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.

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