AFITT-CL 2.1.0

July 2011


  • Updated internal REFMAC and RCSB to current versions.

  • When remapping dictionaries, WRITEDICT now indicates where the matching monomer was sourced.

  • Moved “lookup” out of the -strict settings to a new flag “-lookup” adding this switch will search for a matching monomer from the internal libraries using the current -strict settings.

  • -force options added. WRITEDICT will output the residue name even if it doesn’t match the internal list of known monomers.

  • Various corrections to aniline nitrogen dictionaries.


  • FLYNN now sorts the output fits based on real space correlation coefficient if applicable (RSCC)

  • FLYNN now can automatically fit fragment cocktails. (use -fragment flag)

  • FLYNN adds additional scores to all ligands besides the default MMFF Tanimoto/Shape, these are RSCC (Real space correlation coefficient), PLP (Piecewise-linear potential, requires protein) and Chemscore (requires protein).

  • -resname now forces the ligand to use the given residue name even if it conflicts with the internal monomer library.

  • -chainid Output the ligands with the given chain id.