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PyMol saves mmCIF without auth_seq_id, fall back to label_seq_id #325

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merged 1 commit into from
Jul 9, 2024
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PyMol saves mmCIF without auth_seq_id, fall back to label_seq_id #325

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7 changes: 5 additions & 2 deletions src/mmcif.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -701,7 +701,7 @@ Structure make_structure_from_block(const cif::Block& block_) {
"occupancy",
"B_iso_or_equiv",
"?pdbx_formal_charge",
"auth_seq_id",
"?auth_seq_id",
"?auth_comp_id",
"?auth_asym_id",
"?auth_atom_id",
Expand All @@ -715,10 +715,13 @@ Structure make_structure_from_block(const cif::Block& block_) {
// we use only one comp (residue) and one atom name
const int kCompId = atom_table.first_of(kAuthCompId, kLabelCompId);
const int kAtomId = atom_table.first_of(kAuthAtomId, kLabelAtomId);
const int kSeqId = atom_table.first_of(kAuthSeqId, kLabelSeqId);
if (!atom_table.has_column(kCompId))
fail("Neither _atom_site.label_comp_id nor auth_comp_id found");
if (!atom_table.has_column(kAtomId))
fail("Neither _atom_site.label_atom_id nor auth_atom_id found");
if (!atom_table.has_column(kSeqId))
fail("Neither _atom_site.label_seq_id nor auth_seq_id found");

st.has_d_fraction = atom_table.has_column(kDeuterium);

Expand All @@ -740,7 +743,7 @@ Structure make_structure_from_block(const cif::Block& block_) {
resi = nullptr;
}
ResidueId rid = make_resid(cif::as_string(row[kCompId]),
cif::as_string(row[kAuthSeqId]),
cif::as_string(row[kSeqId]),
row.has(kInsCode) ? &row[kInsCode] : nullptr);
if (!resi || !resi->matches(rid)) {
resi = chain->find_or_add_residue(rid);
Expand Down