# Bio Applied Structural Methods > Parse PDB CRYST1/header for unit cell, space group, resolution, R-factors; apply symmetry operators; pick X-ray vs cryo-EM vs NMR. Use when checking structure quality, parsing CRYST1, or choosing a method. - Skill: `pavel-kravchenko/bio-applied-structural-methods` (Agent Skill) - Install (CLI): `npx skillmds@latest add pavel-kravchenko/bio-applied-structural-methods` - Raw SKILL.md: https://api.skillmd.com/api/skills/pavel-kravchenko/bio-applied-structural-methods/raw - Safety review: pending - Works with: Claude Code, Claude.ai, OpenAI Codex - Category: Coding & Dev Tools - Author: pavel-kravchenko (https://skillmd.com/u/pavel-kravchenko) - Updated: 2026-09-17 - Page: https://skillmd.com/skills/pavel-kravchenko/bio-applied-structural-methods --- # Structural Determination Methods ## When to Use - Deciding whether X-ray crystallography, cryo-EM, or NMR fits a target (protein size, flexibility, membrane context, need for a ligand Kd) - Parsing a PDB `CRYST1` record to get unit cell dimensions, space group, and crystal system - Generating symmetry-related copies of an atom/domain from a crystallographic symmetry operator - Evaluating whether a downloaded PDB structure is good enough to use for docking, homology modeling, or mutagenesis design (resolution, R-work/R-free) - Interpreting a PDB header's `EXPDTA`, `REMARK 2`, and `REMARK 3` records ## Version Compatibility - Biopython >=1.81 (`Bio.PDB.PDBParser` as an alternative to manual header parsing) - NumPy >=1.24, Python >=3.10 - wwPDB legacy PDB format (fixed-width `CRYST1`/`REMARK` records) — stable since PDB format v2; also present, differently formatted, in mmCIF (`_cell.*`, `_refine.*` tags) ## Prerequisites - `pip install biopython numpy` - Basic PDB file layout (ATOM/HETATM records) — see `bio-core-protein-structure` - Fractional vs. Cartesian coordinates helps but isn't required for the symmetry example below ## Parsing the Unit Cell (CRYST1) and Crystal System **Goal:** extract unit cell parameters and space group from a PDB file, and classify the crystal system. **Approach:** `CRYST1` is fixed-width, not whitespace-delimited — some space groups (e.g. `P 21 21 21`) contain internal spaces, so split on column positions per the wwPDB spec, not `str.split()`. ```python def parse_cryst1(pdb_file: str) -> dict: """ Extract unit cell parameters from the CRYST1 record of a PDB file. CRYST1 column layout (0-indexed, fixed-width): cols 6-15 a (Angstrom) cols 15-24 b (Angstrom) cols 24-33 c (Angstrom) cols 33-40 alpha (deg) cols 40-47 beta (deg) cols 47-54 gamma (deg) cols 55-66 space group cols 66-70 Z (copies of the asymmetric unit per cell) """ with open(pdb_file) as fh: for line in fh: if line.startswith("CRYST1"): return { "a": float(line[6:15]), "b": float(line[15:24]), "c": float(line[24:33]), "alpha": float(line[33:40]), "beta": float(line[40:47]), "gamma": float(line[47:54]), "spacegroup": line[55:66].strip(), "Z": int(line[66:70].strip()) if len(line) > 66 and line[66:70].strip() else None, } return None def classify_crystal_system(a: float, b: float, c: float, alpha: float, beta: float, gamma: float, tol: float = 0.5) -> str: """Classify the 7 crystal systems from unit cell parameters (tol in Angstrom/degrees).""" eq = lambda x, y: abs(x - y) < tol is90 = lambda x: eq(x, 90.0) if eq(a, b) and eq(b, c) and is90(alpha) and is90(beta) and is90(gamma): return "Cubic" if eq(a, b) and is90(alpha) and is90(beta) and eq(gamma, 120.0): return "Hexagonal/Trigonal" if eq(a, b) and is90(alpha) and is90(beta) and is90(gamma): return "Tetragonal" if is90(alpha) and is90(beta) and is90(gamma): return "Orthorhombic" if is90(alpha) and is90(gamma) and not is90(beta): return "Monoclinic" return "Triclinic" ## Synthetic monoclinic example (P 1 21 1 space group) line = "CRYST1 40.960 18.650 22.520 90.00 90.77 90.00 P 1 21 1 2\n" import tempfile, os with tempfile.NamedTemporaryFile(mode="w", suffix=".pdb", delete=False) as tmp: tmp.write(line) tmp_path = tmp.name params = parse_cryst1(tmp_path) os.unlink(tmp_path) print(params["spacegroup"], classify_crystal_system( params["a"], params["b"], params["c"], params["alpha"], params["beta"], params["gamma"])) ## P 1 21 1 Monoclinic ``` ## Applying Crystallographic Symmetry Operations **Goal:** generate the coordinates of a symmetry-related copy of an atom from a space-group operator. **Approach:** every space-group symmetry operation is `x' = R @ x + t` in fractional coordinates; apply the rotation matrix and translation vector from the space-group tables (e.g. International Tables for Crystallography). ```python import numpy as np def apply_symmetry_operation(coords, rotation, translation) -> np.ndarray: """ Apply one crystallographic symmetry operation to fractional coordinates. coords : array-like, shape (3,) — fractional coordinates of an atom rotation : array-like, shape (3, 3) — rotation matrix of the operator translation : array-like, shape (3,) — translation vector of the operator """ return np.dot(rotation, coords) + translation ## 2-fold screw axis along b, space group P 1 21 1: (-x, y + 1/2, -z) rotation_P21 = np.array([[-1, 