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

• 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

General Note:

• This release will have a fundamental change in how dependencies are managed. We are moving towards using conda, which will provide better compatibility and consistency across all platforms (linux, macOS, and Windows). Please contact us at bugs@phenix-online.org if you have any issues.

• This installer does not come with the Microsoft Visual C++ 2008 Redistributable Package. This is required if you do not already have it installed. You can get a copy from here. Just run the "vcredist_x64.exe" installer. The next release candidate will contain this file.

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

Known issues

• phenix.map_to_model - GUI not working since it has not been updated to changes in CLI yet
• phenix.real_space_refine - FSC curve in validation after refinement in GUI is not correct; run validation separately for correct curve
• phenix.erraser

• Fix GUI application in macOS installer

Known issue with macOS installation:

• Starting the Phenix GUI with the icon causes an error
• Workaround is to start the Phenix GUI from the terminal (type "source /Applications/phenix-dev-3082/phenix_env.sh" and then "phenix" from a terminal)

• Missing 32-bit installer for CentOS 5