Phenix: Difference between revisions

A short help, such as usage and options, is printed out by all PHENIX command line tools: just type phenix.TOOLNAME and hit Enter (or Return).

* [http://www.phenix-online.org/documentation/xtriage.htm phenix.xtriage] - assessing data quality

* [http://www.phenix-online.org/documentation/explore_metric_symmetry.htm phenix.explore_metric_symmetry] <font face="Courier">--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</font> - investigate different settings

* phenix.cif_as_mtz

* [http://www.phenix-online.org/documentation/autosol.htm phenix.autosol] - "wizard" using HYSS, SOLVE, Phaser, RESOLVE, xtriage and phenix.refine to solve a structure and generate experimental phases with the MAD, MIR, SIR, or SAD methods

* [http://www.phenix-online.org/documentation/sculptor.htm phenix.sculptor] - automate selection and editing of molecular replacement (MR) models

* [http://www.phenix-online.org/documentation/ensembler.htm phenix.ensembler] - multiple superposition tool to automate construction of ensembles for MR

* [http://www.phenix-online.org/documentation/automr.htm phenix.automr] - "wizard" providing an interface to Phaser molecular replacement and feeding the results of molecular replacement directly into the AutoBuild Wizard for automated model rebuilding

* http://www.phenix-online.org/documentation/reel.htm phenix.reel - restraints editor especially for ligands

* [http://www.phenix-online.org/documentation/elbow.htm phenix.elbow] - electronic Ligand Builder and Optimisation Workbench

* [http://www.phenix-online.org/documentation/autobuild.htm phenix.autobuild] - "wizard" for model rebuilding and completion. phenix.phase_and_build, phenix.build_one_model are fast ways to obtain results.

* [http://www.phenix-online.org/documentation/ligandfit.htm phenix.ligandfit] - "wizard" carrying out fitting of flexible ligands to electron density maps

* phenix.phase_and_build and  phenix.build_one_model - fast autobuild

* [http://www.phenix-online.org/documentation/find_helices.htm phenix.find_helices] - rapid helix fitting to a map

* phenix.ligand_identification

  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 ...

  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 \

''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.  

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

If no PDB file for a ligand is available, its SMILES string should be input to phenix.elbow, and phenix.ready_set should run to generate the LINK records (e.g. for a non-natural amino acid that is part of the polypeptide chain), using phenix.elbow's CIF file.

Use phenix.ready_set to add hydrogens to your PDB file, and (except at ultra-high resolution)  the riding hydrogen model in phenix.refine (this is the default so you do not have to specify anything).

See the [http://www.phenix-online.org/documentation/refinement.htm#anch32 phenix.refine documentation].

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

Automatic detection of NCS groups:

  }

  phenix.refine model.pdb data.mtz main.secondary_structure_restraints=true

You can find more information about secondary structure restraints in the [http://www.phenix-online.org/newsletter/CCN_2010_07.pdf PHENIX Newsletter] (pages 12-17).

Use an existing high resolution model (e.g. in a different spacegroup) for restraining the dihedrals:

See the [http://www.phenix-online.org/documentation/refinement.htm#anch26 full documentation].

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

  }

example for file rigid_body.def defining 2 rigid bodies:

  }

Use

to automatically flip these sidechains to make them better fit the density and/or hydrogen bonding pattern.  

e.g.

  phenix.refine model.pdb data.mtz refine.sites.individual="not (chain A and resseq 123:156)"

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:

   }

  }

== See also ==