Python for Structural Biology Cheat Sheet: BioPython and MDAnalysis Essential Commands
Every essential command for BioPython and MDAnalysis — organized by task, not alphabetically. Bookmark this and keep it open while you code.
Environment setup
| Command | What it does |
|---|---|
| conda create -n structbio python=3.10 -y | Create dedicated conda environment |
| conda activate structbio | Activate before every session |
| conda install -c conda-forge biopython mdanalysis numpy pandas matplotlib -y | Install all essential packages at once |
| conda install -c conda-forge pymol-open-source -y | Add PyMOL to the same environment |
| conda env export > structbio.yml | Save environment spec for reproducibility |
| conda env create -f structbio.yml | Recreate environment from saved spec |
BioPython — loading structures
| Command | What it does |
|---|---|
| Parsers | |
| PDBParser(QUIET=True) | Parser for .pdb and .ent files |
| MMCIFParser(QUIET=True) | Parser for .cif and .mmcif files — use for AlphaFold and newer PDB downloads |
| parser.get_structure(“name”, “file.pdb”) | Load a structure — returns a Structure object |
| Downloading | |
| PDBList().retrieve_pdb_file(“4XYZ”, pdir=”.”) | Download PDB file from RCSB |
| requests.get(f”https://alphafold.ebi.ac.uk/files/AF-{uid}-F1-model_v4.pdb”) | Download AlphaFold structure via API — no auth required |
| Command | What it does |
|---|---|
| SMCRA hierarchy — Structure → Model → Chain → Residue → Atom | |
| structure[0] | First model (almost always the only one for X-ray / AF) |
| model[“A”] | Chain A by identifier string |
| chain[100] | Residue by PDB author number — not zero-indexed |
| residue[“CA”] | Alpha carbon atom by name |
| structure[0][“A”][185][“OG”] | Full path to a specific atom in one expression |
| Iteration | |
| model.get_chains() | Iterate all chains |
| chain.get_residues() | Iterate all residues including HETATM — filter with res.id[0]==” “ |
| residue.get_atoms() | Iterate all atoms in a residue |
| structure.get_atoms() | Iterate every atom in the entire structure |
| Residue identity | |
| residue.id | Tuple (het_flag, seq_num, icode) — ” ” = standard AA, “W” = water |
| residue.id[0] == ” “ | True for standard amino acids — use to filter HETATM |
| residue.get_resname() | Three-letter residue name e.g. “GLU” |
| residue.id[1] | Residue sequence number from PDB |
| Atom properties | |
| atom.get_coord() | NumPy array [x, y, z] in ångströms |
| atom.get_bfactor() | B-factor — holds pLDDT in AlphaFold structures |
| atom.get_name() | Atom name string e.g. “CA”, “OG”, “NZ” |
| atom.element | Element symbol e.g. “C”, “N”, “O” |
| atom1 – atom2 | Distance in ångströms between two atoms |
BioPython — calculations
| Command | What it does |
|---|---|
| Neighbor search — use instead of nested loops | |
| NeighborSearch(atom_list) | Build k-d tree from list of Atom objects |
| ns.search(coords, radius, level=”R”) | Find residues within radius of a point — “A”=atoms, “R”=residues |
| Structure superposition | |
| Superimposer() | Create superimposer object |
| sup.set_atoms(ref_atoms, mob_atoms) | Calculate optimal superposition and RMSD — does not move anything |
| sup.rms | RMSD value in ångströms after set_atoms() |
| sup.apply(mobile.get_atoms()) | Apply transformation to move mobile structure in-place |
| Protein analysis (sequence-based) | |
| ProteinAnalysis(sequence_str) | Create analysis object from one-letter sequence string |
| analysis.molecular_weight() | Molecular weight in Daltons |
