Description

This tool is for renumbering residues in FAB chaings according to appropriate scheme. Supported schemes are Kabat, Chothia and Martin.

Requirements: model and sequence.

Sequence should contain the full sequence of the FAB and it should at least cover whole chains in the model.

!!! 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

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