Find Cavities

The pyKVFinder package is integrated into UCSF ChimeraX as the Find Cavities tool, available from version 1.9. This tool allows the user to run pyKVFinder in ChimeraX and visualize the results directly on the ChimeraX viewer.

Tool

The Find Cavities tool can be accessed from:

• Tools > Binding Analysis > Find Cavities

or,

• Tools > Structure Analysis > Find Cavities

For further details on Find Cavities tool, please refer to https://www.cgl.ucsf.edu/chimerax/docs/user/tools/findcavities.html.

Command

The Find Cavities tool uses the kvfinder command. The command can be used in the ChimeraX command line interface (CLI) as follows:

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

For further details on kvfinder command, please refer to https://www.cgl.ucsf.edu/chimerax/docs/user/commands/kvfinder.html.