Renumbering PDB files

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Chemical groups (residues) in [[atomic coordinate files]] are numbered. For polymers (protein, DNA, RNA), the amino acid and nucleotide groups are given ''sequence'' numbers. For non-polymer groups ([[hetero atoms|hetero]] groups in PDB terminology), the numbers are arbitrary. Unfortunately, the [[wwPDB]] allows arbitrary numbering which may be frustrating when comparing structures of similar macromolecules. See examples at [[Unusual sequence numbering]].
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Chemical groups (residues) in [[atomic coordinate files]] are numbered. For polymers (protein, DNA, RNA), the amino acid and nucleotide groups are given ''sequence'' numbers. For non-polymer groups ([[hetero atoms|hetero]] groups in PDB terminology), the numbers are arbitrary. The [[wwPDB]] allows arbitrary numbering. See examples at [[Unusual sequence numbering]]. Discrepancies in numbering are confusing and frustrating when comparing structures of similar macromolecules.

Revision as of 20:59, 27 March 2021

Chemical groups (residues) in atomic coordinate files are numbered. For polymers (protein, DNA, RNA), the amino acid and nucleotide groups are given sequence numbers. For non-polymer groups (hetero groups in PDB terminology), the numbers are arbitrary. The wwPDB allows arbitrary numbering. See examples at Unusual sequence numbering. Discrepancies in numbering are confusing and frustrating when comparing structures of similar macromolecules.

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