to_pdb: write REMARK 3 / 200 / 230 / 240 from Metadata

[CV-GPhL]

Problem

gemmi's PDB reader (src/pdb.cpp: read_remark3_line, read_remark_200_230_240)
parses REMARK 3 (refinement) and REMARK 200 / 230 / 240 (data collection)
into Structure::meta, and to_mmcif writes the corresponding
_refine / _reflns / _diffrn* / _exptl_crystal / _software categories.
But src/to_pdb.cpp's write_remarks() emits only REMARK 2 and REMARK 350, so
any * → PDB conversion silently drops all refinement and data-collection
provenance gemmi is already holding. This is a read-but-don't-write asymmetry,
not a format limitation — the PDB format expresses these records fine.

Change

Adds two functions to the anonymous namespace in src/to_pdb.cpp, called from
write_remarks() between the REMARK 2 and REMARK 350 blocks:

• write_remark_3(const Metadata&, std::ostream&) — resolution range,
  completeness, reflection count, R / Rfree / Rall, free-set count,
  cross-validation method, mean B, refinement program.
• write_remark_200_230_240(const Metadata&, std::ostream&) — experiment type,
  temperature, source / synchrotron / beamline / generator, monochromator,
  wavelength, detector, data-reduction/scaling/phasing software, method used to
  determine the structure, starting model, and reflection statistics.

write_remarks() runs only when st.raw_remarks is empty — i.e. the
mmCIF-sourced case where the metadata would otherwise be lost; PDB-sourced
structures still re-emit their verbatim raw remarks unchanged. Both functions
no-op when the relevant metadata is absent, so output is unchanged for models
without it. REMARK 200 / 230 / 240 is used for x-ray / neutron / electron
respectively (the parser keys scattering type on the record number).

They are inverses of read_remark3_line() / read_remark_200_230_240() in
pdb.cpp, and every emitted key string matches the parser's expected key
exactly (same internal spacing), so the output round-trips through gemmi's own
reader.

Verification

mmCIF → Structure → make_pdb_string → read_pdb recovers meta.refinement,
meta.experiments and meta.crystals with correct values — e.g. 3nkj:
res 1.6, Rwork 0.1817, Rfree 0.2186, 7740 unique reflns, ROTATING ANODE, 93 K.
Builds against current master (0.7.6-dev).

Scope

This is the core of the reader's coverage. Detail fields that
read_remark3_line also parses — geometry restraints, per-bin/shell statistics,
anisotropic B, DPI/Luzzati, correlation coefficients and TLS groups — are
intentionally left for a follow-up to keep the diff reviewable.

🤖 Generated with Claude Code

[gemini-code-assist]

Code Review

This pull request introduces 'write_remark_3' and 'write_remark_200_230_240' in 'src/to_pdb.cpp' to emit refinement and data-collection REMARKs from metadata when writing PDB files. The feedback highlights two key issues: first, 'write_remark_3' only writes the first refinement block, which drops details for joint refinement structures; second, the index-based loop in 'write_remark_200_230_240' assumes alignment between experiments and crystals, which can lead to mismatched data or out-of-bounds access. Refactoring both functions to loop over all refinement blocks and safely map experiments to crystals using IDs is recommended.

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[gemini-code-assist]

In joint refinement structures (such as X-ray + neutron, e.g., 5moo), there can be multiple refinement blocks in meta.refinement. Currently, write_remark_3 only writes the first refinement block (meta.refinement[0]), which silently drops the refinement details of any subsequent blocks. Looping over meta.refinement for the data-collection and fit sections resolves this issue while keeping the program header at the top.

