1.21.2 Changes

• Fix issue where X-ray data parameters (e.g. resolution) are not used
• Fix issue where non-default map coefficient parameters cause map names to be numbered
• Fix issue where phenix.refine parameter diff could not be saved
• Differences in DataManager PHIL are now included when using getting non-default parameters
• Additional filtering is applied to Miller array selections to avoid ambiguity
• The const_shrink_donor_acceptor default has been changed from 0.6 to 0

• Add support for joint X-ray/neutron refinement to phenix.refine GUI
• Fix DMSO restraint
• Fix excessive printing when processing PAE matrix file
• Add tutorial for low resolution restraints
• Bugfix for LigandPipeline
• Bugfix for PredictAndBuild
• phenix.renumber_fab: (NEW!) renumber FAB chains using Kabat, Chothia or Martin conventions

• Full support for structure determination with AlphaFold models in Phenix GUI
• PredictAndBuild X-ray and Cryo-EM structure solution from data and sequences
• Phenix AlphaFold server
• Video tutorials for prediction, X-ray structure solution and Cryo-EM map interpretation
• Cryo-EM tools support ChimeraX visualization
• Cryo-EM density modification and anisotropic scaling display local resolution
• Tutorials available for automated structure determination with PredictAndBuild
• New em_placement and emplace_local tools
• likelihood-based docking of models into cryo-EM maps
• Quantum Mechanical Restraints (QMR) to calculate ligand restraints in situ
• Available in phenix.refine and separate command-line tool, mmtbx.quantum_interface
• Defaults to MOPAC's PM6-D3H4
• Higher level QM available via 3rd-party Orca package
• Restraints
• Approximately 27k of 37k restraints (QM calculated and validated) deployed in the GeoStd
• Automated tests for programs in the Phenix GUI
• ERRASER no longer supported and removed from installation
• Remove rebuild_predicted_model (duplicated by predict_and_build)
• JSON output added to MolProbity structure validation scripts

1.20.1 Changes

• Add backwards compatibility for new solvent masking algorithm
• Bug fix SHELX HKLF format output
• Bug fix for phenix.dock_and_rebuild where no model is obtained
• Bug fix for map and model from phenix.douse not aligning
• Add --without-dials option to installation script

• New tools and methods
• Phenix AlphaFold2 notebook: Run AlphaFold on Google Colab from Phenix GUI
• phenix.process_predicted_model: Identify useful domains in AlphaFold model
• phenix.dock_predicted_model: Dock domains of AlphaFold model into cryo-EM
• phenix.rebuild_predicted_model: Rebuild AlphaFold model in cryo-EM map using docked domains
• phenix.dock_and_rebuild : Process, dock and rebuild AlphaFold model with cryo-EM map
• phenix.model_completion: Connect fragments and fill in gaps based on a map
• phenix.rebuild_model: Rebuild a model using a map and keeping connectivity
• phenix.replace_with_fragments_from_pdb: Rebuild a model using fragments from PDB
• phenix.search_and_morph: SSM search PDB; morph to match target
• phenix.fragment_search: Search for a fragment in PDB matching target
• phenix.reverse_fragment: Reverse chain direction of a fragment
• phenix.superpose_and_morph: SSM or least-squares superpose one model on another; optionally trim and morph to match
• phenix.voyager.casp_rel_ellg: Calculate relative eLLG score for predicted model quality

• phenix.match_maps:
• Bug fix (superposed map was not matching target map)

• phenix.real_space_refine:
• Symmatry multiprocessing aware individual ADP and occupancy refinement
• Multiple changes to improce runtime (for certain refinement strategies)
• Make NQH flips symmetry aware

• phenix.superpose_pdbs:
• Add feature to transform additional models with matrix found with moving model

• phenix.dock_in_map:
• Allow splitting model into domains based on chain ID from phenix.process_predicted_model

• Restraints
• GeoStd updated with 12k plus entity restraints files
• cis-PRO default updated to EH99

• phenix.fetch_pdb, iotbx.cif_as_mtz:
• Bug fix: Multiple datasets with different unit cells in a cif file now preserved as multiple crystals in mtz file.

