phenix

Reflection tools

• Xtriage: reflection data analysis and quality assessment; used to detect twinning and other pathologies.
• Reflection file editor: utility for merging reflection files and creating or extending R-free flags. (GUI only)
• Calculate F(model): utility for generating structure factors (as real or complex numbers) from a model alone.
• Import CIF structure factors: convert a CIF file (used by the PDB to store deposited experimental data) to an MTZ file. This will automatically fetch data for a known ID from the PDB, or you may supply your own files.

Model tools

• PDB Tools: various model manipulations such as modifying atom records, geometry minimization, and generating "fake" structure factors.
• Combine PDB files: simple utility for merging models split over several PDB files (such as massive complexes like the ribosome). Chain IDs will be modified if necessary (using up to two characters).
• Superpose PDB files: structure alignment program.
• NCS identification: determine appropriate NCS operators and/or restraint groups based on a set of heavy-atom sites, macromolecule chains, or electron density.
• Apply NCS: apply NCS operators to a PDB file to generate the complete asymmetric unit.

Note that a simpler NCS GUI is also available as a plugin to the phenix.refine GUI, and does not necessarily need to be run separately.

Phasing

• AutoSol: automated experimental phasing for all experiment types (SAD, MAD, MIR, etc.); also performs simple model-building after phasing. Combines HySS, Phaser, SOLVE, RESOLVE, and phenix.refine.
• Phaser-EP: Another Phaser interface, for SAD and MR-SAD phasing. We recommend trying AutoSol first, but this GUI exposes additional parameters.

Molecular replacement

• AutoMR: automated molecular replacement using Phaser; feeds directly into AutoBuild. (This is also the starting point for running MR-SAD.)
• Phaser-MR: Interface for molecular replacement using standalone Phaser, with all parameters available as well as different modes of operation. We recommend starting with AutoMR first, but this GUI is useful for tough cases.
• Sculptor: prepare a search model for molecular replacement by trimming the structure, modifying B-factors, etc.
• Sculptor - Coot interface: a Coot plugin for running Sculptor interactively and visualizing results.
• Ensembler: tool for creating superimposed ensembles of related MR search models.

Model building

• AutoBuild: automated model-building and refinement with RESOLVE and phenix.refine. This GUI only encapsulates the building functions; a separate GUI is available for omit-map calculations.
• Find Helices and Strands: fast building of secondary structure (as poly-ALA) into maps with RESOLVE and PULCHRA. Especially good for low-resolution data.
• Fit Loops: simple GUI for building missing loops into a map based on a sequence and start model.

Refinement

• phenix.refine: automated refinement, supporting both X-ray and neutron data. In addition to the features available in the command-line program, the GUI version includes graphical atom selection, simplified setup of restraints, automatic addition of hydrogens, and post-refinement validation.
• ReadySet: preparation of input files for refinement, including generating restraints (CIF) files and adding hydrogens.

Maps

• Create map coefficients: simple GUI for generating likelihood-weighted maps, including 2mFo-DFc, mFo-DFc, anomalous, and others, including averaged "kick" maps. Currently works only on untwinned data. (GUI only)
• AutoBuild - create omit map: similar to the main AutoBuild GUI, but used for omit map generation rather than building.
• Density modification: This is just a simplified interface for running the AutoBuild wizard in map-only mode.
• Isomorphous difference map: simple utility for creating a map from two sets of amplitudes. Corresponds to the command-line program phenix.fobs_minus_fobs_map.
• Superpose maps: given two PDB files and accompanying map coefficients (in MTZ format), superposes the PDB files and reorients the maps to follow them. Output is the reoriented PDB files and maps in CCP4 format.

Ligands

• LigandFit: wizard for placing ligands in electron density maps, accounting for necessary conformational changes.
• eLBOW: electronic Ligand Builder and Optimization Workbench, a tool for generating restraints (and geometries) for any molecule, using a variety of inputs including PDB file and SMILES string.
• REEL: "Restraints Editor Especially Ligands", a graphical editor for CIF files, also serves as a frontend to eLBOW. Currently runs as a separate program. (GUI only)
• Ligand search: program for identifying unknown blobs of electron density and placing appropriate ligand(s).

Validation

Although these programs exist only in the GUI, some of the individual analyses are available as command-line tools (phenix.ramalyze, phenix.rotalyze, phenix.cbetadev, and phenix.clashscore). Because all three programs are subsets of the same functionality, their documentation is lumped together.

• Comprehensive validation: reports R-work and R-free, statistics for geometry restraints, Ramachandran plot, sidechain rotamers, C-beta deviation, all-atom contacts, and real-space correlation with electron density. Outlier lists are linked to graphics programs such as Coot, and clicking a residue or atom will zoom in on that site in the graphics window. Coot will also display clashes detected by PROBE.
• POLYGON: graphical comparison of user-selected model statistics with similar structures in the PDB.
• PDB Statistics Overview: This very simple application uses the same database as POLYGON, but presents it in a different format. Useful when you simply want to view a histogram of a statistic for a filtered subset of the PDB.
• Structure comparison: a tool for evaluating assorted model features and validation criteria for multiple related structures, and highlighting regions of difference. Automatically superposes model and maps into a common frame of reference for viewing in Coot or PyMOL.

We recommend including reflections in validation, since the model geometry ideally needs to be analyzed along with experimental data. However, the validation GUI will also run with just a PDB file. The phenix.refine GUI will also display a complete validation report at the end of refinement.

Utilities

• Calculate map correlations: interface to phenix.get_cc_mtz_mtz.
• Calculate model-map correlations: interface to phenix.get_cc_mtz_pdb.
• Generate Table 1: utility for extracting statistics from PDB, reflection, and log files required for publication.