This application in Rosetta3 was created and documented by David Johnson, et al.

Purpose and Algorithm

This application takes in a PDB file and specified target residue/residue pair and, generates a (localized) PocketGrid, and outputs the total "deep volume" of all target pockets and the largest pocket. See the referred paper for Pocket algorithm details.


Johnson DK and Karanicolas J. Druggable protein interaction sites are more predisposed to surface pocket formation than the rest of the protein surface. PLoS Comput Biol. 2013;9(3):e1002951

Command Line Options

Sample command

pocket_measure.linuxgccrelease -database ~/Rosetta/main/database -in:file:s input.pdb -central_relax_pdb_num 97:A,143:A -pocket_num_angles 100

pocket_measure options

General Rosetta Options
   -database                   Path to rosetta databases
   -in:file:s                  Input pdb file(s)

Pocket Identification Options
   -pocket_num_angles          Number of different pose angles to measure pocket score at, default is 1, but at least 100 is recommended to reduce grid and orientation artifacts
   -pocket_grid_size           Defines the dimensions of the PocketGrid centered on the target residue(s), or 10 Angstroms by default
   -pocket_psp                 Mark Pocket-Solvent-Pocket events as well, default=false
   -pocket_sps                 Unmark Solvent-Pocket-Solvent events, default=true
   -pocket_surface_dist        Distance to consider pocket point being "surface" and excluded from "deep volume"
   -pocket_max_spacing         Maximum residue-residue distance to be considered a pocket, default is 8 Angstroms
   -pocket_min_size            Minimum pocket size to score, in cubic Angstroms, default is 10 cubic Angstroms
   -pocket_max_size            Maximum pocket size to report, in cubic Angstroms, 0 for no limit (default)
   -pocket_probe_radius        Radius of surface probe molecule, default 1.0 Angstroms
   -pocket_side                Include only side chain atoms for target surface, default=false
   -pocket_filter_by_exemplar  Additional filter generates an exemplar and then restricts the pocket to that exemplars, defaul=false
   -pocket_ignore_buried       Ignore pockets that are not solvent exposed, default=true
   -pocket_only_buried         Identify only pockets buried in the protein core (automatically sets -pocket_ignored_buried false), default=false
   -pocket_static_grid         By default the PocketGrid expands if pocket points are identified near the edge, this flag disables the autoexpanding feature.
   -pocket_grid_spacing        Defines the spacing of the PocketGrid, 0.5 by default

Pocket Output Options
   -pocket_dump_pdbs           Generate PDB files of all PocketGrid points marked as pocket, for debugging/visualization of underlying PocketGrid
   -pocket_debug_output        Print any and all debugging output related to pockets, default=false


  • Because orientation of the protein can affect the exact identification of the pocket, which can have profound effects on the measured pocket volume, it is recommended to use the -pocket_num_angles flag with at least 100 to generate PocketGrids at multiple rotations and return the average pocket volume.

See Also