Atomic coordinate file: Difference between revisions

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The most popular macromolecular data format among crystallographers is the one developed and used by the early (1970's) [[Protein Data Bank]], called the ''Protein Data Bank Format'', ''PDB Format'', or ''legacy PDB format''. Data files in this format are called ''PDB Files'' (file type .pdb). Although this format has serious limitations, it remains popular partly because the data files are in plain text, and are relatively easy to read by humans.

PDB format cannot accommodate >99,999 atoms/model, or >62 chains (see [[Jmol/Visualizing large molecules]]). In August, 2021, the PDB format accommodates >99% of [[X-ray crystallography ~~entries~~]], but only about 86% of [[cryo-EM]] entries<ref>The ''advanced search'' at RCSB.org has a field ''Deposition'', ''Compatible with PDB format''.</ref>. The remainder are available in mmCIF format (see below). 88% of entries were determined by X-ray, and 4.5% by cryo-EM. For the entire database as a whole, 98.8% of entries are available in PDB format (August, 2021).

PDB format cannot accommodate >99,999 atoms/model, or >62 chains (see [[Jmol/Visualizing large molecules]]). In August, 2021, the PDB format accommodates >99% of [[X-ray crystallography]] entries, but only about 86% of [[cryo-EM]] entries<ref>The ''advanced search'' at RCSB.org has a field ''Deposition'', ''Compatible with PDB format''.</ref>. The remainder are available in mmCIF format (see below). 88% of entries were determined by X-ray, and 4.5% by cryo-EM. For the entire database as a whole, 98.8% of entries are available in PDB format (August, 2021).

Atomic coordinate file: Difference between revisions

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 The most popular macromolecular data format among crystallographers is the one developed and used by the early (1970's) [[Protein Data Bank]], called the ''Protein Data Bank Format'', ''PDB Format'', or ''legacy PDB format''. Data files in this format are called ''PDB Files'' (file type .pdb). Although this format has serious limitations, it remains popular partly because the data files are in plain text, and are relatively easy to read by humans.
-PDB format cannot accommodate >99,999 atoms/model, or >62 chains (see [[Jmol/Visualizing large molecules]]). In August, 2021, the PDB format accommodates >99% of [[X-ray crystallography entries]], but only about 86% of [[cryo-EM]] entries<ref>The ''advanced search'' at RCSB.org has a field ''Deposition'', ''Compatible with PDB format''.</ref>. The remainder are available in mmCIF format (see below). 88% of entries were determined by X-ray, and 4.5% by cryo-EM. For the entire database as a whole, 98.8% of entries are available in PDB format (August, 2021).
+PDB format cannot accommodate >99,999 atoms/model, or >62 chains (see [[Jmol/Visualizing large molecules]]). In August, 2021, the PDB format accommodates >99% of [[X-ray crystallography]] entries, but only about 86% of [[cryo-EM]] entries<ref>The ''advanced search'' at RCSB.org has a field ''Deposition'', ''Compatible with PDB format''.</ref>. The remainder are available in mmCIF format (see below). 88% of entries were determined by X-ray, and 4.5% by cryo-EM. For the entire database as a whole, 98.8% of entries are available in PDB format (August, 2021).
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