extract

Overview

Summary: Extract an active-site pocket from a protein-ligand PDB to define the ML region and surrounding MM environment. Specify substrates with -c by residue name, residue ID, or a PDB path. Link hydrogens are added to cap cut bonds when --add-linkh is enabled. Use --ligand-charge for non-standard residue charges.

mlmm extract creates an active-site pocket from a protein-ligand PDB to define the ML region. It selects residues near the substrate, truncates the model according to backbone/side-chain rules, optionally caps severed bonds with link hydrogens, and can process single structures or ensembles.

This is typically the first step in an mlmm-toolkit workflow, producing a smaller, computationally tractable model from a full protein-ligand complex.

If you run into misclassification (e.g., unusual residue/atom naming), see the appendix below on naming requirements and the internal reference lists.

Minimal example

mlmm extract -i complex.pdb -c A:123 -o pocket.pdb -l -3

Output checklist

  • pocket.pdb (or custom path via -o)

  • Charge summary logged via INFO (amino acids, ions, substrates, total)

Common examples

  1. Minimal (ID-based substrate) with explicit total ligand charge.

mlmm extract -i complex.pdb -c A:123 -o pocket.pdb -l -3

  1. Substrate provided as a PDB; per-resname charge mapping.

mlmm extract -i complex.pdb -c substrate.pdb -o pocket.pdb \
 -l "GPP:-3,MMT:-1"

  1. Multi-structure to single multi-MODEL output with hetero-hetero proximity.

mlmm extract -i complex1.pdb complex2.pdb -c A:123 \
 -o pocket_multi.pdb --radius-het2het 2.6 -l -3 --verbose

Usage

mlmm extract -i COMPLEX.pdb [COMPLEX2.pdb...]
 -c SUBSTRATE_SPEC
 [-o POCKET.pdb [POCKET2.pdb...]]
 [--radius Å] [--radius-het2het Å]
 [--include-h2o/--no-include-h2o]
 [--exclude-backbone/--no-exclude-backbone]
 [--add-linkh/--no-add-linkh]
 [--selected-resn LIST]
 [-l, --ligand-charge MAP_OR_NUMBER]
 [--verbose/--no-verbose]

Examples

# Minimal (ID-based substrate) with explicit total ligand charge
mlmm extract -i complex.pdb -c '123' -o pocket.pdb -l -3

# Substrate provided as a PDB; per-resname charge mapping (others remain 0)
mlmm extract -i complex.pdb -c substrate.pdb -o pocket.pdb -l 'GPP:-3,SAM:1'

# Name-based substrate selection including all matches (WARNING is logged)
mlmm extract -i complex.pdb -c 'GPP,SAM' -o pocket.pdb -l 'GPP:-3,SAM:1'

# Multi-structure to single multi-MODEL output with hetero-hetero proximity enabled
mlmm extract -i complex1.pdb complex2.pdb -c 'GPP,SAM' -o pocket_multi.pdb --radius-het2het 2.6 -l 'GPP:-3,SAM:1'

# Multi-structure to multiple outputs with hetero-hetero proximity enabled
mlmm extract -i complex1.pdb complex2.pdb -c 'GPP,SAM' -o pocket1.pdb pocket2.pdb --radius-het2het 2.6 -l 'GPP:-3,SAM:1'

Workflow

Residue inclusion

  • Always include the substrate residues from -c/--center.

  • Standard cutoff (--radius, default 2.6 Å):

  • When --no-exclude-backbone, any atom within the cutoff qualifies a residue.

  • When --exclude-backbone, amino-acid residues must contact the substrate with a non-backbone atom (not N/H*/CA/HA*/C/O). Non-amino acids use any atom.

  • Independent hetero-hetero cutoff (--radius-het2het): adds residues when a substrate hetero atom (non C/H) lies within the specified Å of a protein hetero atom. With backbone exclusion enabled the protein atom must be non-backbone.

  • Water handling: HOH/WAT/H2O/DOD/TIP/TIP3/SOL are included by default (--include-h2o).

  • Forced inclusion: --selected-resn accepts IDs with chains/insertion codes (e.g., A:123A).

  • Neighbor safeguards:

  • When backbone exclusion is off and a residue contacts the substrate with a backbone atom, auto-include the peptide-adjacent N/C neighbors (C-N <= 1.9 Å). Termini keep caps (N/H* or C/O/OXT).

  • Disulfide bonds (SG-SG <= 2.5 Å) bring both cysteines.

  • Non-terminal PRO residues always pull in the N-side amino acid; CA is preserved even if backbone atoms are removed, and when --exclude-backbone, the neighbor’s C/O/OXT remain to maintain the peptide bond.

Truncation/capping

  • Isolated residues retain only side-chain atoms; amino-acid backbone atoms (N, CA, C, O, OXT plus N/CA hydrogens) are removed except for PRO/HYP safeguards.

