AFITT-CL 2.0.1

September 2010

Package renamed from FLYNN to AFITT-CL. None of the internal programs have been renamed. AFITT and AFITT-CL will be released simultaneously with the same version numbers from this point forward.


  • Added correct dictionary creation including connection table. This is required for newer versions of coot

  • CIF dictionaries properly encode all LINK records.

  • CIF dictionaries now encode proper planarity for guanine and no longer have duplicate planar atoms when using MMFF94s.

  • CIF Dictionaries now look up known non-peptide residues. If the residue is not consistent with the known dictionary, the residue name is changed and a new MMFF94 derived dictionary is generated.

  • Updated COOT integration to 0.6+


  • Enhanced automatic density location. Blobs are now slightly larger than before making better targets for fitting.

  • Added experimental fragment fitting. See the documentation for more information about this command line option. For version 2.0.1 this requires the fragment feature of the FLYNN license. This requirement will be removed when this feature is considered non-experimental. If you are interested in helping us test this feature, please contact for more details.

  • Refinement dictionaries are always written out for the ligand. Please note that these are written as if the -split flag is set to true. Refer to the documentation or type “flynn –help” at the command line for more details.

  • Updated COOT integration to 0.6+