NanoShaper

A recent addition to VMD's molecular surface representations is support for NanoShaper, a molecular surface engine that uses a ray casting and grid-based method to find molecular surfaces, pockets, and cavities, on multi-core CPUs [44]. NanoShaper can successfully compute molecular surfaces in many cases that cause problems for both Surf and MSMS, and without being limited to the Gaussian surfaces of QuickSurf. The key limitation for NanoShaper, similar to QuickSurf, relates to memory use which grows with the volume of the bounding box containing the molecular structure of interest.

See the web page https://www.electrostaticszone.eu/ for more details. Available options include

• Surface Type - SES, Skin, or Blobby for molecules with more than one thousand atoms and 3.0 for smaller molecules)
• Representation Method - The surface can optionally be drawn using lines rather than solid triangles
• SES Probe Radius - Probe radius used to construct the solvent-excluded molecular surface
• Skin Parameter - Parameter used to construct the molecular skin surface
• Blob Parameter - Gaussian exponent scaling factor used to construct the Gaussian (Blobby) surface