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Electrostatic Potential Surface Panel |
Calculate the electrostatic potential on a grid, using a Poisson-Boltzmann solver with the partial charges of the input structure, and generate isosurfaces and a mapping to the molecular surface.
To open the Electrostatic Potential Surface panel, you can:
Choose Workspace → Surface → Poisson-Boltzmann Electrostatic in the main window.
The electrostatic potential is generated by solving the Poisson-Boltzmann equations, using the partial charges of all the atoms in the entry that is in the Workspace, which must be a single, named entry. Two grids are used—a fine grid for the region of interest ("focusing" grid) that is defined by an atom selection, and a coarse grid for the rest of the system. The structure in the Workspace is considered to be immersed in a solvent, whose parameters you can specify; the default is water.
Once the potential is evaluated, surfaces are generated by interpolation on the grid. If a mapping to the molecular (Connolly) surface is needed, this surface is also generated.
Use the standard picking controls to select the atoms that define the fine (focusing) grid used in the Poisson-Boltzmann calculation.
In this section you can specify various settings for solution of the Poisson-Boltzmann equations.
Specify the dielectric constant for the solute (the structure for which the potential is being calculated) in this text box. You should not normally have to change it from the default value of 1.0.
Specify the dielectric constant for the solvent. The default value is 80.0, corresponding to water as the solvent. For the electrostatic potential in a vacuum, set the value to 1.
Specify the radius of the solvent molecules. The default value of 1.4 is the value for water.
Set the temperature at which the calculation is performed.
In this section you can specify the form of the output. The electrostatic potential is calculated on a grid (producing a volume), which can be displayed in more than one way.
Map the values of the electrostatic potential onto the molecular surface for the Workspace atoms, which is also calculated.
The surface is created using interpolation on a cubic grid. This option menu allows you to specify the resolution of the resulting surface. Higher resolution means a smoother surface, which is slower to generate and draw. Lower resolution means a rougher surface but is faster to generate and and draw (and hence rotating will be faster). These controls affect the grid spacing for the surface. When you select Low, Medium, or High, the grid spacing in angstroms is displayed in the text box. If you want to specify the grid spacing, choose Custom and enter the desired value in the text box.
Generate isosurfaces of the electrostatic potential, one for positive values and one for negative values.
Choose the initial isovalue for the surfaces, in units of kT/e, from this option menu. Surfaces are generated for these isovalues, but you can change them in the Manage Surfaces panel.
Create the surface. There might be a small delay while the surface is created if you have a lot of atoms in the entry used for the surface.
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