[phenixbb] New CCI Apps

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Sun Aug 19 15:03:54 PDT 2007

On behalf of the Phenix development team I'm pleased to announce
the release of a new CCI Apps version:


Send bug reports to: bugs at phenix-online.org
For help write to: help at phenix-online.org

Version 2007_08_18_1856
  phenix.reduce updated to produce PDB-V3 hydrogen names (Duke group)
  phenix.refine updated to handle the new atom names from the remediated
    PDB-V3. Currently protein and RNA/DNA only. For ligands with new names,
    use elbow.builder to generate CIF files with matching restraints.
  phenix.refine manual significantly re-worked
  phenix.refine bug fixes:
    - Proper handling of chain breaks, to avoid incorrect angle,
      dihedral, chirality and planarity restraints. This bug
      was likely to lead to bad restraints for structures with
      alternative conformations.
    - Avoid Wilson B crash for no data if low resolution omitted
    - Proper handling of NCS + remove_h=true
    - Proper handling of negative residue numbers
    - Avoid segfault in twin refinement
    - Cumulative fixes and enhancements in picking and refinement of
      interatomic scatterers (IAS)
  phenix.refine vdw_1_4_factor changed from 2/3 to 0.8 (to improve
    geometry and MolProbity clash scores in particular)
  phenix.refine obsolete remove_hydrogens option removed
  New phenix.pdbtools (use --help)
  Command aliases removed (i.e. mmtbx.xtriage is now only available
    as phenix.xtriage)
  Most major commands renamed to phenix.*, e.g.
    iotbx.emma -> phenix.emma
    iotbx.pdb.hierarchy -> phenix.pdb.hierarchy
    Use phenix<TAB> (in most shells) to get a full list of available
    phenix commands.
    - Perform simple eLBOW jobs in COOT
    - Automatically perform the appropriate calculations on all the unknown
      ligands in a PDB file and combine the CIF results into one file
    - Covalent bonding of ligands to macromolecules (phase I implementation)
    - Print the sequence of PDB file (elbow.print_sequence)
    - User control of addition and writing of Hydrogens
    - Output of TRIPOS mol2 files
    - User control over naming of output files
    - elbow.join_cif_files has re-ordered arguments (target as last argument)
    - elbow.link_edits will generate "edits" from PDB LINK records for input
      to phenix.refine
    - elbow.metal_coordination will generate phenix.refine "edits"
      for metal coordination spheres including angles

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