PDB & mmCIF 3D Macromolecular Structure (.pdb, .cif, .mmcif)

@modelscript/pdb (languages/pdb) provides native WebAssembly GLR parsing, backbone Ramachandran $(\varphi ,\psi )$ dihedral angle and steric clash verification, radius of gyration ($R_g$) calculation, Gaussian Network Model (GNM) elastic normal-mode fluctuation analysis, DAEBuilder lowering, and OpenSCAD / Modelica projections for Protein Data Bank (.pdb) and PDBx/mmCIF (.cif) 3D macromolecular structures.

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Supported Extensions & Standards

Extension	Format	Description
.pdb, .ent	Legacy PDB Format	Fixed-column records (HEADER, TITLE, SEQRES, HELIX, SHEET, SSBOND, ATOM, HETATM, CONECT, END)
.cif, .mmcif	PDBx / mmCIF	Macromolecular Crystallographic Information File (data_, loop_, _atom_site.*)

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Key Capabilities

1. Atomic Coordinates, Secondary Structure & Disulfide Bridges

• Extracts multi-chain 3D atomic coordinates $(x,y,z)$, occupancy, isotropic temperature factors ($B$-factors), $\alpha$-helices (HELIX), $\beta$-sheets (SHEET), disulfide bonds (SSBOND), and ligand connectivity (CONECT).
• Computes backbone torsion angles $(\varphi ,\psi ,\omega )$, center of mass, and mass-weighted radius of gyration $R_g$.

2. Gaussian Network Model (GNM) Elastic Normal Modes

• Constructs the $C_{\alpha }$ Kirchhoff contact matrix $\mathbf{\Gamma }$ ($r_c=7.0\text{AA}$) to compute theoretical residue mean-square fluctuations $⟨(\mathrm{\Delta }{\mathbf{R}}_i{)}^2⟩\propto [{\mathbf{\Gamma }}^{-1}{]}_{ii}$ and correlate them against crystallographic $B$-factors.

3. DAE Arena Lowering & 3D CSG / Modelica Export

• Lowers coarse-grained $C_{\alpha }$ harmonic spring networks into @modelscript/runtime's DAEBuilder arena and projects structures into Modelica (pdbToModelica) and OpenSCAD 3D ball-and-stick CSG geometry (pdbToScad).

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Pre-Flight Diagnostics

10 rules6 error4 warning

Code	Rule	Severity	Message
M9251	steric-clash	error	Severe steric clash between non-bonded atoms '<atomA>' (serial '<serialA>') and '<atomB>' (serial '<serialB>') at distance '<distance>' Å (< 1.20 Å).
M9252	broken-peptide-backbone	warning	Broken peptide backbone in chain '<chainId>' between '<resA><seqA>' (C) and '<resB><seqB>' (N) at distance '<distance>' Å (> 2.00 Å).
M9253	invalid-occupancy	error	Atom '<atomName>' (serial '<serial>') has invalid occupancy '<occupancy>' outside allowed bounds [0.0, 1.0].
M9254	non-positive-b-factor	warning	Atom '<atomName>' (serial '<serial>') has non-positive isotropic temperature factor (B-factor) '<bFactor>' Å^2 (<= 0.0).
M9255	ramachandran-outlier	warning	Residue '<resName><resSeq>' in chain '<chainId>' has Ramachandran backbone torsion angles (phi='<phi>' deg, psi='<psi>' deg) in a disallowed steric region.
M9256	missing-backbone-atoms	error	Standard amino acid residue '<resName><resSeq>' in chain '<chainId>' is missing required main-chain backbone atoms '<missingAtoms>'.
M9257	invalid-disulfide-distance	warning	Disulfide bond (SSBOND) between 'CYS<seq1>' (chain '<chain1>') and 'CYS<seq2>' (chain '<chain2>') has invalid SG-SG distance '<distance>' Å outside [1.80, 2.50] Å.
M9258	unresolved-conect-serial	error	CONECT record for atom serial '<conectSerial>' references unresolved atom serial '<missingSerial>'.
M9259	duplicate-atom-serial	error	Duplicate atom serial number '<serial>' declared on atom '<atomName>'.
M9260	empty-pdb-structure	error	Macromolecular structure '<structureId>' contains zero atomic coordinate records.

Generated from languages/pdb/src/errors.ts. All languages →

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CLI Usage

# Validate steric clashes, peptide bond lengths, occupancy, and B-factors
msx lint CrambeTrypsinInhibitor.pdb

# Parse and inspect PDB or mmCIF macromolecular records
msx parse CrambeTrypsinInhibitor.pdb