extract

pdb2reaction extract carves an active-site cluster model (binding pocket) from a protein–ligand PDB (single structure or ensemble) for downstream MEP / TSOPT / freq / DFT runs. Specify the substrate with -c/--center as a residue name ('GPP,SAM'), residue ID ('A:123A'), or a PDB path. Cap hydrogens are placed at severed bonds when --add-linkh is on (default). Use --ligand-charge/-l for non-standard residue charges.

Examples

Command form:

pdb2reaction extract -i COMPLEX.pdb [COMPLEX2.pdb ...]
    -c SUBSTRATE_SPEC
    [-o MODEL.pdb [MODEL2.pdb ...]]
    [--radius Å] [--radius-het2het Å]
    [--include-h2o / --no-include-h2o]
    [--exclude-backbone / --no-exclude-backbone]
    [--add-linkh / --no-add-linkh]
    [--selected-resn LIST] [--modified-residue LIST]
    [-l, --ligand-charge MAP_OR_NUMBER]
    [--out-json / --no-out-json]
    [-v LEVEL]

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

# Minimal (ID-based substrate) with explicit total ligand charge
pdb2reaction extract -i complex.pdb -c '123' -o model.pdb -l -3

Substrate provided as a PDB; per-resname charge mapping (others remain 0):

# Substrate provided as a PDB; per-resname charge mapping (others remain 0)
pdb2reaction extract -i complex.pdb -c substrate.pdb -o model.pdb -l 'GPP:-3,SAM:1'

Name-based substrate selection — all matches included (WARNING logged):

# Name-based substrate selection — all matches included (WARNING logged)
pdb2reaction extract -i complex.pdb -c 'GPP,SAM' -o model.pdb -l 'GPP:-3,SAM:1'

Multi-structure → single multi-MODEL output with hetero-hetero proximity:

# Multi-structure → single multi-MODEL output with hetero-hetero proximity
pdb2reaction extract -i complex1.pdb -i complex2.pdb -c 'GPP,SAM' \
    -o model_multi.pdb --radius-het2het 2.6 -l 'GPP:-3,SAM:1'
# Multi-structure → multiple outputs: pass -o model1.pdb -o model2.pdb instead

Workflow

Residue inclusion

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

• Standard cutoff (--radius, default 2.6 Å): with --no-exclude-backbone (default), any atom within the cutoff makes its residue qualify (i.e. includes the residue). With --exclude-backbone, amino-acid residues must contact the substrate with a non-backbone atom (not N / H* / CA / HA* / C / O / OXT). Non-amino acids always 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 residue IDs (e.g. A:123A). See --selected-resn takes residue IDs (not names) in CLI Conventions for the residue-ID requirement.

• Neighbor safeguards:

  • When backbone exclusion is off and a residue contacts the substrate with a backbone atom, the peptide-adjacent N / C neighbors (C–N ≤ 1.9 Å) are auto-included; 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 when backbone atoms are removed, and under --exclude-backbone the neighbor’s C / O / OXT remain to maintain the peptide bond.

Truncation and 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).

Cap hydrogens (--add-linkh)

• Cap hydrogens are placed at 1.09 Å along severed bond vectors at carbon boundaries only (CB–CA, CA–N, CA–C; PRO / HYP use CA–C only); non-carbon boundaries are not capped.

• Inserted after a TER as contiguous HETATM records named HL in residue LKH (chain L). Serial numbers continue from the main block.

• In multi-structure mode the same bonds are capped across all models; coordinates remain model-specific.

Charge summary (--ligand-charge/-l)

Amino acids and common ions draw charges from internal dictionaries; waters are zero. Unknown residues default to 0 unless --ligand-charge/-l supplies either a total charge (distributed across unknown substrate residues, or across all unknown residues when there is no unknown substrate residue) or a per-resname mapping like GPP:-3,SAM:1.

Multi-structure ensembles

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

Output policy	Layout
No -o, multiple inputs	per-file model_<original_basename>.pdb
One -o path	single multi-MODEL PDB
N outputs matching N inputs	N individual PDBs

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

Outputs

<output>.pdb        # Active-site model PDB(s) with optional cap hydrogens after a TER record
                    # Single input → model.pdb by default
                    # Multiple inputs without -o → model_<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": {...}, "n_link_hydrogens": N}.

CLI options

Defaults shown are used when the option is not specified. The full flag list is in the generated command reference; the table below covers the options that need explanation.

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...	Active-site model PDB output(s); see Outputs for naming/layout.	Auto (model.pdb or model_<input>.pdb)
-r, --radius FLOAT	Atom–atom distance cutoff (Å) for inclusion (internally 0.001 Å when zero).	2.6
--radius-het2het FLOAT	Independent hetero–hetero cutoff (Å, non C/H).	0.0 (internally 0.001 Å when zero)
--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 cap hydrogens at 1.09 Å along severed bonds at carbon boundaries only (non-carbon boundaries are not capped).	True
--selected-resn TEXT	Force-include residues by residue ID (with optional chains / insertion codes, e.g. A:123A). See --selected-resn takes residue IDs (not names).	""
--modified-residue TEXT	Comma-separated residue names (with optional per-residue charge) to treat as amino acids for backbone truncation and charge assignment (e.g. HD1,HD2,HD3 or HD1:0,SEP:-2). A residue given without a trailing :charge defaults to charge 0.	""
-l, --ligand-charge TEXT	Total charge or per-resname mapping (e.g. GPP:-3,SAM:1).	None
--out-json / --no-out-json	Write a machine-readable result.json alongside the extracted PDB(s). Schema: JSON Output Schema.	False

Substrate specification (-c/--center)

• PDB path: 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, case-insensitive. If multiple residues share a name, all matches are included and a warning is logged.

