Surfnet

Surfnet finds and displays molecular cavities and indentations. The method is an adaptation of that described in:

R.A. Laskowski, "SURFNET: A program for visualizing molecular surfaces, cavities, and intermolecular interactions" J Mol Graph 13:323 (1995).

There are several ways to start Surfnet, a tool in the Surface/Binding Analysis category.

Surfnet comes in two flavors called SurfNet - option, where option can be Interface (find cavities between molecules) or Selected Atoms (find cavities and surface indentations adjacent to the specified atoms). If Surfnet - Selected Atoms is chosen, it is necessary to enter an atom specification. If Surfnet - Interface is chosen, atom specifications for the receptor and ligand(s) are required. The receptor and ligand(s) may be in the same model or different models.

A brief description of the method is needed to explain the remaining options:

1. Pairwise combinations of atoms are examined for intervening void space. If the type of calculation is Interface, only receptor atom/ligand atom pairs are examined; if there are multiple ligands, they are treated collectively. If the type of calculation is Selected Atoms, only pairs of atoms included in the input atom specification are examined. In all cases, only pairs of atoms no farther apart than the Distance Cutoff (in angstroms) are examined. A "gap sphere" is placed directly between the two atoms and shrunk until it no longer intersects the VDW surface of any atom. Atomic radii are assigned by Chimera based on inferred atom types. Gap spheres with radii equal to or greater than the Grid Interval (also see below) are retained.
2. The Density of each gap sphere is smeared out from its center according to a Gaussian or Quadratic function such that the value at its radius (100.0 in arbitrary units) is half the value at its peak (200.0).
3. At each point in a 3-dimensional grid, only the largest density contribution from a gap sphere is stored (not necessarily the contribution from the nearest gap sphere center, since the decrease in density with distance depends on radius). The resolution of the grid in angstroms (Grid Interval) is under user control.
4. The grid values are used to generate a contour surface at the level of 100.0. The Compact option collapses small triangles in the contour surface into single points.
5. The contour surfaces are displayed as a Mesh or solid Surface Representation opened as a VRML object into the lowest available model number.

To assign a Color other than the default cyan to the contour surface, click the color well in the dialog before clicking OK or Apply. This will bring up the Color Editor, in which a new color can be created. OK executes a Surfnet calculation and dismisses the dialog. Apply runs the calculation without closing the dialog; each successive click on Apply will create and display another contour surface according to the current settings. Close closes the dialog, and Help opens this manual page in a browser window.