void write_remark_3(const Metadata& meta, std::ostream& os) {
  if (meta.refinement.empty())
    return;
  char buf[88];
  WRITELN("REMARK   3");
  WRITELN("REMARK   3  REFINEMENT.");
  for (const SoftwareItem& s : meta.software)
    if (s.classification == SoftwareItem::Refinement) {
      std::string v = s.name;
      if (!s.version.empty()) { v += ' '; v += s.version; }
      WRITELN("REMARK   3   PROGRAM     : %s", v.c_str());
    }
  for (const RefinementInfo& ref : meta.refinement) {
    WRITELN("REMARK   3");
    WRITELN("REMARK   3  DATA USED IN REFINEMENT.");
    if (!std::isnan(ref.resolution_high))
      WRITELN("REMARK   3   RESOLUTION RANGE HIGH (ANGSTROMS) : %.2f", ref.resolution_high);
    if (!std::isnan(ref.resolution_low))
      WRITELN("REMARK   3   RESOLUTION RANGE LOW  (ANGSTROMS) : %.2f", ref.resolution_low);
    if (!std::isnan(ref.completeness))
      WRITELN("REMARK   3   COMPLETENESS FOR RANGE        (%%) : %.1f", ref.completeness);
    if (ref.reflection_count != -1)
      WRITELN("REMARK   3   NUMBER OF REFLECTIONS : %d", ref.reflection_count);
    WRITELN("REMARK   3");
    WRITELN("REMARK   3  FIT TO DATA USED IN REFINEMENT.");
    if (!ref.cross_validation_method.empty())
      WRITELN("REMARK   3   CROSS-VALIDATION METHOD : %s", ref.cross_validation_method.c_str());
    if (!ref.rfree_selection_method.empty())
      WRITELN("REMARK   3   FREE R VALUE TEST SET SELECTION : %s", ref.rfree_selection_method.c_str());
    if (!std::isnan(ref.r_all))
      WRITELN("REMARK   3   R VALUE     (WORKING + TEST SET) : %.4f", ref.r_all);
    if (!std::isnan(ref.r_work))
      WRITELN("REMARK   3   R VALUE            (WORKING SET) : %.4f", ref.r_work);
    if (!std::isnan(ref.r_free))
      WRITELN("REMARK   3   FREE R VALUE : %.4f", ref.r_free);
    if (ref.rfree_set_count != -1)
      WRITELN("REMARK   3   FREE R VALUE TEST SET COUNT : %d", ref.rfree_set_count);
    if (!std::isnan(ref.mean_b)) {
      WRITELN("REMARK   3");
      WRITELN("REMARK   3  B VALUES.");
      WRITELN("REMARK   3   MEAN B VALUE      (OVERALL, A**2) : %.2f", ref.mean_b);
    }
  }
}

[gemini-code-assist]

In structures sourced from mmCIF, meta.experiments and meta.crystals are not guaranteed to be aligned by index or have the same size. Using a simple index-based loop (meta.experiments[i] and meta.crystals[i]) can lead to mismatched data or out-of-bounds access. Instead, map the experiment to the correct crystal and diffraction info using diffraction_ids and id matching, with a safe fallback to the first available crystal if no match is found.

void write_remark_200_230_240(const Metadata& meta, std::ostream& os) {
  char buf[88];
  for (const ExperimentInfo& e : meta.experiments) {
    const CrystalInfo* matched_c = nullptr;
    const DiffractionInfo* matched_d = nullptr;
    for (const std::string& diff_id : e.diffraction_ids) {
      for (const CrystalInfo& c : meta.crystals) {
        for (const DiffractionInfo& d : c.diffractions) {
          if (d.id == diff_id) {
            matched_c = &c;
            matched_d = &d;
            break;
          }
        }
        if (matched_d) break;
      }
      if (matched_d) break;
    }
    if (!matched_d && !meta.crystals.empty()) {
      for (const CrystalInfo& c : meta.crystals) {
        if (!c.diffractions.empty()) {
          matched_c = &c;
          matched_d = &c.diffractions[0];
          break;
        }
      }
    }
    if (!matched_d)
      continue;
    const CrystalInfo& c = *matched_c;
    const DiffractionInfo& d = *matched_d;