| analysis.isoelectric_point() | Theoretical isoelectric point (pH) |
| analysis.gravy() | GRAVY hydrophobicity score — negative = soluble |
| analysis.instability_index() | Predicted stability — <40 stable, ≥40 unstable |
| analysis.secondary_structure_fraction() | (helix, turn, sheet) fractions — Chou-Fasman, sequence-based |
BioPython — file I/O
| Command | What it does |
|---|---|
| PDBIO().set_structure(structure); io.save(“out.pdb”) | Write whole structure to PDB file |
| io.save(“chain_A.pdb”, ChainASelect()) | Write subset using a Select subclass — override accept_residue() |
| PPBuilder().build_peptides(structure) | Extract polypeptide sequences from structure — returns list of Polypeptide objects |
| str(pp.get_sequence()) | Get sequence string from a Polypeptide object |
MDAnalysis — loading
| Command | What it does |
|---|---|
| mda.Universe(“topology.gro”, “traj.xtc”) | Load GROMACS topology + trajectory |
| mda.Universe(“topology.prmtop”, “traj.nc”) | Load AMBER topology + trajectory |
| mda.Universe(“topology.psf”, “traj.dcd”) | Load NAMD/CHARMM topology + trajectory |
| mda.Universe(“protein.pdb”) | Single structure with one frame — no trajectory |
| mda.Universe(“top.gro”, [“r1.xtc”, “r2.xtc”]) | Concatenate multiple trajectory files |
| Trajectory info | |
| u.atoms.n_atoms | Total atom count |
| len(u.trajectory) | Number of frames |
| u.trajectory.dt | Timestep in picoseconds |
| u.trajectory.totaltime | Total simulation time in picoseconds |
| u.trajectory[N] | Seek to frame N |
MDAnalysis — selections
| Selection string | What it selects |
|---|---|
| Molecular type keywords | |
| “protein” | All protein residues |
| “backbone” | Protein backbone: N, CA, C, O |
| “water” | Water molecules (TIP3P, SPC etc.) |
| “not protein and not resname SOL NA CL” | Ligands and non-standard residues only |
| Residue and atom identity | |
| “resname GLU” | All glutamate residues |
| “resid 100:200” | Residues 100 through 200 |
| “resid 85 100 173” | Specific residues by ID (space-separated list) |
| “name CA” | Alpha carbon atoms only |
| “name CA CB” | Multiple atom names |
| “not type H” | Heavy atoms only (no hydrogens) |
| Spatial and boolean | |
| “protein and around 5 resname LIG” | Protein atoms within 5 Å of ligand — updates each frame |
| “(resname ASP GLU) or (resname LYS ARG)” | Charged residues — parentheses group OR clauses |
| “protein and not water” | Boolean NOT — everything protein that isn’t water |
| AtomGroup properties | |
| ag.positions | NumPy array (n_atoms, 3) — coordinates at current frame |
| ag.n_atoms | Number of atoms — check this is > 0 after any selection |
| ag.resids | Array of residue numbers for each atom |
| ag.resnames | Array of residue names for each atom |
| ag.center_of_mass() | Center of mass [x, y, z] |
| ag.radius_of_gyration() | Radius of gyration in ångströms |
MDAnalysis — trajectory analysis
| Command | What it does |
|---|---|
| Alignment (run before RMSD/RMSF) | |
| align.AlignTraj(u, u, select=”backbone”, in_memory=True).run() | Align trajectory on backbone — required before RMSD/RMSF |
| align.AlignTraj(u, u, select=”backbone”, filename=”aligned.xtc”).run() | Align and write to disk — use for large systems |
| RMSD and RMSF | |
| rms.RMSD(u, select=”backbone”).run() | RMSD over trajectory — results in .results.rmsd[:, 2] (Å) |
| rms.RMSD(u, select=”backbone”).run(start=50) | Skip equilibration frames — start from frame 50 |
| rms.RMSF(ca_atoms).run() | Per-residue RMSF — results in .results.rmsf (Å) |
| H-bond analysis | |
| HBA(universe=u).run() | All intra-system H-bonds (requires H atoms in topology) |
