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).

Surfnet is an extension in the Docking category. There are several ways to start an extension.

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 border of the color well in the dialog box before clicking "OK" or "Apply." This will bring up the Color Editor, in which a new color or colors can be created and stored. Clicking "OK" executes a Surfnet calculation and dismisses the dialog box; "Apply" runs the calculation without closing the dialog box, and each successive click on "Apply" creates and displays another contour surface according to the current set of input parameters, including color.