Data analysis and manipulation

• Xtriage: comprehensive reflection data analysis and quality assessment; used to detect twinning and other pathologies. Also used internally in the AutoSol and AutoBuild wizards.
• Calculate merging statistics: calculate R-sym, R-meas, mean I/sigma, CC1/2, and related statistics starting from scaled, unmerged intensities.
• Analyze anomalous signal in a SAD experiment
• Scale unmerged anomalous data or multiple datasets
• Reflection file editor: utility for merging reflection files and creating or extending R-free flags. (GUI only)
• 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.
• French & Wilson data correction: procedure for estimating appropriate values for weak and negative intensities. This is also run automatically as part of several programs, including phenix.refine and the Phaser GUIs.
• 3D and 2D data viewers: these display data from reflection files (usually amplitudes or intensities) as they appear in reciprocal space, either in a full 3D view or a pseudo-precession camera section.

Validation and map-based comparisons

• Comprehensive validation: based on the MolProbity server (and sharing much of the same code), with added analysis of experimental data. 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.
• 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.
• Comparison of unmerged data quality with refined model, as described in Karplus & Diederichs (2012). Phenix.cc_star.
• EMRinger: Model validation for de novo electron microscopy structures
• Map correlations and offset: Map-map correlation allowing translational offset
• Model-map correlations and offset: Map-model correlation allowing translational offset
• POLYGON: graphical comparison of user-selected model statistics with similar structures in the PDB.

Experimental 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.
• Hybrid substructure search: heavy-atom site identification program. Used automatically as part of AutoSol.
• Phaser-EP: Another Phaser interface, for SAD and MR-SAD phasing. We recommend trying AutoSol first, but this GUI exposes additional parameters.
• Plan a SAD experiment: Estimate required data quality for successful SAD phasing given experimental parameters

Molecular replacement

• MRage: automated molecular replacement using Phaser;
• Phaser-MR: Interface for molecular replacement using standalone Phaser, with all parameters available as well as different modes of operation. We recommend starting with MRage first, but this GUI is useful for tough cases.
• MR-Rosetta: automation pipeline for exceptionally difficult structures, which uses the Rosetta software for protein structure prediction and design to rebuild poor MR solutions, along with Phaser and AutoBuild. (Separate installation of Rosetta is required.)
• 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.

Maps (create, manipulate, compare)

• 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)
• Generate composite omit maps: Tool for creating a composite omit map.
• 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.
• Cut out density: extracts a section of electron density from input map coefficients, and outputs new map coefficients (suitable for running molecular replacement in Phaser).
• 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.
• Map sigma level comparison: Calculate equivalent sigma levels when visually comparing two maps
• Find difference map peaks and holes: Identify local maxima and minima in mFo-DFc map (and anomalous map if available) and flag waters with excess density
• Model-based phases: calculate phases and structure factors in a variety of formats (including Hendrickson-Lattman coefficients).
• Create a map from map coefficients: convert an MTZ file containing map coefficients to one or more CCP4 or XPLOR-format maps suitable for viewing in PyMOL, etc. (Note that the main maps GUI and many other programs can also output these files, and the GUI will generate them for you as necessary for PyMOL.)
• Auto-sharpen/blur a map: Automatic or manual map sharpening/blurring.
• Calculate F(model): utility for generating structure factors (as real or complex numbers) from a model alone.

Enhanced maps (Polder, FEM, density-modified...)

• Calculate Polder maps: compute omit map excluding bulk solvent <polder.html>`_
• RESOLVE density modification: This is just a simplified interface for running the AutoBuild wizard in map-only mode.
• Solvent flipping density modification: Simple density modification by solvent flipping
• Multi-crystal averaging: performs density modification on different crystal forms of the same structure and averages the maps around the models.
• Maximum entropy map: Statistical map modification procedure to remove artifacts due to missing data
• Feature Enhanced Map (FEM): Calculate a 2mFo-DFc map locally scaled and density-modified to enhance fine details

Model building

• PredictAndBuild: Solve an X-ray structure using AlphaFold models.
• 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.
• Phase and build: similar to AutoBuild, but significantly faster (although less accurate).
• Find Helices and Strands: fast building of secondary structure (as poly-ALA) into maps with RESOLVE and PULCHRA. Especially good for low-resolution data.
• Morph model: improvement of poor molecular replacement solutions by "morphing" into density and rebuilding.
• Map to model: Model-building into cryo-EM and low-resolution maps

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.
• phenix.real_space_refine: automated refinement using a map and model (CCP4 format or MTZ format with map coefficients)
• DEN refinement: Deformable elastic network refinement using simulated annealing, for low-resolution and molecular replacement structures
• Ensemble refinement: Time-averaged molecular dynamics refinement - models disorder using a combination of multiple models and TLS
• Rosetta refinement: Hybrid Rosetta/Phenix refinement for low-resolution X-ray crystal structures
• ReadySet: preparation of input files for refinement, including generating restraints (CIF) files and adding hydrogens.
• AmberPrep: Utility for preparing files for refinement automatically generate the four files needed for Phenix-Amber

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.
• Ligand pipeline: Automated molecular replacement, refinement, and ligand placement for high-throughput crystallography
• 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).
• Guided ligand replacement: Ligand fitting based on an existing protein-ligand complex

Map analysis, symmetry, manipulation

• Mtriage: Analyze quality of cryo-EM maps and models
• Local resolution: Calculate a local resolution map
• Map symmetry: Find map reconstruction symmetry
• Map box: Extract box of density with model or extract unique part
• Local resolution: Calculate a local resolution map
• Auto-sharpen/blur a map: Automatic or manual map sharpening/blurring.

