Python-based Hierarchical ENvironment for Integrated Xtallography

PHENIX nightly build distribution

These installers are built automatically using the current source code and are automatically tested. We do not release installers that have known major problems, so these builds should be suitable for most purposes. Official releases and builds deemed to be "stable" are noted as such and highlighted in bold type.

If you do use the nightly builds, we recommend updating frequently; once a build disappears from the list here, it can be assumed to be obsolete.

If you encounter errors when using any of these builds, please update to the most recent build before sending a bug report. (It is generally a good idea to update frequently anyway, since the code changes rapidly.)

Note: Phenix installers are available for 64-bit Windows systems (Windows 7 or newer). Some programs or features are not available because of limitations of the Windows platform; please read the platform support notes for details. We appreciate any feedback about bugs or inconsistencies.

You will need proper authentication to download the installer; see the main download page for details.

VersionDateStatus LogsInfo
dev-38852020-05-28successful ci, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6, intel-windows-x86_64 docs; changelog
1.18.2-38742020-05-17successful ci, intel-windows-x86_64, intel-linux-2.6-x86_64-centos6, mac-intel-osx-x86_64 docs; changelog
User notes for 1.18.2-3874:

1.18.2 Changes

  • Fix weighting for iron sulfur clusters

1.18.1 Changes

  • General bug fixes
1.18 Changes
  • 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

User notes for 1.18.1-3865:

1.18.1 Changes

  • General bug fixes
1.18 Changes
  • 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

User notes for 1.18-3861:

1.18 Changes

  • 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

User notes for 1.18-3855:

1.18 Changes

  • 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

User notes for 1.18-3845:

1.18 Changes

  • 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

User notes for 1.18rc2-3793: Updated conda dependencies for linux and macOS.
User notes for dev-3742: Known pickling issue with phenix.refine GUI
1.17.1-36602019-10-16successful ci, intel-windows-x86_64, intel-linux-2.6-x86_64-centos6, mac-intel-osx-x86_64 Official 1.17.1 release; docs; changelog
User notes for 1.17.1-3660:

1.17.1 Changes

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

User notes for 1.17-3644:

1.17 Changes

  • 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

User notes for 1.17rc2-3619: Release Candidate 3, even though it's labeled rc2
1.16-35492019-06-27successful ci, intel-linux-2.6-x86_64-centos6, mac-intel-osx-x86_64, intel-windows-x86_64 Official 1.16 release; docs; changelog
User notes for 1.16-3549:

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

User notes for 1.16-3546:

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

1.15.2-34722019-04-11successful ci, intel-windows-x86_64, intel-linux-2.6-x86_64-centos6, mac-intel-osx-x86_64 Official 1.15.2 release; docs; changelog
User notes for 1.15.2-3472:

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
Other improvements
  • 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

User notes for 1.15.1-3469:
  • Improved phenix.map_to_model behavior
User notes for 1.15-3459:

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
Other improvements
  • 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

User notes for 1.15rc3-3435: Fonts on linux should work again.
User notes for 1.15rc2-3433: Font issues persist on linux.
User notes for 1.15rc2-3428: There may be some font issues on linux.
User notes for 1.15rc1-3423: Same as previous build
User notes for 1.15rc1-3420:

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.
Windows Note:
  • 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.

User notes for dev-3406: Remove grid in Ramachandran plots from dev-3405
User notes for dev-3395: Windows installer not available
User notes for dev-3304: 32-bit Windows version no longer available
1.14-32602018-09-11successful ci, mac-intel-osx-x86_64, intel-windows-x86_64, intel-windows, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-centos5, intel-linux-2.6-x86_64-centos5 Official 1.14 release; docs; changelog
User notes for 1.14-3260:

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
Phaser
  • Bug fixes
  • Improved data information content functionality
Ligands
  • Better support for metals and metal clusters
  • Added support for QM package, Orca
Other improvements
  • 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
User notes for 1.14-3235: Windows installers are missing.
User notes for 1.14rc1-3161: Cryo-EM validation GUI still under development
User notes for dev-3150: Structure validation for CryoEM is temporarily unavailable until a redesign is complete. Please use the official 1.13-2998 for CryoEM validation.
User notes for dev-3139: Fix Windows issue with plotting
User notes for dev-3126: Plotting on Windows can cause a crash (error message relating to axes).
User notes for dev-3120: Fixed phenix.map_to_model GUI
User notes for dev-3112:

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
User notes for dev-3084:
  • Fix GUI application in macOS installer
User notes for dev-3082:

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)
User notes for dev-3079:
  • Missing 32-bit installer for CentOS 5
User notes for 1.13-2998:

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
User notes for 1.13-2997:

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
User notes for 1.13rc2-2981: macOS graphical installer has correct location for SSL certificates.
User notes for 1.13rc2-2975:

Known Issues:

  • Stand-alone Polygon GUI is not working
  • Graphical macOS installer does not have correct SSL certificate location. Web-related functions may fail (e.g. BLAST).
User notes for 1.13rc1-2961: Improved compatibility with Rosetta on macOS
User notes for 1.13rc1-2960: Improved Rosetta support on macOS
User notes for 1.13rc1-2958: Restore backwards compatibility for old phenix.refine/validation jobs
User notes for dev-2919: Users with nightly builds from dev-2876 to dev-2918 should upgrade to this nightly build. Release 1.12 is fine.
User notes for dev-2917: Testing

Testing

User notes for dev-2906: Bug fix for restraints files Hidden due to TLS bug in refinement
User notes for dev-2902: PDBTools GUI works
User notes for dev-2890:
  • Refactoring of underlying code
  • PDBTools GUI does not work
User notes for dev-2880: phenix.real_space_refine GUI: bug fix in new file interface for map coefficients files
User notes for dev-2875:
  • phenix.real_space_refine GUI bug fix: secondary structure restraints are not always enabled
  • phenix.real_space_refine GUI: updated file input interface to be similar to phenix.refine GUI
User notes for dev-2873: bug fix for saving FSC file
User notes for dev-2863:
  • phenix.fem bug fix
  • macOS point-and-click installer bug fix related to SSL_CERT_FILE
User notes for 1.12-2829:

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