The Volume plugin performs three actions:
This plugin does not have a GUI.
The following commands compute grid based on currently selected atoms, create triangles, and map atoms:
Connollythe typical molecular surface
VanderWaalsbased on Vander-der-Waals distance
SolventAccessiblebased on Vander-der-Waals distance plus probe radius
ElectronDensityEXPERIMENTAL
GaussianEXPERIMENTAL
These commands work on selected, existing grids and require a contour level to be specified as parameter:
AddSurface double*Triangulate on grid and map atoms to surface.
ContourHigh double*Create contour from grid, where greater values are inside.
ContourLow double*Create contour from grid, where greater values are outside.
The creation of triangles from a grid is based on algorithm
by Jules Bloomenthal:
Bloomenthal, Jules, An Implicit Surface Polygonizer, Graphics Gems IV, p. 324-349, (Paul Heckbert ed.),
Academic Press (Morgan Kaufmann) 1994.
Section Key ValuetypeDescription
Volume GridSpacing floatSpacing (Å) on created grids (default 0.4)
Volume SolventRadius floatRadius (Å) off solvent probe (default 1.4)