[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:
http://phenix-online.org/download/cci_apps/
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.
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
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