Renumbering PDB files: Difference between revisions
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Eric Martz (talk | contribs) New page: 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-polym... |
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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]] 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]]. | 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]]. | ||
Revision as of 23:56, 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. Unfortunately, the wwPDB allows arbitrary numbering which may be frustrating when comparing structures of similar macromolecules. See examples at Unusual sequence numbering.