Release Notes¶

Platform Support¶

• Support has been added for Ubuntu 16, OSX 10.10, OSX 10.11, and OSX 10.12.
• OSX 10.7, OSX 10.8, OSX 10.9, SuSe 11, and Redhat 5 x86 are no longer supported.

Coot Support¶

• Support has been added for Coot 0.8.
• Coot versions 0.6 and earlier are no longer supported.

Bug Fixes¶

• A bug in WRITEDICT that caused inappropriate bond lengths to be written for some cyclic systems has been fixed. Originally, WRITEDICT outputted the MMFF bond potential minimum as the bond length. However, for aromatic rings this value is inappropriately large since MMFFs angle and torsion potentials also affect the bond length significantly. In these cases, the equilibrium bond lengths are used by WRITEDICT.
• A bug that caused PDB remark data that was more than 72 characters long to be clipped from the refined output has been fixed. Practically, this only occurred when the input and output file formats were both PDB.
• On Windows, the default “save” location has been changed from C:Program Files (x86)AFITT 2.4.0 to the Users Home directory.
• Previously, if an older version of AFITT was installed on Windows, users could not overwrite the old preferences. This issue has been fixed.
• A crash that occurred on Windows 10 after selecting the Refmac option without a locally installed copy of Refmac has been fixed.
• The AFITT suite ships with a simple Python-based do_gold.py test script, to make sure AFITT-CL (FLYNN) is functioning as intended. This script analyzes the Gold dataset (protein+ligand complexes) available from the Electron Density Server (EDS) and included with the distribution. The do_gold.py test script has been modified to run correctly with either Python 2 or Python 3.

Major Features¶

• Added Phenix support through the use of afitt_helpers to drive ligand fitting MMFF94/AM1 and PM3 forcefields during Phenix refinement
• Added a command line application for very fast peptide bond and sidechain fitting (rotfit). The user can select the quality of the electron-density where it is being refit.
• Alter the protein masking to not remove density that may be created by hydrogen or covalent bonds. This was causing density very close to the protein to be truncated and hard to find automatically.
• AFITT now post-processes equilibrium angles in a fit molecule to see if they are compatible with geometric forcefields. If they are not, they are replaced with fully MMFF94 optimized angles. This mostly affects 6-5 aromatic systems, but is a general fix ensuring the geometric forcefield will work properly given the constraints in the CIF dictionary.
• Dictionary writing now properly fails if the input protein has duplicate serial numbers. Most refinement programs cannot handle this state.
• AFITT now always outputs disulfide bridges if they are present in the input PDB files and in general, has much better handling of data in PDB files.

Minor Features¶

• 2D Depictions have been enhanced using OEDepict 2.0
• -nolookup has been renamed -forceExistingResidueNames for clarity and to fix confusion with the -lookup flag which works differently. The old -nolookup flag is aliase to -forceExistingResidueNames and still has the same effect.

Bug Fixes¶

• Updated to current VIDA infrastructure
• Data in the input PDB file is now taken from the largest input fragment, not removed entirely.
• AFITT tries hard to prevent duplication of CRYST1 records in the writedict output.

Other¶

Note: Last release for Redhat 5 and SUSE Linux Enterprise 11.

Other¶

Note: Last release for SUSE Linux Enterprise 10.

Major Features¶

• PM3 Optimization has been added to the molecule builder (to employ, click the PM3 icon in the builder)
• All molecules fit to a blob can be rejected at once by clicking the checkbox next to the blob when inspecting results.
• More density regions are returned when fitting to assist locating poor density. The same default regions are still selected.
• Changing the contour level in the density location window will select/unselect the appropriate density based on the current contour.
• The spreadsheet can be separated from the main window (See the Edit/Options menu)
• Protein residue fitting, including rotamer searches, peptide flips and full residue geometry optimization, has been added.
• Visualization of hydrogen bonds is now on by default.
• Conflicting deposited residues in RSCB or the REFMAC5 library are now visualized.
• Optimization fixes for molecules with high strain.

Bug Fixes¶

• Fixed symmetry operations on cubic lattices.
• In some cases, the Tip dialog could not be closed except by clicking on the close icon in the title bar, this is now fixed.
• AFITT no longer generates long titles.
• When reviewing molecules in the spreadsheet, the scene doesn’t change when changing molecules.
• Editing aromatic bonds in the sketcher doesn’t generate radical carbons any more.
• Various speed improvements when going forwards and backwards in the wizard.
• When a molecule is overstrained ( or moved out the density ) during optimization, AFITT now falls back to the original conformation.

Major Features¶

• Phenix support has been added to CIF dictionaries.
• AFITT has been updated to support REFMAC 5.6 and 5.7
• Monomers in CIF files are given IUPAC names when possible
• AFITT now sorts the output fits based on real space correlation coefficient if applicable (RSCC)
• AFITT now can automatically fit fragment cocktails, simply select multiple ligands in the Molecule selection page
• Additional ligand scores are now added to all ligands besides the default MMFF94 Tanimoto/Shape, these are RSCC (Real space correlation coefficient), PLP (Piecewise-linear potential, requires protein) and Chemscore (requires protein).
• Hydrogen naming now fully supports RSCB and REFMAC standards (COOT may not currently recognize these standards)
• When remapping dictionaries, AFITT now indicates where the matching monomer was sourced and outputs a graphical representation of the monomer

Minor Features¶

• Updated internal REFMAC and RCSB to current versions.
• A better indication is shown when a ligand has unsupported atom types.
• An options was added to force AFITT to keep the current residue name. AFITT will output the residue name even if it doesn’t match the internal list of known monomers.
• Various corrections to aniline nitrogen dictionaries.
• LINK records are validated against the link record in the PDB file to be in the correct order.
• AFITT’s graphics subsystem has been overhauled to work better on inexpensive hardware (INTEL HD GRAPHICS for instance)
• AFITT now properly supports rendering against a white background.
• Stability has been improved by integrating updates to the latest VIDA infrastructure.
• The integrated 3D editor has been upgraded.
• Fixed memory leak in internal optimizer.