DelPhiController

DelPhiController is an interface to the program DelPhi, which uses the finite-difference Poisson-Boltzmann equation to calculate electrostatic potentials in and around molecules. DelPhi incorporates the effects of ionic strength and molecular shape; any values for the dielectric constants of the molecule and solvent may be used.

DelPhi is not included in Chimera, and must be obtained separately. DelPhiController interfaces to the academic version of DelPhi, which is available from the Honig Laboratory for for SGI IRIX, Linux, PC, AIX IBM, and Macintosh systems. DelPhiController will only interface to DelPhi on UNIX platforms.

The associated feature DelPhiViewer can display molecular surfaces colored by electrostatic potential, isopotential surfaces, and volumes containing a range of potential values. However, Surface Color and Volume Viewer are recommended instead, as they provide more general and capable interfaces for displaying electrostatic potentials with surface colors and volumes, respectively.

There are several ways to start DelPhiController, a tool in the Surface/Binding Analysis and Volume Data categories. Starting DelPhiController brings up a panel with three sections organized like index cards with their names on tabs across the top: Input, Parameter, and Output. Clicking a tab brings the corresponding card to the front.

In the Input section, the user must specify the input molecule, an atomic radii file, and an atomic charge file. For the Chimera Model input option, the Browse... button should be used to specify a model that has already been opened in Chimera. For the PDB File input option, the name of the file should be typed in or located with Browse.... Several radii (.siz) and charge (.crg) files are supplied in the data subdirectory of the DelPhi installation; these may be used as appropriate, or the user may specify customized versions. Note that the molecule input should be edited so that only the atoms of interest for the electrostatic potential calculation are included; it may be desirable to remove any solvent molecules, ions, and/or ligand molecules. Even if atoms are not displayed in Chimera, it is their presence in the original input file that matters. The atom and residue names are used for radius and charge assignment; if no match is found for an atom, values of zero are assigned. If the charge file includes charges for hydrogens, hydrogens should be present in the input molecule. Warnings will appear in the DelPhi log file for residues with strange net charges.

The potential file input is not required unless focusing is being done. Focusing is when a potential map from a previous run is used to set the boundary conditions for a subsequent run in which the grid occupies a smaller volume (has a larger box fill percentage). The PDB input for site potentials is not required unless an output site potentials file is also specified (in the Output section).

The Parameter section allows specification of parameters for the DelPhi run, such as the dielectric constants of the solvent and the molecule. Defaults are supplied, so it is possible to execute the calculation without entering anything in this section; however, what values are optimal will depend on the situation. Since discussions of the parameters are beyond the scope of this page, users are strongly encouraged to consult the documentation in the doc subdirectory of the DelPhi installation. If the Calculate GRASP Surface box is activated, a file named grasp.srf will be generated. Note that Grid Scale is in grid units per angstrom; larger values give finer grids.

The Output section allows the user to name the output file(s). The outputs always generated are the electrostatic potential map (.phi file) and a log file. If names are not supplied, the electrostatic potential file will be named default.phi and the log file will be named delphi.out. The results of any requested energy calculations will be reported in the log file. Other output files may be specified as desired; their contents and formats are described in the DelPhi documentation. To check if radii and charges have been assigned properly, it is often useful to write out a Modified PDB File, which includes these values.

Clicking Run initiates the DelPhi calculation; Cancel dismisses the DelPhiController panel. The calculation time depends on the system and parameters; in general, it ranges from nearly instantaneous to about a minute.

Upon completion of an electrostatic potential calculation initiated via DelPhiController, DelPhiViewer is started automatically. However, displaying the potential with Surface Color (for surface coloring) or Volume Viewer (for isosurfaces and transparent solids) is recommended instead. These tools are more general and capable than DelPhiViewer.

To use DelPhiViewer to display the electrostatic potential, enter the name of the map file from DelPhi (or browse to its location). There are three general types of display:

• The Isosurface is a contour surface at a specified kT/e value. Positive-valued surfaces are blue and negative-valued surfaces are red. The isosurface will be opened in the lowest available Chimera model number. The surface Representation may be solid Surface or Mesh.
• The Molecular Surface option allows coloring by electrostatic potential at the molecular surface (as in the figure above). Three color wells are provided for specifying colors to use for negative, zero, and positive potentials. Positive potentials range from the zero color (white by default) to the positive color (blue by default); negative potentials range from the zero color to the negative color (red by default). The default colors include transparency. Potentials at or above the Cutoff value are the positive color, and potentials at or below the negative of the Cutoff value are the negative color. For the MSMS Surface setting, the molecular surface should first be generated and then specified using the Browse... button. The molecular surface does not need to be saved to a file. For the Grasp SRF File setting, the name of a pre-existing Grasp surface file must be typed in or located with the Browse... button. Grasp surface creation is an option in the Parameter section of DelPhiController. The Grasp surface is opened as a model of class Surface_Model in the lowest available Chimera model number, whereas the MSMS surface occupies the same model number as the corresponding molecule. Recolor surface can be used to recolor an existing surface after color well settings have been changed.
• Volume Visualization allows display of regions containing a specified range of potential values (caution: this option may be very slow on some machines). Regions where the magnitude of the electrostatic potential falls within the specified range are displayed as transparent (at the low value) to opaque (at the high value) volumes; red indicates a negative potential and blue indicates a positive potential. The 3-dimensional data set is continuously projected into the viewing plane, and this is facilitated by dividing the data into slices along the viewing axis. The number of slices must be a power of 2. Using fewer slices decreases both resolution and computational time. The volume display is opened in the lowest available Chimera model number.