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Introduction To The AFITT SUITE

Welcome To The AFITT Suite of Tools

AFITT is a crystallographic tool for correctly placing small molecules in real-space density.

AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry. The AFITT GUI also provides an interface to external refinement programs and tools to validate the refinement including interactive Ramachandran plots and real-space correlation coefficient calculation (RSCC).

This manual describes both the AFITT GUI and the Command Line portions of the AFITT suite.

All GUI users should read the Getting Started chapter prior to using AFITT. Command line users should become familiar with the FLYNN Usage section of the documentation.


The AFITT GUI is a wizard based ligand fitting application. Each section of the wizard assists in the completion of a single task, loading the coordinates and density files and locating the ligand in density are two such examples.

Command Line

There are a number of command line components.

  • FLYNN, the ligand fitting application

  • WRITEDICT, a comprehensive refinement dictionary generator that properly

    handles covalent bond restraints between the ligand and the protein.

  • ROTFIT carries out very fast automated refitting of sidechains and peptide


  • RSCC performs real-space correlation coefficient and real-space R-factor


  • ALIGNGRID aligns proteins with electron-density maps on a single reference.


This package also includes command line programs afitt_helper_am1, afitt_helper_mmff, afitt_helper_pm3, buster_helper_am1, buster_helper_mmff, buster_helper_pm3. These programs are directly called by the PHENIX and BUSTER refinement packages, and not intended for use by the end user.


Highlights of AFITT include:

  • real-space fitting of ligands in density.
  • integrated with REFMAC, PHENIX, BUSTER, CNX, and COOT.
  • fragment and cocktail fitting (simply select more than one ligand to fit).
  • generation of high-quality refinement dictionaries for use during reciprocal space refinement.
  • use of forcefield (MMFF) and semi-empircal (AM1, PM3) methods during reciprocal space refinement for BUSTER and Phenix.
  • real space fitting of protein residues.
  • proper handling of covalently bonded ligands.
  • proper handling of multiple occupancy ligands.

Additional highlights of the GUI interface:

  • tightly integrated with REFMAC, PHENIX, and COOT.
  • integrated molecular builder
  • post-refinement analysis of ligands and residues