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

Reorganization and addition of cryo-EM tools

• phenix.mtriage - assess map and model quality
• phenix.auto_sharpen - map sharpening
• phenix.map_symmetry - identify symmetry in maps
• phenix.map_box - cut out unique parts of maps
• phenix.combine_focused_maps - combine different maps
• phenix.dock_in_map - automatically place a model into a map
• phenix.map_to_model - automatically build model into a map
• phenix.sequence_from_map - identify sequence from a map
• phenix.real_space_refine - improved refining to models
• phenix.validation_cryoem - separate tool for comprehensive validation of models and maps

• Bug fixes
• Improved data information content functionality

• Better support for metals and metal clusters
• Added support for QM package, Orca

• Better performance
  • NCS search
  • Generating secondary structure restraints
  • Clashscore calculation
• phenix.ligand_identification - option to generate ligand library based on sequence and structural homologs of input

Improvements:

• phenix.map_to_model - better symmetry support and improved runtime efficiency
• phenix.structure_search - structural library and internal support for mmCIF
• phenix.ligand_identification - limit ligand size for search
• Phaser 2.8.1 - various bug fixes
• Structure Comparison - more/improved validation information (ligands, waters, cis/trans peptides, HIS protonation)
• GUI - automatic validation after phenix.real_space_refine; visual improvements in validation
• Internal bug fixes and performance improvements

New Tools: phenix.secondary_structure_validation, Structure Comparison, phenix.mtriage, phenix.real_space_diff_map

Improvements: better sharpening algorithms in phenix.auto_sharpen; better iterative map improvement in phenix.map_to_model; individual mapping in phenix.map_to_object; better outlier rejection in ssm-rmsd calculation in phenix.find_alt_orig_sym_mate; Secondary structure restraints use angles for restraining hydrogen bonds; User-defined box in phenix.polder in addition to atom selection; various improvements to phenix.real_space_refine; can have different restraints for different copies of the same ligand in the same model; better control of peptide planes and omega angles; faster calculation of clashscore; improved handling of cis-peptides in ramalyze; various bug fixes and updated dependencies

GUI: new interfaces for phenix.mtriage, phenix.map_box, phenix.auto_sharpen, phenix.map_to_model, phenix.ncs_average, phenix.sculpt_ensemble