should be prepared for APBS calculations by reconstructing missing heavy atoms, adding hydrogens, and assigning atomic charges and radii. These tasks can be done with PDB2PQR alone or in combination with parts of Dock Prep. Atomic charges can be assigned with Add Charge or PDB2PQR, although the latter may be preferred because it includes force fields developed specifically for Poisson-Boltzmann calculations. By default, any explicit solvent (typically water) will be omitted from the APBS calculation.

The resulting electrostatic potential map will be opened as a new model in Chimera and the Electrostatic Surface Coloring tool for coloring molecular surfaces by potential will appear. Alternatively, the map can be shown as isopotential surfaces; these are not displayed automatically, but can be shown by starting Volume Viewer and clicking the eye icon or by using the volume command.

See also: Coulombic Surface Coloring, DelPhiController

There are several ways to start APBS, a tool in the Surface/Binding Analysis category. It is also implemented as the command apbs.

Options:

Focusing will be performed automatically; that is, there will be an initial electrostatics calculation on a larger grid with relatively coarse divisions, followed by another calculation on a smaller grid with finer divisions, for which the boundary conditions are determined from the first run (APBS keyword mg-auto). Default grid sizes (see dime, cglen, and fglen below) are based on the dimensions of the input structure. APBS keywords are shown in parentheses below; see the documentation at the APBS site for details on specific options.

Executable location:

OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The job will be run in the background; clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Close dismisses the dialog, and Help opens this manual page in a browser window.

The electrostatic potential map will be opened as a new model in Chimera, and the Electrostatic Surface Coloring tool for coloring molecular surfaces by potential will appear. Alternatively, the map can be shown as isopotential surfaces; these are not displayed automatically, but can be shown by starting Volume Viewer and clicking the eye icon or by using the volume command.

UCSF Computer Graphics Laboratory / September 2020