Surfnet

Surfnet finds and displays molecular cavities and indentations. 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 comes in two flavors:

• Surfnet - Interface - find cavities between two specified sets of atoms, Receptor and Ligands. The two sets of atoms do not really have to be a receptor and ligand(s). They can be in the same or different models.
  
  
• Surfnet - Selected Atoms - find any cavities formed by the specified atoms (the Midas Selection).

1. Pairwise combinations of atoms are examined for intervening void space. If the type of calculation is Interface, only pairs with one atom from each specified set are examined. If the type of calculation is Selected Atoms, pairwise combinations of atoms in the specified set are examined. Either way, 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, which is opened as a SurfaceModel in Chimera and shown in the specified Representation (Mesh or solid Surface) and Color (default white). The surface can be closed (deleted) or hidden using the Model Panel.