Phenix

PHENIX (Python-based Hierarchical ENvironment for Integrated Xtallography) is a new software suite for the automated determination and refinement of macromolecular structures using X-ray crystallography and other methods. It integrates well with CCP4-formatted files for I/O, is highly automated, and very straightforward to use.

The suite has a GUI program (phenix) which can be used to run the programs, but they also work from the command line:

• phenix.refine - refinement program
• phenix.xtriage - assessing data quality
• phenix.find_helices - rapid helix fitting to a map
• phenix.pbdtools - PDB model manipulations and statistics; e.g. phenix.pbdtools your_model.pdb --show-adp-statistics will show you complete statistics about B-factors; phenix.pbdtools your_model.pdb --show-geometry-statistics will show you complete statistics about stereochemistry, and so on
• phenix.elbow - electronic Ligand Builder and Optimisation Workbench
• phenix.reduce - tool for adding hydrogens to a PDB model
• ...

Example

phenix.refine model.pdb data.mtz strategy=rigid_body+individual_sites+individual_adp \
   simulated_annealing=true optimize_wxc=true optimize_wxu=true main.number_of_macro_cycles=5

Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ...

This will do the following:

1. Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius);
2. Refinement of individual xyz and b-factors every cycle with optimized weights;
3. Simulated annealing at 2nd and one before the last cycles;

Ligands

If some ligand in model.pdb is unknown, phenix.refine will complain:

Sorry: Fatal problems interpreting PDB file:
 Number of atoms with unknown nonbonded energy type symbols: 18
 Please edit the PDB file to resolve the problems and/or supply a
 CIF file with matching restraint definitions, along with
 apply_cif_modification and apply_cif_link parameter definitions
 if necessary (see phenix.refine documentation).
 Also note that phenix.elbow is available to create restraint
 definitions for unknown ligands.

In that case, just running

phenix.elbow model.pdb --do-all --output=all_ligands

will produce all_ligands.cif, which may be fed to phenix.refine by

phenix.refine model.pdb data.mtz all_ligands.cif ...

== Occupancy refinement

Adding "occupancy" to the "strategy" options will refine the occupancies of those parts of the model that have alternate conformations.

NCS

Automatic detection of NCS groups:

phenix.refine data.hkl model.pdb main.ncs=True

Manual specification of NCS groups:

phenix.refine data.hkl model.pdb ncs_groups.params main.ncs=True

where ncs_groups.params contains:

refinement.ncs.restraint_group {
  reference = chain A 
  selection = chain B 
  selection = chain C
}
refinement.ncs.restraint_group {
  reference = chain E
  selection = chain F
}

TLS

• run your model through TLSMD server to identify TLS domains (it will produce PHENIX friendly TLS groups selections);

http://skuld.bmsc.washington.edu/~tlsmd/

• use these selections for TLS refinement in PHENIX: see http://www.phenix-online.org/documentation/refinement.htm

for example:

phenix.refine model.pdb data.hkl strategy=individual_sites+individual_adp+tls  tls_selections.txt

See also

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