Tool: Renumber Residues

Renumber Residues changes the residue numbering in atomic models starting from 1 or another integer given by the user. The corresponding command is renumber.

To switch between numbering schemes already defined for biopolymer structures from the wwPDB, instead use setattr to change the atomic-model attribute res_numbering, with possible values author, canonical, or uniprot. See also: Change Chain IDs, Build Structure, Altloc Explorer, Check Waters, rename, save

Renumber Residues can be opened from the Structure Editing section of the Tools menu and manipulated like other panels (more...).

Either the currently selected residues or one or more chains chosen from the list in the dialog can be designated for renumbering. For chains, the following option is available:

• Chain renumbering starts at beginning of sequence (if known) even if initial residues are missing (default on) – whether to map the specified starting number to the first residue in the PDB SEQRES records (or mmCIF equivalent) for the chain instead of the first residue in the chain's atomic coordinates; these could differ if N-terminal residues are missing due to disorder. Using this option allows consistent numbering of multiple copies of the same protein despite their having N-terminal disordered regions of different lengths.

Other settings:

• Start from: [N] (default 1) – zero or a positive or negative integer
• Maintain relative numbering within renumbered residues (default on) – whether to renumber the remaining designated residues per chain to maintain a constant offset from their current numbering (which keeps any existing insertion codes and gaps in numbering). Turning this option off means to renumber consecutively in increments of 1 regardless of current numbering.

Clicking Apply (or OK, which also dismisses the dialog) renumbers the residues. If the requested renumbering would result in multiple residues in the same chain having the same number, an error message will appear and the renumbering will not occur. Close simply closes the dialog, while Help opens this page in the Help Viewer.