Surfnet

H-ras (121p) protein vs. ligand

Surfnet identifies molecular cavities and indentations and displays them as surfaces. The method is an adaptation of that described in:

SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions. Laskowski RA. J Mol Graph. 1995 Oct;13(5):323-30, 307-8.

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

Surfnet finds cavities between two specified sets of atoms, Atom Set 1 and Atom Set 2. The two sets of atoms can be identical, overlapping, or completely different, and in the same or different models. If Atom Set 2 is left blank, it is assumed to be the same as Atom Set 1.

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

1. Pairwise combinations of atoms, one from each set, are examined for intervening void space. Only pairs of atoms no farther apart than the Distance Cutoff (in Å) 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 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 with Grid Interval spacing (in Å), only the largest density contribution from a gap sphere is stored. This is not necessarily the contribution from the nearest gap sphere center, since the decrease in density with distance depends on radius.
   
   
4. The grid values are used to generate a contour surface at the level of 100.0, shown in the specified Representation (Mesh or solid Surface) and Color (default white).

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