Structure Preparation

The --prepare flag enables automatic structure preparation before pocket scouting. This includes selecting the best alternate locations, adding missing hydrogen atoms according to the CHARMM force field, and assigning terminal caps to chains. When preparation is enabled, the extraction flag (-e) is automatically turned on so that the protonated structure is written to the output.

poke -dvp --prepare protein.pdb

Tip

When --prepare is used without -ss, the scouter selection is automatically set to the prepared atoms (proteins, nucleic acids, cofactors, and structural ions) instead of all atoms.

Alt-location selection

When atoms have alternate locations (alt-locs), the preparator selects the best conformer for each residue based on highest occupancy. In case of a tie, the conformer with the lowest temperature factor is preferred.

Hydrogen addition

Missing hydrogen atoms are added based on the CHARMM force field definitions. By default all existing hydrogens are removed and re-added. Use --keep-hydrogens to retain existing hydrogens and only add the missing ones:

poke -dvp --prepare --keep-hydrogens protein.pdb

Capping

Terminal caps are automatically added to chain ends. The preparator detects chain separations based on several criteria: changes in species type (protein, nucleic acid), segment ID (chain) changes, large jumps in residue IDs, and explicit termini indices.

The default caps are NH3+/COO- for proteins and 5TER/3TER for nucleic acids. These can be customized:

Flag	Description
--caps-types TYPE N_TERM C_TERM ...	Cap types for each species (e.g., protein NH3+ COO-)
--caps-exclude NAME ...	Residue names to skip when capping (default: ACE NME)
--ignore-segid	Do not use segment IDs to detect chain separations
--max-other-len LEN	Max “other” residues before a chain is considered interrupted (default: 5)
--resid-threshold LEN	Residue ID jump to consider a chain interrupted (default: 50, used only if segid is absent)
--ter-indices IX ...	Explicit 0-based residue indices to treat as terminal

Protonation states

Residues with titratable side chains can be assigned specific protonation states. The default is auto, which uses the presence of specific hydrogen atoms or geometric criteria (covalent/hydrogen bond detection) to determine the correct state.

Flag	Options	Auto-detection method
--his TYPE	auto, bond, HSP, HSE, HSD	Presence of HD1/HE2 or hydrogen bonding
--cys TYPE	auto, bond, CYS, CYS2	Presence of HG1 or covalent bonding (disulfide)
--lys TYPE	auto, LYS, LSN	—
--arg TYPE	auto, ARG, ARGN	—
--glu TYPE	auto, GLU, GLUP	—
--asp TYPE	auto, ASP, ASPP	—

For fine-grained control, --custom-restype IX TYPE can be used to override the residue type at specific 0-based indices:

poke -dvp --prepare --custom-restype 42 HSE 105 CYS2 protein.pdb

Preparation selection

By default, only proteins, nucleic acids, and common cofactors and structural ions are prepared. Use --selection-prepare with an MDAnalysis selection string to control which atoms undergo preparation:

poke -dvp --prepare --selection-prepare "protein" protein.pdb