Command: renumber

Usage:
renumber residue-spec [ start N ] [ seqstart M ] [ relative true | false ]

The command renumber renumbers residues starting from 1 or another integer given by the user. The corresponding tool is Renumber Residues.

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: changechains, rename, build, combine, save

Within each atomic model, the specified residues are grouped by chain ID, and of these, the lowest-numbered residue per chain is assigned a new number with start or seqstart:

start specifies the starting number directly
seqstart specifies the starting number directly for chains without any biopolymer residues specified, and indirectly for chains with any biopolymer residues specified. If any biopolymer residues were specified for that chain, the specified number is mapped to the first residue in the PDB SEQRES records (or mmCIF equivalent) for that chain. This may be different from the first residue in the chain's atomic coordinates (one or more N-terminal residues may be missing from the coordinates due to disorder). Using seqstart allows consistent numbering of multiple copies of the same protein despite their having N-terminal disordered regions of different lengths.

The specified number can be zero or a positive or negative integer (default start 1).

The remaining residues specified from each chain are then numbered either consecutively from the start (relative false), or to maintain a constant offset from their current numbering (relative true, default). The default relative true maintains any existing insertion codes and gaps in numbering.

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.

Examples:

renumber /A:10-50 start 310

– renumber chain A residues 10-50 as 310-350

renumber #1/A start 1 relative false

– in model #1, renumber all chain A residues that have 3D coordinates consecutively starting with 1

renumber /B,D,F seqstart -3

– renumber chains B, D, and F, using -3 as the number for the first residue in the SEQRES records of each

UCSF Resource for Biocomputing, Visualization, and Informatics / June 2022

Command: renumber

Usage: renumber residue-spec [ start N ] [ seqstart M ] [ relative true | false ]

Usage:
renumber residue-spec [ start N ] [ seqstart M ] [ relative true | false ]