  • Continuous peptide stretches keep internal backbone atoms; only terminal caps (N/H* or C/O/OXT) are removed. TER awareness prevents capping across chain breaks.

  • With --exclude-backbone, main-chain atoms on all non-substrate amino acids are stripped (subject to PRO/HYP safeguards and PRO neighbor retention).

  • Non-amino-acid residues never lose atoms named like backbone (N/CA/HA/H/H1/H2/H3).

Charge summary (--ligand-charge)

  • Amino acids and common ions draw charges from internal dictionaries; waters are zero.

  • Unknown residues default to 0 unless --ligand-charge supplies either a total charge (distributed across unknown substrate residues, or all unknowns when no unknown substrate) or a per-resname mapping like GPP:-3,SAM:1.

  • Summaries (protein/ligand/ion/total) are logged for the first input when verbose mode is enabled.

Substrate specification (-c/--center)

  • PDB path: the coordinates must match the first input exactly (tolerance 1e-3 Å); residue IDs propagate to other structures.

  • Residue IDs: '123,124', 'A:123,B:456', '123A', 'A:123A' (insertion codes supported).

  • Residue names: comma-separated list (case insensitive). If multiple residues share a name, all matches are included and a warning is logged.

Multi-structure ensembles

  • Accepts multiple input PDBs (identical atom ordering is validated at the head/tail of each file). Each structure is processed independently and the union of selected residues is applied to every model so that outputs remain consistent.

  • Output policy:

  • No -o, multiple inputs -> per-file pocket_<original_basename>.pdb.

  • One -o path -> single multi-MODEL PDB.

  • N outputs where N == number of inputs -> N individual PDBs.

  • Diagnostics echo raw vs. kept atom counts per model along with residue IDs.

CLI options

Note: Default values shown are used when the option is not specified.

Option

Description

Default

-i, --input PATH...

One or more protein-ligand PDB files (identical atom ordering required).

Required

-c, --center SPEC

Substrate specification (PDB path, residue IDs, or residue names).

Required

-o, --output PATH...

Pocket PDB output(s). One path => multi-MODEL, N paths => per input.

Auto (pocket.pdb or pocket_<input>.pdb)

-r, --radius FLOAT

Atom-atom distance cutoff (Å) for inclusion.

2.6

--radius-het2het FLOAT

Independent hetero-hetero cutoff (Å, non C/H).

0.0

--include-h2o/--no-include-h2o

Include HOH/WAT/H2O/DOD/TIP/TIP3/SOL waters.

True

--exclude-backbone/--no-exclude-backbone

Remove backbone atoms on non-substrate amino acids (PRO/HYP safeguards).

False

--add-linkh/--no-add-linkh

Add carbon-only link hydrogens at 1.09 Å along severed bonds.

False

--selected-resn TEXT

Force-include residues (IDs with optional chains/insertion codes).

""

--modified-residue TEXT

Comma-separated residue names (with optional charge) to treat as amino acids for backbone truncation and charge assignment. Examples: HD1,HD2,HD3 or HD1:0,SEP:-2. Useful for modified amino acid residues with non-standard names.

""

-l, --ligand-charge TEXT

Total charge or per-resname mapping (e.g., GPP:-3,SAM:1).

None

-v, --verbose/--no-verbose

Emit INFO-level logging (True) or keep warnings only (False).

True

Tip

If the extracted pocket is too small, calculated energies and barriers may be unreliable. In such cases, increasing the extraction radius (e.g., -r 4.0 or higher) can improve accuracy by including more of the protein environment.

Outputs

<output>.pdb # Pocket PDB(s) with optional link hydrogens after a TER record
 # Single input -> pocket.pdb by default
 # Multiple inputs without -o -> pocket_<original_basename>.pdb per structure
 # One -o path with multiple inputs -> single multi-MODEL PDB
 # Output directories are not created automatically; ensure they exist

  • Charge summary (protein/ligand/ion/total) is logged for model #1 when verbose mode is enabled.

  • Programmatic use (extract_api) returns {"outputs": [...], "counts": [...], "charge_summary": {...}}.

Systems with non-standard residues (MCPB, etc.)

When metal-coordinating amino acid parameters are generated by tools such as Amber’s MCPB.py (Metal Center Parameter Builder), the coordinating residues are assigned non-standard names (e.g., HD1, HE1, CM1, AP1). These are not included in extract’s internal AMINO_ACIDS dictionary, so backbone truncation and link-hydrogen capping will not be applied correctly.

When such residues are detected, extract will display a warning:

[extract] WARNING: Residue HD1 83 may be an amino acid (has N, CA, C, O)
but is not recognized as a standard residue name.
Backbone truncation was not applied.
Consider preparing the pocket model manually.

