DelPhiController DelPhiController icon

molecular surface colored by potential

DelPhiController is an interface to DelPhi, which uses the finite-difference Poisson-Boltzmann equation to calculate electrostatic potentials in and around molecules. DelPhi is not included with Chimera; DelPhiController works with the academic version available from the Honig Lab. For more details than provided here, consult the DelPhi documentation [online manual] [PDF manual].

The resulting electrostatic potentials can be visualized with Electrostatic Surface Coloring or displayed as isosurfaces with Volume Viewer.

There are several ways to start DelPhiController, a tool in the Surface/Binding Analysis and Volume Data categories (including from the Volume Viewer Tools menu). It has three sections organized like index cards: Input, Parameter, and Output. Clicking a tab brings the corresponding card to the front.

Clicking Run initiates the DelPhi calculation; the time required depends on the system and parameters, but generally ranges from nearly instantaneous to minutes. The Electrostatic Surface Coloring tool will appear after the potential map (*.phi file) has been created. Cancel dismisses the DelPhiController panel, while Help opens this manual page in a browser window.


At a minimum, the required inputs are a structure of interest, a radius file, a charge file, and the location of the DelPhi executable. Any adjustments in Parameter settings and Output file names and locations must be made before the calculation is started.

The structure can be a model already open in Chimera or the contents of a local PDB file, specified using the pulldown menu in the Molecule section of the dialog.

Only the atoms to be included in the calculation should be present in the structure. It may be necessary to delete solvent, ions, ligands, and alternate crystallographic locations of atoms, and in some cases, to add hydrogens. Ultimately, which atoms should be included depends on the specific application and the availability of corresponding radius and charge parameters. Several tasks to prepare a model in Chimera can be performed with the Dock Prep tool (however, any charge assignments performed with Dock Prep will be ignored; DelPhi will only use the values in the charge file specified with DelPhiController).

The locations of other input files can be entered manually or filled in with Browse. When DelPhi has been run successfully with DelPhiController, the input file locations are saved in a user's preferences file.

Radius and charge files from the Honig group may be used, or user-customized versions. Each atom that does not match any specifications in the files will be assigned a radius of 0 and charge of 0. The log file should be checked to see if radii and charges have been assigned properly. It may also be helpful to generate a modified PDB file. To achieve the correct assignments, it may be necessary to


DelPhi uses many parameters, and although reasonable defaults are supplied, what values are optimal will depend on the situation. Note that the defaults in DelPhiController may differ from those described in the DelPhi documentation [parameter list].




The results of any requested Energy calculations will be written to the log file.

Output files:

UCSF Computer Graphics Laboratory / May 2007