Structure Analysis

Protein structure analysis

One PDB entry yields different residue counts, interface lists and hydrogen-bond totals depending on how waters, HETATM records, alternate locations and symmetry copies were treated. Those choices, and every distance or angle cutoff, are part of the result and are reported with it.

Files and identity

1. Prefer PDBx/mmCIF over the legacy PDB format: PDB files break above 99,999 atoms and 62 chains, truncate chain IDs to one character and have no entity concept. Download https://files.rcsb.org/download/<id>.cif or use Biopython PDBList().retrieve_pdb_file("1abc", pdir=".", file_format="mmCif"). Record the entry id, the model used (NMR ensembles have many; state the index) and the download date.
2. Chains and entities: mmCIF has label_asym_id (internal chain), auth_asym_id (the author chain that papers and viewers use) and label_entity_id; a homodimer is one entity with two chains. Residue numbering is auth_seq_id (author numbering with gaps, insertion codes and negatives) or label_seq_id (1..n over the entity sequence). UniProt numbering is a third scheme, mapped by SIFTS. Say which one every residue number in the report follows.
3. HETATM policy: ligands, ions, modified residues inside the polymer (MSE, SEP, TPO) and waters (HOH, DOD) are all HETATM. Decide and state whether waters are removed, ions kept, and modified residues counted as protein. Biopython encodes this in residue.id[0] (" " standard, "W" water, "H_XXX" hetero) and Bio.PDB.Polypeptide.is_aa(res, standard=True); gemmi offers st.remove_waters(), st.remove_ligands_and_waters(), st.remove_hydrogens() and Residue.het_flag. Call st.setup_entities() after reading PDB files with gemmi.
4. Alternate locations: pick one conformer consistently. Biopython's PDBParser wraps them in DisorderedAtom objects that default to the highest occupancy (atom.is_disordered()); gemmi st.remove_alternative_conformations() keeps the first; MDAnalysis selects with altloc A. Counting all altlocs doubles some contacts.
5. Insertion codes: a Biopython residue id is (hetflag, resseq, icode), so 52 and 52A are distinct residues; parsing the number alone merges them. Antibody numbering schemes rely on them.
6. Assemblies: the asymmetric unit may hold half a dimer or two copies of a monomer. The biological assembly applies the operators in _pdbx_struct_assembly (REMARK 350). gemmi: gemmi.make_assembly(st.assemblies[0], st[0], gemmi.HowToNameCopiedChain.AddNumber) or st.transform_to_assembly("1", how); PyMOL set assembly, 1 before fetch; ChimeraX sym #1 assembly 1; RCSB serves <id>-assembly1.cif. Interfaces across symmetry mates exist only in the assembly. Report which assembly, or that the asymmetric unit was used.
7. Hydrogens: crystal structures rarely include them. Angle-based hydrogen-bond criteria need added hydrogens (PDBFixer or OpenMM Modeller.addHydrogens, PyMOL h_add, ChimeraX addh); heavy-atom-only criteria are the alternative. State which.

Criteria

8. Hydrogen bonds: heavy-atom donor-acceptor distance <= 3.5 angstroms is the common loose criterion, 3.2 or 3.0 strict; with hydrogens, D-H...A angle >= 120 degrees loose or

   = 150 strict. MDAnalysis HydrogenBondAnalysis defaults to d_a_cutoff=3.0 and d_h_a_angle_cutoff=150; ChimeraX hbonds applies Mills and Dean geometric criteria with default distSlop 0.4 and angleSlop 20 tolerances; PyMOL distance ..., mode=2 uses a 3.5 angstrom default cutoff with its own polar-contact heuristics. Counts from different tools are not comparable; always name tool, version and numbers.

9. Interface residues by distance: any heavy atom within 4.0 angstroms of the partner chain (5.0 is the generous variant). Biopython NeighborSearch(atoms).search_all(4.0, level="R"); gemmi NeighborSearch(st[0], st.cell, 5).populate() with ContactSearch(4.0) and ignore = ContactSearch.Ignore.SameChain, which also finds contacts to symmetry images; MDAnalysis select_atoms("chainID A and around 4.0 chainID B").
10. Interface residues by solvent accessibility: a residue is interfacial when its SASA drops on complexation (thresholds in use include > 0, > 1 square angstrom, and >= 5%). Buried surface area BSA = SASA(A) + SASA(B) - SASA(AB); PDBePISA reports interface area as BSA / 2, so say which convention a number follows. SASA with Shrake-Rupley and a 1.4 angstrom probe: Biopython ShrakeRupley(probe_radius=1.4, n_points=100) from Bio.PDB.SASA, whose .compute(struct, level="R") fills residue.sasa; freesasa defaults to Lee-Richards; ChimeraX measure buriedarea #1/A withAtoms2 #1/B and measure sasa; PyMOL set dot_solvent, 1 then get_area. Radii sets and point densities move SASA by a few percent. Remove waters and ligands first unless they are the question.
11. Secondary structure: DSSP through Bio.PDB.DSSP(model, path, dssp="mkdssp") (DSSP 4 prefers mmCIF input); collapsing eight states to three (H, G, I to helix; E, B to strand; the rest to coil) is a convention to state.
12. Superposition and RMSD: report which atoms (CA only or all heavy), which residues (aligned core or all), and whether the RMSD is after the fit. PyMOL align rejects outliers over five cycles and reports RMSD on the kept subset, so also give rms_cur over all matched atoms; Bio.PDB.Superimposer and MDAnalysis.analysis.rms.RMSD fit on exactly the atoms you pass.

Report

• Entry, assembly or asymmetric unit, model index, chains (author ids), numbering scheme.
• Altloc policy, HETATM and water policy, hydrogens added or not and by which tool.
• Every cutoff (distance, angle, SASA threshold, probe radius) with the tool and version.
• Counts at each filtering step, so a reader can see where residues went.

Sources

• wwPDB PDBx/mmCIF dictionary: https://mmcif.wwpdb.org/
• wwPDB legacy PDB format v3.3: https://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
• Biopython Bio.PDB tutorial: https://biopython.org/docs/latest/Tutorial/chapter_pdb.html
• gemmi documentation (molecular models, neighbor and contact search): https://gemmi.readthedocs.io/
• MDAnalysis hydrogen bond analysis: https://docs.mdanalysis.org/stable/documentation_pages/analysis/hydrogenbonds.html
• ChimeraX commands hbonds, measure, sym: https://www.cgl.ucsf.edu/chimerax/docs/user/commands/
• PyMOL wiki (align, distance, get_area, assembly): https://pymolwiki.org/
• PDBePISA interface conventions: https://www.ebi.ac.uk/pdbe/pisa/