On behalf of the Phenix development team I'm pleased to announce the release of a new CCI Apps version: http://phenix-online.org/download/cci_apps/ Send bug reports to: [email protected] For help write to: [email protected] 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. eLBOW - 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