Notes

• If the extracted active-site model is too small, calculated energies and barriers may be unreliable — increase -r (e.g. 4.0 Å or higher) to include more of the protein environment.

• INFO logs summarize residue selection, truncation counts, and charge breakdowns.

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 in extract’s internal AMINO_ACIDS dictionary, so backbone truncation and cap-hydrogen placement will not be applied correctly, and a warning is emitted:

[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 active site model manually.

Use --modified-residue to register non-standard residue names as amino acids so backbone truncation and charge assignment apply automatically — useful for phosphoserine, methylated residues, D-amino acids with unusual names, and MCPB-renamed metal-coordinating residues:

# Treat HD1, HD2, HD3 as amino acids (charge defaults to 0)
pdb2reaction extract -i complex.pdb -c 'SUB' -o model.pdb \
    --modified-residue 'HD1,HD2,HD3'

# Specify explicit charges per modified residue
pdb2reaction extract -i complex.pdb -c 'SUB' -o model.pdb \
    --modified-residue 'HD1:0,SEP:-2'

Important

If --modified-residue does not cover your use case, manual active-site model construction is recommended:

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

2. Add a cap 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 cap hydrogen.

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

Appendix: PDB naming requirements and reference lists

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

Important

For extract to work correctly, residue 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.

AMINO_ACIDS

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

Standard 20 (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, Nδ-protonated His), HIE (0, Nε-protonated His), ASH (0, neutral Asp), GLH (0, neutral Glu), LYN (0, neutral Lys), ARN (0, neutral Arg), TYM (−1, deprotonated Tyr phenolate).

Phosphorylated: 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), OCS (−1, cysteic acid), CYM (−1, deprotonated Cys).

Lysine variants / carboxylation: MLY (+1), LLP (+1), KCX (−1, Nz-carboxylic acid).

D-amino acids (19): DAL, DAR, DSG, DAS, DCY, DGN, DGL, DHI, DIL, DLE, DLY, MED, DPN, DPR, DSN, DTH, DTR, DTY, DVA.

Other modified: CGU (−2, γ-carboxy-glutamate), CGA (−1), PCA (0, pyroglutamate), MSE (0, selenomethionine), OMT (0, methionine sulfone), HYP (0, hydroxyproline); also ASA, CIR, FOR, MVA, IIL, AIB, HTN, SAR, NMC, PFF, NFA, ALY, AZF, CNX, CYF.

N-terminal variants (N prefix): NALA (+1), NARG (+2), NASP (0), NGLU (0), NLYS (+2), … plus ACE (0), NTER (+1, generic). C-terminal variants (C prefix): CALA (−1), CARG (0), CASP (−2), CGLU (−2), CLYS (0), … plus NHE (0), NME (0), CTER (−1, generic).

BACKBONE_ATOMS

Atom names treated as backbone for amino acids; under --exclude-backbone these are removed from non-substrate residues:

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

ION

Recognized ion residue names with formal charges:

Charge	Residue names
+1	LI, NA, K, RB, CS, TL, AG, CU1, K+, NA+, NH4, H3O+, HE+, HZ+
+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, CR, DY, EU, EU3, ER, GD3, LA, LU, ND, PR, SM, TB, TM, Y, PU
+4	U4+, TH, HF, ZR
−1	F, CL, BR, I, CL-, IOD

WATER_RES

Recognized water residue names (included by default with --include-h2o, assigned zero charge):

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

Cap hydrogen and frozen atoms

When pdb2reaction extracts an active-site model from a larger structure, severed bonds are capped with cap hydrogens. By default (--freeze-links), the parent atoms of these cap hydrogens are frozen during optimization and path searches to prevent unphysical rearrangement at the boundary.

• Forces — frozen atoms receive zeroed forces.

• Hessian — frozen degrees of freedom are either removed (return_partial_hessian: true) or zeroed in the full matrix.

• Vibrational analysis — when frozen atoms are present, freq automatically performs Partial Hessian Vibrational Analysis (PHVA), diagonalizing only the active block of the Hessian.

Frozen atoms can also be set manually via the geom.freeze_atoms YAML key (1-based indices). CLI-detected cap atoms are merged with YAML-specified atoms.

See Also

• Common Error Recipes — Symptom-first failure routing

• all — End-to-end workflow that calls extract internally via -c/--center

• path-search — MEP search on extracted active-site models

• scan — Staged scan on extracted active site models

• add-elem-info — Fix missing PDB element columns before extraction

• Troubleshooting — Common extraction errors

• Glossary — Definitions of Active Site Model, Cluster Model, Cap Hydrogen