Map improvement

• Local anisotropic sharpening: Optimize a map with local or overall half-map or model-based anisotropic sharpening
• Resolve Cryo EM: Density modify a cryo EM map
• Combine Focused Maps: Align maps and combine the best parts of each

Docking, model building and rebuilding

• PredictAndBuild: Interpret a cryo-EM map using AlphaFold models.
• Dock in map: Dock a model into map
• Map to model: Model-building into cryo-EM maps
• Pathwalker: Chain tracing with cryo-EM maps
• Rebuild model: Rebuild a model, keeping connectivity
• Complete model: Break up and reassemble a model, filling in gaps
• Sequence from map: Determine a sequence from a map
• Fit Loops: Build missing loops into a map based on a sequence and starting model
• Douse (Add waters): Add waters to cryo-EM models
• CryoFit: Flexibly fit a model to a cryo-EM map

Refinement

• phenix.real_space_refine: automated refinement using a map and model (CCP4 format or MTZ format with map coefficients)
• 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.

Superpose, search, compare, analyze symmetry

• Superpose PDB files: structure alignment program.
• Secondary-structure matching: Align with SSM, morph and trim a model
• PDB Search: Match phi-psi angles or sequence: Ramachandran or sequence-based PDB search
• Secondary structure PDB search: SSM match, morph and trim
• Fragment search: Find and morph matching fragments from PDB
• Chain comparison: Find similarity between two main-chains
• Replace with fragments from PDB: Replace entire model with fragments from PDB
• NCS identification: determine appropriate NCS operators and/or restraint groups based on a set of heavy-atom sites, macromolecule chains, or electron density.
• Find alternate-origin symmetry mate: Transform a model to place it in same ASU and frame of reference as another

Modification, minimization and dynamics

• Process predicted model: Replace B-factor field in model and optionally split into domains
• Trim overlapping: Trim parts of a model overlapping another model
• PDB Tools: various model manipulations such as modifying atom records, geometry minimization, and generating "fake" structure factors.
• PDB editor: graphical tool for editing PDB files
• 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.
• Model Reconstruction: Get asymmetric unit or biological unit with BIOMT or MTRX
• Geometry minimization: Regularize geometry for a model (without data)
• Simple dynamics: Shake a model using crude molecular dynamics
• 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).
• Add conformations: Add alternate conformations in bulk, for an entire model or user-defined atom selection
• Perturb model with normal mode analysis: Uses NMA in Phaser to generate perturbed models along the direction of the normal modes
• Identify domains with normal mode analysis (SCEDS): Uses NMA in Phaser to identify approximate rigid domains
• Sort heteroatom groups: Rearrange the non-polymer heteroatom groups in a model to group with the nearest macromolecule chain, similar to the protocol used by the PDB
• Prepare model for PDB deposition: Finalize mmCIF files for deposition to the PDB
• Get PDB validation report: Retrieve a validation report from the PDB
• Generate Table 1: utility for extracting statistics from PDB, reflection, and log files required for publication.
• Find a Program: Search for a program or test

Other tools

A number of simpler tasks involving file modification and visualization can be accessed by clicking the button labeled "Other tools" on the toolbar.

Current options include:

• Fetch PDB data: Download structure data in PDB, FASTA, or CIF/MTZ format. (Command line equivalent: phenix.fetch_pdb.)
• Convert PDB file(s) to FASTA: Extract sequences of polymer chains in a model, with flexible options for handling gaps, insertions, etc. (Command line equivalent: iotbx.pdb_as_fasta.)
• Multiple sequence alignment: uses the public-domain program MUSCLE (Edgar 2005) to perform alignment of sequences in various formats (including automatic extraction of sequences from PDB files). (Command line equivalent: none, but MUSCLE can be run in PHENIX with the command phenix.muscle.)
• Plot average B-factors in PDB file: Plots residue B-factors (for all atoms, backbone, or sidechain) as a horizontal line graph. (Command line equivalent: mmtbx.bfactor_plot.)
• Reindex reflections: Performs change-of-basis operations on reflection files. (Command-line equivalent: phenix.reindex.)
• Modify PDB file: Shortcuts for performing some of the most common tasks in phenix.pdbtools (also available as a full GUI).
• PDB remediation: Convert between versions 2 and 3 of the PDB format. (Command-line equivalent: iotbx.pdb_remediator.)
• Import data and flags: Prepares data for use in refinement; this tool is especially useful when bringing in new high-resolution reflections for an already-refined structure.
• Plot PDB statistics: Generates scatter plots or histograms of statistics output by phenix.model_vs_data for a large fraction of the PDB (nearly all X-ray structures with experimental data available). The same database is used to generate the plots in POLYGON.
• Inspect R-free flags: Plots distribution of R-free flags in a reflections file; this is primarily used to determine whether the flags have been created in thin resolution shells. (Command line equivalent: wxtbx.inspect_r_free_flags.)

References

• Graphical tools for macromolecular crystallography in PHENIX. N. Echols, R.W. Grosse-Kunstleve, P.V. Afonine, G. Bunkóczi, V.B. Chen, J.J. Headd, A.J. McCoy, N.W. Moriarty, R.J. Read, D.C. Richardson, J.S. Richardson, T.C. Terwilliger, and P.D. Adams. J. Appl. Cryst. 45, 581-586 (2012).

• Fast procedure for reconstruction of full-atom protein models from reduced representations. P. Rotkiewicz, and J. Skolnick. J Comput Chem 29, 1460-5 (2008).