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Uses Will Sheffler's packing code (holes) to evaluate voids/holes in packing
You can pass a residue selector to only compute the holes score for that given selection: The holes calculation is performed on the Pose as whole (ignoring the ResidueSelector), but when the time comes to report the score, only the atoms in the residue selector are summed. The Holes score is a sum of individual atoms/residues anyway (technically "PoseBalls"), so by only reporting a specific selection, we should be able to get location-specific data.
How to interpret the holes score output: A value of 0.0 means on par with native structures observed in the PDB; positive is worse (more voids), negative is better (less voids); this is for the default HolesParams used here, which is dec15; it is not recommended to change this unless you know the inner workings of what this code is doing.
<Holes name="(&string)" threshold=“(&real)" residue_selector="(&string)" normalize_per_atom="(&bool)" normalize_per_residue="(&bool)" exclude_bb_atoms="(&bool)" />
#compute holes around h-bond networks; correlates better than using the total holes score <RESIDUE_SELECTORS> # get all network residues as output by HBNet <ResiduePDBInfoHasLabel name="hbnet_residues" property="HBNet" /> # select everything within 5A around the network residues <Neighborhood name="around_hbnet" selector="hbnet_residues" distance="5.0" /> # select only the buried residues within this set <Layer name="hbnet_core" select_core="true" core_cutoff="3.6" /> # select core using sidechain neighbors (don’t use SASA because of potential voids!) <And name="core_around_hbnet" selectors="hbnet_core,around_hbnet"/> </RESIDUE_SELECTORS> <FILTERS> # holes score only around h-bond networks <Holes name="network_holes" threshold="1.8" residue_selector="core_around_hbnet" normalize_per_atom="true" exclude_bb_atoms="true" confidence="0"/> # holes score of the full pose <Holes name="full_holes" threshold="1.8" confidence="0"/> </FILTERS> <PROTOCOLS> <Add filter="network_holes" /> <Add filter="full_holes" /> </PROTOCOLS>
In order to use the -holes::dalphaball flag, you need to first compile the corresponding executable in source/external/DAlpahBall. This is done by navigating to
main/source/external/DAlpahBall and typing
make. (You may need to make platform-specific adjustments to the Makefile.) The pass the path to the executable that is produced to the -holes::dalphaball flag.