AFITT-CL 2.4.0

November 2014

  • Add helper programs to allow ligand forcefields during refinement for PHENIX and BUSTER
  • Updated PHENIX support, including covalent bond support
  • 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.

Platform Support

  • Added support for RedHat 7, Ubuntu 14 and OSX 10.9
  • Dropped support for RedHat 5 32 bit, Ubuntu 10 and OSX 10.6
  • This will be the last release for SuSe 11

FLYNN

  • 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.
  • -box is now called -manualSearch (-box still works)
  • -blobsThenBox is now called -autoThenManualSearch for clarity (-blobsThenBox still works)
  • -ciftype now follows the new writedict convention (accepts both numeric and more readable names such as “refmac”, “xplor”)
  • -ciftype parameter is now in the correct parameter section (Advanced not Fragment)
  • FLYNN always fixes serial numbers when writing CIF output to better enable use in workflow situations. These can be caused when hydrogens are added to ligands outside the context of the protein for instance.

WRITEDICT

  • 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.
  • Writedict now properly fail if the input protein has duplicate serial numbers. Most refinement programs cannot handle this state.
  • Prevent duplication of CRYST1 records in the writedict output.
  • Always output disulfide bridges if input
  • Never rename standard residues hydrogens, this was causing Markly naming violations.
  • Fix phenix covalent link output when covalently linking two residues of the same residue type.
  • WRITEDICT no longers fails if input standard residues have alternate conformations with different graphs.
  • WRITEDICT now defaults to MMFF94s
  • WRITEDICT now understands human readable names for the dictionary type, i.e. -type refmac as opposed to -type 0
  • WRITEDICT now has a -fix_serial_numbers flag that corrects duplicate serial numbers in the resulting pdb output

ROTFIT

  • Added rotfit rotamer driving command line program. This used to live entirely in the GUI.