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 most Windows systems, including both 32-bit (XP or newer) and 64-bit (Windows 7 or newer) versions. 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-32902018-10-11successful ci, mac-intel-osx-x86_64, intel-windows-x86_64, intel-windows, intel-linux-2.6-x86_64-centos5, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-centos5 docs; changelog
dev-32832018-10-04successful ci, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-centos5, mac-intel-osx-x86_64, intel-windows-x86_64, intel-windows, intel-linux-2.6-x86_64-centos5 docs; changelog
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
1.13-29982017-12-23successful ci, intel-windows, intel-windows-x86_64, intel-linux-2.6-centos5, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-x86_64-centos5 Official 1.13 release; docs; changelog
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
1.12-28292017-07-07successful ci, intel-windows-x86_64, mac-intel-osx-x86_64, intel-windows, intel-linux-2.6-x86_64-centos5, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-centos5 Official 1.12 Release; docs; changelog
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

User notes for 1.12rc1-2807: Bug fix for Phaser GUI
User notes for 1.12rc1-2801: Phaser upgraded to version 2.8
User notes for 1.12rc0-2798: bug fix for validation (atom_radius)
User notes for 1.12rc0-2784: Linux installers more compatible with non-RedHat derivatives; phenix.polder in transition (GUI may fail)
User notes for dev-2712: Windows installers are not available.
User notes for dev-2685: macOS build not working correctly due to upgrade for matplotlib
User notes for dev-2666: Missing 32-bit Windows installer
User notes for dev-2665: Only available for Linux, macOS, and 32-bit Windows
User notes for dev-2664: Only available for Linux and macOS
User notes for dev-2621: For Prime
User notes for dev-2614: phenix.real_space_diff_map: new tool to compute model-map difference map (cryo-EM)
1.11.1-25752016-10-26successful ci, intel-windows-x86_64, intel-windows, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-centos5, intel-linux-2.6-x86_64-centos5 Official 1.11.1 Release; docs; changelog
User notes for 1.11.1-2575: Improved geometry restraints, improved NCS search, new map tools (phenix.polder for omit maps without bulk solvent in omitted region, phenix.model_map and phenix.mask for generating maps and bulk solvent masks, phenix.auto_sharpen for cleaning up maps, phenix.segment_and_split_map for segmenting maps), new model-building tools (phenix.map_to_model for low-resolution maps, phenix.chain_comparison for matching residues and direction), improved phenix.real_space_refine and added GUI, improve model geometry (phenix.model_idealization and phenix.geometry_minimization), improved Phaser, improved validation (phenix.reduce and phenix.ramalyze), simplified Rosetta installation, improved support for Amber, updated dependencies, Unicode support in GUI, unified interface for atom selections
User notes for 1.11-2567: Improved geometry restraints, improved NCS search, new map tools (phenix.polder for omit maps without bulk solvent in omitted region, phenix.model_map and phenix.mask for generating maps and bulk solvent masks, phenix.auto_sharpen for cleaning up maps, phenix.segment_and_split_map for segmenting maps), new model-building tools (phenix.map_to_model for low-resolution maps, phenix.chain_comparison for matching residues and direction), improved phenix.real_space_refine and added GUI, improve model geometry (phenix.model_idealization and phenix.geometry_minimization), improved Phaser, improved validation (phenix.reduce and phenix.ramalyze), simplified Rosetta installation, improved support for Amber, updated dependencies, Unicode support in GUI, unified interface for atom selections
User notes for 1.11-2563: Bug fix for displaying clashes from MolProbity
User notes for 1.11-2561: Updated documentation
User notes for 1.11-2558: Phaser bug fixes; backwards compatibility for phenix.refine jobs
User notes for 1.11rc3-2553: bug fixes for Selection Editor
User notes for 1.11rc3-2552: New release candidate
User notes for 1.11rc2-2531: Release candidate
User notes for dev-2499: Bug fix (lots of positive density around protein atoms). Real-space B-factor refinement in phenix.real_space_refine is now parallel and much improved.
User notes for dev-2450: OS X installer should work without "Broken Pipe" errors
User notes for dev-2443: Unix installer has updated dependencies. Please forward any issue to bugs. OS X installer may produce "Broken Pipe" errors. Please use latest installer if that is the case.
User notes for dev-2398: Includes Iota & Prime.