AFITT is a crystallographic tool for correctly placing small molecules in real-space density. AFITT walks users through the process of fitting ligands from start to finish using customizable workflows.
AFITT merges OpenEye’s Shape and MMFF technologies into a new combined forcefield that fits small molecules into crystallographic density while maintaining excellent chemistry. AFITT 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 is divided into several chapters, Installation and Platform Notes should be read by users and administrators that need to install the software on various platforms. All users should read the Getting Started chapter prior to using AFITT.
AFITT 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.
Highlights of AFITT include:
- real-space fitting of ligands in density.
- tightly integrated with REFMAC, PHENIX, 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.
- real space fitting of protein residues
- proper handling of covalently bonded ligands.
- proper handling of multiple occupancy ligands.
- integrated molecular builder.
- post-refinement analysis of ligands and residues.
The Differences From Previous Versions section below describes the changes since the last version. Otherwise, the AFITT Workflows chapter provides a good overview of AFITT and it’s capabilities and can be used as a quick start for the anxious crystallographer.
The following chapters then explain each section of the wizard in more detail. Finally, the Editing 2D Molecules section of the manual describes how to manually modify both the initial 2D structure and the final 3D fitted structure.
- o Added PHENIX support through use of afitt_helpers
- to drive ligand fitting MMFF94/MMFF94S forcefields during PHENIX refinement.
- o Alter the protein masking to not remove density that may be created by
- hydrogen or covalent bonds.
- o AFITT now post-processes equilibrium angles to see if they are compatible with
- geometric forcefields. If they are not, replace them with fully MMFF optimized angles. This mostly affects 6-5 aromatic systems, but is a general fix ensuring the geometric force-field will work properly given the constraints in the CIF dictionary.
- o Dictionary writing now properly fails if the input protein has duplicate serial numbers.
- Most refinement programs cannot handle this state.
- o AFITT now always outputs disulfide bridges if in the input PDB and in general,
- has much better handling of PDB data.
Protein side chain fitting has been reintroduced after a long hiatus. Side chains are refit into density using several methods including rotamer searching, pep flipping and full geometric optimization. To enable side-chain fitting, please select the “Fixup protein geometry” checkbox from the Welcome to AFITT customization page.
Density detection has been updated to include more density regions found at lower densities. These densities are not selected by default, but can be easily investigated and controlled by adjusting the contour slider in the blob fitting page.
Fragment and cocktail fitting has been added to AFITT. To fit multiple ligands, simply select multiple ligands to Fit by clicking on the “LIG” button in the molecule selection page. All ligands are then fit to all located or selected regions of density. Each ligand is then scored using RSCC (real space correlation coefficient) this has proven to be a better indicator of correctness of ligand placement.
The 3D molecule editor has been updated to include a combined 2D or 3D editor. This makes simple editing of molecules much nicer in general. Also a refinement dictionary inspector has been added to investigate dictionary contraints in a more familiar fashion.
Refinement dictionaries have been upgraded to work with REFMAC 5.6 and 5.7. Due to a change in hydrogen naming, usage of versions of REFMAC prior to 5.6 are not recommended.
AFITT 1.3 and previous were designed to be a general modelling application including protein modeling. AFITT 2.0 focuses mainly on ligand fitting and is, as a consequence, much simpler to use. Much effort has been made to create easy to use workflows and interactions, in general, all that is required to fit a ligand to density is to load the appropriate data and click the Next button in the wizard.
However, some elements of AFITT 1.3 are not in AFITT 2.0, these include:
- Protein Building
- Protein Rotamer Searching and Validation
- Protein MMFF/Shape Minimization
- VIDA style operations such as state saving and bookmarking.
Essentially, any operation that made the Ligand fitting workflow overly complex was rejected and removed from AFITT 2.0. Many of these elements are planned to be introduced in future versions of AFITT once they are redesigned to become part of the AFITT workflow.