Description

The renumber_fab tool is designed to streamline the renumbering process for FAB chains. It performs a search among a set of supplied sequences to find the most similar sequence. Once identified, this sequence is sent to the server to retrieve the appropriate numbering. The tool supports various renumbering schemes, such as Kabat, Chothia, and Martin.

Requirements: A model and its corresponding sequence.

Ensure that the sequence encompasses the entire FAB structure and adequately covers the entire chains in the model.

Additionally, the tool will update HELIX/SHEET records describing secondary structure. However, it will neither renumber nor output SSBOND, LINK, and certain other records.

You can customize the similarity threshold by adjusting the 'identity' parameter in case the sequences are not closely matched. The tool generates detailed logs, giving insights into similarity and matched chains.

!!! WARNING !!! This program sends supplied sequence to AbNum server at http://www.bioinf.org.uk/abs/abnum/ Please acknowledge the server authors: Abhinandan KR, Martin AC. Mol Immunol. 2008 Aug; 45(14):3832-9. https://doi.org/10.1016/j.molimm.2008.05.022

Command line usage examples

% phenix.renumber_fab model.pdb sequence.fa

% phenix.renumber_fab 2jjj.cif sequence.fa scheme=chothia identity=0.4

GUI

This tool is available in the Phenix GUI in the "PDB deposition" section.

List of all available keywords

• scheme = *kabat chothia martin which scheme to use
• verbose = True More log output
• identity_cutoff = 0.5 chains with less identity between model and sequence file will be skipped. If you have a chain with a lot of deletions in sequence, lower this number.
• job_title = None Job title in PHENIX GUI, not used on command line
• output
  • suffix = None Suffix string added to automatically generated output filenames. If None, _fab_renumbered and scheme name will be used.
• guiGUI-specific parameter required for output directory
  • output_dir = None