Renumbering PDB files: Difference between revisions
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==PDB Tools Web== | ==PDB Tools Web== | ||
[https://wenmr.science.uu.nl/pdbtools/ PDB Tools Web] is a server that has many options for modifying PDB files. The complete list of operations is explained in the [https://wenmr.science.uu.nl/pdbtools/manual Manual]. Operations can be applied to selected subsets of residues. Those affecting group numbering: | [https://wenmr.science.uu.nl/pdbtools/ PDB Tools Web] is a server that has many options for modifying PDB files. The complete list of operations is explained in the [https://wenmr.science.uu.nl/pdbtools/manual Manual]. Operations can be applied to selected subsets of residues. Those affecting group numbering: | ||
*pdb_delinsertion: "'''Deletes insertion codes''' in a PDB file, shifting the residue numbering of downstream residues. Allows for picking specific residues too." | *pdb_delinsertion: "'''Deletes insertion codes''' in a PDB file, shifting the residue numbering of downstream residues. Allows for picking specific residues too." (For examples with insertion codes, see [[Unusual sequence numbering]].) | ||
*pdb_gap: "'''Detects gaps''' between consecutive residues in the sequence, both by a distance criterion or discontinuous residue numbering. Only applies for protein residues." | *pdb_gap: "'''Detects gaps''' between consecutive residues in the sequence, both by a distance criterion or discontinuous residue numbering. Only applies for protein residues." | ||
*pdb_reres: "'''Renumbers the residues''' of the PDB file starting from a given number (default 1)." | *pdb_reres: "'''Renumbers the residues''' of the PDB file starting from a given number (default 1)." | ||