1.19.2 Changes

• Avoid GUI crash when running validation after phenix.real_space_refine
• Other bug fixes

• phenix.real_space_refine
• Fix bug in restoring previous jobs
• Clarify NCS options

• phenix.real_space_refine
• Improved rotamer fitting (use multiprocessing, in case of NCS constraints work on one copy only and propagate changes to all related copies, various performace improvements and bug fixes)
• Improved map/restraints weight calculation
• Morphing can now use multiprocessing (nproc)
• phenix.map_to_model and phenix.trace_and_build
• Improved high-resolution model-building including detection of insertions and deletions
• New methods
• phenix.local_resolution: calculates a local resolution map
• phenix.local_aniso_sharpen: optimizes a map taking into account local resolution-dependence and anisotropy of the map and its errors
• New scripting tools
• High-level scriptable Python tools are now available for map and model analyses and manipulation as well as for model-building
• Restraints
• Adjusting the "positions" of atom names is (pseudo-)symmetric amino acid side chains is now the default
• Improved restraints for ARG allows more flexibility of the CD atom
• Bug fixes
• Chains with modified amino or nucleic acids can be aligned
• Fixed handling of modified amino/nucleic acids in sequence alignment

1.18.2 Changes

• Fix weighting for iron sulfur clusters

1.18.1 Changes

• General bug fixes

• Amber
• Automatic creation of Amber files in phenix.refine GUI
• Added AmberPrep GUI
• Restraints
• Engh & Huber restraints (2001) for cis-peptides now implemented
• Restraints added for FeS
• Metal coordination library is default to Zn+2 and FeS clusters
• Rama-Z: New global Ramachandran score for identifying protein structures with unlikely stereochemistry in CLI (phenix.rama_z, mmtbx.rama_z) and GUI (validation reports).
• Density modification for cryo-EM
• Includes model-based density modification with automatic model generation
• Optimized defaults and additional documentation
• Real-space refinement
• Hydrogen atoms no longer included in map target function, which improves fit.
• Add NQH flip option (enabled by default)
• Other
• New tool for ordered solvent picking in cryo-EM maps (phenix.douse)
New map and model superposition tool (phenix.match_maps)
• New FindProgram toll to find any Phenix program with a text search
• Project details now has a button for opening the README file for tutorials

1.17.1 Changes

• Fix bug on Windows where Xtriage results would fail to display
• Other bug fixes

• Improved handling of SHELX data in phenix.reflection_file_converter
• eLBOW can output files for Amber
• eLBOW supports QM package Orca
• dials.image_viewer is used for viewing diffraction images
• Updated map smoothing
• Fix inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model

1.16 Changes

• New GUI for mmtbx.prepare_pdb_deposition to make mmCIF files for deposition into the PDB
• New tool (CLI and GUI) for getting a validation report from the PDB (phenix.get_pdb_validation_report)
• Added sequence checking to Comprehensive Validation for Cryo-EM
• Amber functionality is available by default

1.15.2 Changes

• Fix phenix.rosetta_refine issue
• Fix PDB/CIF conversion in GUI

1.15.1 Changes

• Improved phenix.map_to_model behavior

New and improved tools

• New algorithm for phenix.map_to_model is faster and builds longer chains
• phenix.trace_and_build can build protein into maps at resolutions as low as 4.5 A
• phenix.fix_insertions_deletions can build models in places where the map is poor
• phenix.refine_ca_model for optimizing C-alpha only models
• phenix.comparama for generating Kleywegt-like plots that show how residues moved in the Rakmachandran plots before and after refinement
• eLBOW can find unique instances of a ligand from the PDB and optionally create Polder OMIT maps
• Updated structural library for phenix.structure_search
• Updated ligand library for phenix.ligand_identification
• Improved reporting of cis-peptides for residues with altloc atoms

• Updated mmCIF support (stuct_conn loop, ligand restraints, sequence)
• phenix.refine, phenix.real_space_refine, and phenix.pdbtools will also output models in mmCIF format by default
• Dependencies are now based on conda packages, which will be more compatible with new operating systems and will improve consistency across all platforms (macOS, linux, Windows)
• Bug fixes