0, 0], [0, 1, 0], [0, 0, -1]], dtype=float) translation_P21 = np.array([0.0, 0.5, 0.0]) original = np.array([0.12, 0.34, 0.56]) sym_copy = apply_symmetry_operation(original, rotation_P21, translation_P21) print(f"Original: {original} -> Symmetry mate: {sym_copy}") ## Original: [0.12 0.34 0.56] -> Symmetry mate: [-0.12 0.84 -0.56] ``` ## Assessing Structure Quality from the PDB Header **Goal:** decide whether a downloaded PDB entry is trustworthy enough for downstream analysis (docking, mutagenesis design, homology templates). **Approach:** pull `EXPDTA` (method), resolution, and R-work/R-free from `REMARK` lines; a large `R_free - R_work` gap (>0.05-0.10) signals overfitting regardless of nominal resolution. ```python def parse_pdb_header(pdb_text: str) -> dict: """Extract experiment type, resolution, R-factors, unit cell, and space group.""" info = {} for line in pdb_text.splitlines(): if line.startswith("EXPDTA"): info["experiment"] = line[10:].strip() elif "RESOLUTION." in line: parts = line.split() for i, p in enumerate(parts): if p == "ANGSTROMS." and i > 0: info["resolution_A"] = float(parts[i - 1]) elif "R VALUE" in line and "WORKING" in line: info["R_work"] = float(line.split()[-1]) elif "FREE R VALUE" in line and "SET" not in line: info["R_free"] = float(line.split()[-1]) elif line.startswith("CRYST1"): info["space_group"] = line[55:66].strip() return info def evaluate_structure_quality(info: dict) -> str: """Return a one-line quality verdict from a parsed PDB header dict.""" res = info.get("resolution_A") band = ("atomic (<1.5A)" if res and res < 1.5 else "good (1.5-2.5A)" if res and res < 2.5 else "acceptable (2.5-3.5A)" if res and res < 3.5 else "low, side chains uncertain" if res else "unknown resolution") r_work, r_free = info.get("R_work"), info.get("R_free") overfit = "" if r_work is not None and r_free is not None: gap = r_free - r_work overfit = f", R_free-R_work={gap:.3f} ({'OVERFIT WARNING' if gap > 0.10 else 'OK'})" return f"{info.get('experiment', 'Unknown')}: {res} A ({band}){overfit}" header = """ EXPDTA X-RAY DIFFRACTION REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 R VALUE (WORKING SET) : 0.196 REMARK 3 FREE R VALUE : 0.229 CRYST1 69.850 69.850 103.180 90.00 90.00 90.00 P 41 21 2 8 """ print(evaluate_structure_quality(parse_pdb_header(header))) ## X-RAY DIFFRACTION: 2.0 A (good (1.5-2.5A)), R_free-R_work=0.033 (OK) ``` ## Choosing a Structural Method | Feature | X-ray crystallography | Cryo-EM (single particle) | NMR | |---|---|---|---| | Size range | Any (needs crystal) | ~100 kDa+ (best); smaller now feasible | <30-40 kDa (assignment-limited) | | Sample state | Crystal (ordered lattice) | Vitrified, non-crystalline | Concentrated solution | | Best for | Small/medium, well-ordered proteins | Large complexes, membrane proteins, multiple conformations | Dynamics, ligand Kd, disordered regions | | Resolution | 1-3.5A typical | 2-4A typical (improving) | Ensemble, no single resolution number | ```python def recommend_method(mw_kda: float, dynamic: bool = False, membrane: bool = False, need_ligand_kd: bool = False) -> str: """Rule-of-thumb structural method recommendation (not a substitute for expert judgment).""" if need_ligand_kd and mw_kda < 30: return "NMR (15N-HSQC titration gives per-residue CSP and Kd)" if mw_kda > 150 or membrane or dynamic: return "Cryo-EM (large/flexible/membrane targets; 3D classification separates states)" if mw_kda < 40: return "X-ray crystallography (small proteins crystallize readily; NMR also feasible)" return "X-ray crystallography (default for well-behaved 40-150 kDa targets)" print(recommend_method(450, dynamic=True)) # Cryo-EM ... print(recommend_method(15)) # X-ray crystallography ... ``` ## Pitfalls - **`CRYST1` is fixed-width, not whitespace-split**: space groups like `P 21 21 21` contain internal spaces; splitting on whitespace corrupts the space-group and Z fields. - **R-work always improves with more refinement parameters**: only `R_free` (computed from reflections withheld from refinement) is a fair quality check; trust the `R_free - R_work` gap, not R-work alone. - **Resolution number alone is not sufficient**: check R-free, and for cryo-EM also check local resolution — global resolution can hide poorly resolved flexible regions. - **Low-resolution cryo-EM maps (>4A) cannot reliably place side chains** — backbone tracing may still be trustworthy. - **NMR "structures" are ensembles** (multiple `MODEL` records in one PDB entry) representing conformational dynamics, not competing guesses of one static structure — do not just pick MODEL 1 and discard the rest. - **mmCIF vs legacy PDB**: unit cell/resolution live in `_cell.*`/`_refine.*` mmCIF tags, not `CRYST1`/`REMARK`, for structures only distributed in mmCIF. ## See Also - `bio-core-protein-structure` — Bio.PDB SMCRA hierarchy, RMSD, DSSP - `structural-bioinformatics` — Ramachandran plots, PWM/PROSITE, broader Bio.PDB workflows - `alphafold-structure-prediction` — predicted-model alternative when no experimental structure exists - `bio-applied-proteomics` — mass-spectrometry side of protein characterization (not covered here)