Command: kvfinder

Usage:
kvfinder  model-spec  [ probeIn  r1 ] [ probeOut  r2 ] [ surfaceType  SAS | SES ] [ removalDistance  d ] [ volumeCutoff  minvol ] [ gridSpacing  s ] [ showTool  true | false ] [ replace  true | false ] [ boxOrigin  x,y,z ] [ boxExtent  length | lx,ly,lz ]

The kvfinder command detects cavities or pockets in an atomic structure using KVFinder, a method based on surface shape, as described in:

parKVFinder: A thread-level parallel approach in biomolecular cavity detection. Guerra JVDS, Ribeiro-Filho HV, Bortot LO, Honorato RV, Pereira JGC, Lopes-de-Oliveira PS. SoftwareX. 2020 Jul-Dec;100606.
pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. Guerra JVDS, Ribeiro-Filho HV, Jara GE, Bortot LO, Pereira JGC, Lopes-de-Oliveira PS. BMC Bioinformatics. 2021 Dec 20;22(1):607.

The kvfinder command installs and runs pyKVFinder locally. It is also implemented as the Find Cavities tool. The authors of KVFinder (at the Brazilian Biosciences National Lab) also provide a web service, but it is not used in the ChimeraX implementation. See also: measurements, Protein-Ligand Binding Sites tutorial, MOLE Channel Coloring tutorial, recipe for reading CASTp pockets

Conceptually, the KVFinder method uses two spherical probes to identify cavities:

• probeIn with smaller radius r1 (default 1.4 Å) is rolled over the VDW spheres of the macromolecule to define a molecular surface. Where the surface of this probe can go defines the solvent-excluded surface (SES), and where the center of this probe can go defines the solvent-accessible surface (SAS). By default, the SES is used, but the surfaceType option can be used to specify SAS instead.
  
  
• probeOut with larger radius r2 (default 4.0 Å) is rolled over the VDW spheres of the macromolecule to get an initial estimate of the outer limits of the cavities. The cavities are then trimmed further from the exterior by the removalDistance d (default 2.4 Å) to avoid finding too many shallow indentations. Using a larger probeOut increases the calculation time.

PDB HET residues (solvent, ligands, and ions) are ignored. KVFinder calculates the volume and surface area of each identified cavity, given the parameters above, and reports them in the Log. Cavities with volume less than volumeCutoff minvol (default 5.0 ų) are omitted from the results.

The cavities are discretized as points on a grid with gridSpacing s (default 0.6 Å). Using a smaller spacing gives a higher-resolution result, but can significantly increase the calculation time. These collections of dots are opened as (pseudo)atomic models in ChimeraX, each cavity as a separate submodel assigned a unique color.

The showTool option indicates whether to also tabulate the results in an interactive cavity list (default true).

With replace true (default), running the calculation again on the same atomic model will overwrite the previously created cavity models and cavity list. If false, a new cavity list and additional cavity models will be created without closing the existing ones.

By default, the entire macromolecular surface will be examined. However, the calculation can be limited to a rectangular box by specifying both of the following:

• boxOrigin x,y,z – coordinates of the corner of the box separated by commas only
• boxExtent length | lx,ly,lz – box side length given as a single number in Å for a cubic box, or as three numbers separated by commas only for the box dimensions along X, Y, and Z