Important

For systems containing non-standard residues, manual pocket model construction is recommended. Steps:

  1. Select residues around the active site and determine truncation points

  2. Add a link hydrogen on the parent atom (the atom that remains) of each severed covalent bond

  3. Use residue name LKH (chain L) and atom name HL for the link hydrogen

  4. Place it at 1.09 Å along the original bond direction

Appendix: PDB naming requirements and reference lists

This appendix is mainly for debugging cases where extract misclassifies residues due to non-standard residue/atom naming. If your inputs follow standard PDB conventions, you can usually skip it.

Important

For extract to work correctly, residue names and atom names in the input PDB must conform to standard PDB naming conventions. The tool relies on internal dictionaries to recognize amino acids, ions, water molecules, and backbone atoms. Non-standard naming will cause residues to be misclassified or charges to be incorrectly assigned.

The following internal constants define the recognized names:

AMINO_ACIDS

A dictionary mapping residue names to their nominal integer charges. Membership in this dictionary determines whether a residue is treated as an amino acid for backbone handling, truncation, and charge calculation.

Standard 20 amino acids (charges reflect physiological pH):

  • Neutral: ALA, ASN, CYS, GLN, GLY, HIS, ILE, LEU, MET, PHE, PRO, SER, THR, TRP, TYR, VAL

  • Positive (+1): ARG, LYS

  • Negative (-1): ASP, GLU

Canonical extras:

  • SEC (selenocysteine, 0), PYL (pyrrolysine, +1)

Protonation/tautomer variants (Amber/CHARMM style):

  • HIP (+1, fully protonated His), HID (0, Nd-protonated His), HIE (0, Ne-protonated His)

  • ASH (0, neutral Asp), GLH (0, neutral Glu), LYN (0, neutral Lys), ARN (0, neutral Arg)

  • TYM (-1, deprotonated Tyr phenolate)

Phosphorylated residues:

  • Dianionic (-2): SEP, TPO, PTR

  • Monoanionic (-1): S1P, T1P, Y1P

  • Phospho-His (phosaa19SB): H1D (0), H2D (-1), H1E (0), H2E (-1)

Cysteine variants:

  • CYX (0, disulfide), CSO (0, sulfenic acid), CSD (-1, sulfinic acid), CSX (0, generic derivative)

  • OCS (-1, cysteic acid), CYM (-1, deprotonated Cys)

Lysine variants / carboxylation:

  • MLY (+1), LLP (+1), DLY (+1), KCX (-1, Nz-carboxylic acid)

D-amino acids (19 residues):

  • DAL, DAR, DSG, DAS, DCY, DGN, DGL, DHI, DIL, DLE, DLY, MED, DPN, DPR, DSN, DTH, DTR, DTY, DVA

Other modified residues:

  • CGU (-2, gamma-carboxy-glutamate), CGA (-1), PCA (0, pyroglutamate), MSE (0, selenomethionine), OMT (0, methionine sulfone), HYP (0, hydroxyproline)

  • Various others: ASA, CIR, FOR, MVA, IIL, AIB, HTN, SAR, NMC, PFF, NFA, ALY, AZF, CNX, CYF

N-terminal variants (prefix N): NALA (+1), NARG (+2), NASP (0), NGLU (0), NLYS (+2), etc., plus ACE (0), NTER (+1, generic)

C-terminal variants (prefix C): CALA (-1), CARG (0), CASP (-2), CGLU (-2), CLYS (0), etc., plus NHE (0), NME (0), CTER (-1, generic)

BACKBONE_ATOMS

A set of atom names considered backbone atoms for amino acids. These are used when --exclude-backbone to determine which atoms to remove from non-substrate residues:

N, C, O, CA, OXT, H, H1, H2, H3, HN, HA, HA2, HA3

ION

A dictionary mapping ion residue names to their formal charges. Recognized ions are automatically assigned correct charges in the charge summary.

Charge

Residue Names

+1

LI, NA, K, RB, CS, TL, AG, CU1, Ag, K+, Na+, NH4, H3O+, HE+, HZ+, Tl

+2

MG, CA, SR, BA, MN, FE2, CO, NI, CU, ZN, CD, HG, PB, Be, PD, PT, Sn, Ra, YB2, V2+

+3

FE, AU3, AL, GA, IN, CE, Ce, CR, Cr, Dy, EU, EU3, Er, GD3, LA, LU, Nd, PR, SM, Sm, TB, Tm, Y, Pu

+4

U4+, Th, Hf, Zr

-1

F, CL, BR, I, Cl-, IOD

WATER_RES

A set of residue names recognized as water molecules. Waters are included by default (--include-h2o) and assigned zero charge:

HOH, WAT, H2O, DOD, TIP, TIP3, SOL

See Also