Renumbering PDB files
From Proteopedia
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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 of polymer sequences. See examples at [[Unusual sequence numbering]]. Discrepancies in numbering are confusing and frustrating when comparing structures of similar macromolecules. | + | Chemical groups (residues) in [[atomic coordinate files]] ([[PDB 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 of polymer sequences. See examples at [[Unusual sequence numbering]]. Discrepancies in numbering are confusing and frustrating when comparing structures of similar macromolecules. |
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| + | Below are servers that will re-number atomic coordinate files. | ||
Revision as of 21:11, 27 March 2021
Chemical groups (residues) in atomic coordinate files (PDB 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 of polymer sequences. See examples at Unusual sequence numbering. Discrepancies in numbering are confusing and frustrating when comparing structures of similar macromolecules.
Below are servers that will re-number atomic coordinate files.