| HBA(universe=u, between=[[“protein”], [“resname LIG”]]).run() | Protein-ligand H-bonds only |
| hba.results.hbonds | Array of (frame, donor_idx, H_idx, acceptor_idx, dist, angle) |
| Distance calculation | |
| distance_array(ag1.positions, ag2.positions) | Fast pairwise distance matrix — returns (n1, n2) NumPy array |
| np.linalg.norm(atom1.positions[0] – atom2.positions[0]) | Distance between two specific atoms at current frame |
| Trajectory iteration | |
| for ts in u.trajectory: | Iterate every frame — positions update automatically |
| for ts in u.trajectory[::5]: | Every 5th frame (stride) — faster for large trajectories |
| for ts in u.trajectory[50:]: | From frame 50 onward — skip equilibration |
| ts.frame, ts.time, ts.dimensions | Current frame index, time (ps), box dimensions [a,b,c,α,β,γ] |
MDAnalysis — writing output
| Command | What it does |
|---|---|
| protein.write(“protein_only.pdb”) | Write current frame of selection to PDB |
| with mda.Writer(“out.xtc”, n_atoms) as w: w.write(ag) | Write trajectory frames to XTC file |
| for ts in u.trajectory[::10]: w.write(protein) | Write every 10th frame — reduces file size |
| u.trajectory[50]; protein.write(“frame50.pdb”) | Write a specific frame as PDB for PyMOL |
Cross-library workflows
AlphaFold pLDDT extraction (BioPython)
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=True)
struct = parser.get_structure(“af”, “AF-P04637-F1-model_v4.pdb”)
plddt = {res.id[1]: res[“CA”].get_bfactor()
for res in struct[0][“A”].get_residues()
if res.id[0] == ” “ and “CA” in res}
# plddt = {resid: score, …} — filter: {k: v for k, v in plddt.items() if v >= 70}
Standard MD analysis setup (MDAnalysis)
import MDAnalysis as mda
from MDAnalysis.analysis import align, rms
u = mda.Universe(“topology.gro”, “md_vis.xtc”)
align.AlignTraj(u, u, select=“backbone”, in_memory=True).run() # align first
rmsd_data = rms.RMSD(u, select=“backbone”).run().results.rmsd[:, 2]
rmsf_data = rms.RMSF(u.select_atoms(“backbone and name CA”)).run().results.rmsf
Interface residues — BioPython NeighborSearch
from Bio.PDB import NeighborSearch
ns_b = NeighborSearch(list(model[“B”].get_atoms()))
iface_a = {res_a for res_a in model[“A”].get_residues()
if res_a.id[0] == ” “
for atom in res_a.get_atoms()
if ns_b.search(atom.get_coord(), 5.0, level=“R”)}
Protein-ligand contact occupancy — MDAnalysis
from MDAnalysis.lib.distances import distance_array
from collections import Counter
lig = u.select_atoms(“resname LIG”)
protein = u.select_atoms(“protein”)
counts = Counter()
for ts in u.trajectory:
mask = (distance_array(lig.positions, protein.positions) < 5.0).any(axis=0)
counts.update(protein.atoms[mask].resids)
# occupancy_pct = {r: c/len(u.trajectory)*100 for r, c in counts.items()}
RMSD comparison — BioPython Superimposer
from Bio.PDB import Superimposer
sup = Superimposer()
# Build equal-length lists of paired Cα atoms
ca_ref = [chain_ref[r][“CA”] for r in common_resids]
ca_mob = [chain_mob[r][“CA”] for r in common_resids]
sup.set_atoms(ca_ref, ca_mob)
print(f“RMSD: {sup.rms:.3f} Å over {len(ca_ref)} Cα atoms”)
sup.apply(mobile.get_atoms()) # move mobile to aligned position
Three checks before any analysis
(1) After every BioPython parse: print(len(list(structure.get_atoms()))) — confirm atoms loaded. (2) After every MDAnalysis selection: assert sel.n_atoms > 0, "Empty selection" — catch silent mismatches. (3) After alignment: check RMSD is physically reasonable (backbone RMSD < 5 Å for a stable protein) before running RMSF or H-bond analysis.