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 (Phenix home page; documentation) 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, phenix.pbdtools your_model.pdb set_b_iso=25.3 selection="chain A and resname ALA and name CA" - this will set all B=25 for all CA atoms in all ALA residues of chain A.
- phenix.elbow - electronic Ligand Builder and Optimisation Workbench
- phenix.reduce - tool for adding hydrogens to a PDB model
- phenix.explore_metric_symmetry --unit_cell=145,44,67,90,110.5,90 --space_group=C2 --other_unit_cell=67,44,136,90,96,90 --other_space_group=p2 - investigate different settings
- phenix.polygon - starts the GUI and runs calculations resulting in a POLYGON drawing of important characteristics of your PDB file in relation to the data
Example for use of phenix.refine
basic usage
phenix.refine model.pdb data.mtz
Here "data.mtz" is your reflection data file. PHENIX automatically recognizes most of the known file formats, so it can be MTZ, CNS or ...
advanced usage
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
This will do the following:
- Rigid body refinement first cycle only (MZ protocol = VERY high convergence radius);
- Refinement of individual xyz and b-factors every cycle with optimized weights (warning: optimize_wxc=true optimize_wxu=true makes the program use much more time!)
- Simulated annealing at 2nd and one before the last cycles;
Warning: the file model.pdb in this example should not have any ANISOU records! If it has any, these would be refined as individual anisotropic which is most likely not desired.
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 ...
Restraints in real space
Occupancy
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 e.g.:
refinement.ncs.restraint_group {
reference = chain A
selection = chain B
selection = chain C
}
refinement.ncs.restraint_group {
reference = chain E
selection = chain F
}
Secondary structure restraints
phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true
You can find more information about secondary structure restraints in the PHENIX Newsletter (pages 12-17).
reciprocal space
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.def
with tls_selections.def something like:
refinement.refine {
adp {
tls = chain 'A'
tls = chain 'B'
}
}
Rigid body
example for file rigid_body.def defining 2 rigid bodies:
refinement.refine.sites {
rigid_body = chain 'A' or chain 'B'
rigid_body = chain 'L' or chain 'M'
}
Atom selection
e.g.
phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)"
Switching off specific interactions
To switch off the interaction between a specific atom and its environment, e.g. to obtain unbiased (by restraints) estimates of distances, see http://www.phenix-online.org/documentation/refinement.htm#anch80 - you just add restraints of the form:
refinement.geometry_restraints.edits {
zn_selection = chain X and resname ZN and resid 200 and name ZN
his117_selection = chain X and resname HIS and resid 117 and name NE2
bond {
action = *add
atom_selection_1 = $zn_selection
atom_selection_2 = $his117_selection
distance_ideal = 2.1
sigma = 0.02
# use slack=None if you _want_ to restrain, use large slack if not
slack = 1
}
}
See also
http://phenix-online.org/presentations/neutron_japan_2009/phenix_japan_part1.pdf
http://cci.lbl.gov/~afonine/for_ak/validation.pdf
- 42 pages of general introduction to structure refinement: [1]
- 45 pages of phenix.refine overview (including extended details about its use from the command line): [2]
- 42 pages of "Some Facts About Maps": [3]
- 50 pages of "Crystallographic Structure Validation": [4]
- 31 pages of introduction to PHENIX: [5]
server producing custom RNA/DNA base pairing restraints