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.

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VersionDateStatus LogsInfo
2.0-57292025-06-15successful docs; changelog
1.21.2-54192024-08-11successful mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6 Official 1.21.2 release; docs; changelog
User notes for 1.21.2-5419:

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
1.21.1 Changes
  • 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
1.21 Changes
  • 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
User notes for 1.21.1-5286:

1.21.1 Changes

  • 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
1.21 Changes
  • 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
User notes for 1.21-5207:

1.21 Changes

  • 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
User notes for 1.21rc1-5109: Fixes GUI crash on macOS Sonoma (14)
User notes for 1.21rc1-5084: Phenix Workshop
User notes for 1.21rc1-5058:

IUCR 2023 Phenix Workshop

Only the Python 3 installer is available for Windows

User notes for 1.21rc1-5049: IUCR 2023 Phenix Workshop
User notes for 1.21rc1-4958:

MCCS 2023 (Madrid) workshop build

This build will not restore old phenix.refine jobs properly.

User notes for 1.21rc1-4957:

MCCS 2023 (Madrid) workshop build

This build will not restore old phenix.refine jobs properly.

User notes for 1.21rc1-4899: Fixed Apple Silicon installer
User notes for dev-4753: Cold Spring Harbor Workshop
User notes for dev-4746: Cold Spring Harbor Workshop
User notes for dev-4742: Cold Spring Harbor Workshop
User notes for dev-4694: Release for Frederick National Lab Workshop
User notes for dev-4674: ACA 2022 Phenix Workshop
1.20.1-44872022-01-20successful ci, intel-linux-2.6-x86_64-centos6, intel-windows-x86_64, mac-intel-osx-x86_64 Official 1.20.1 release; docs; changelog
User notes for 1.20.1-4487:

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
1.20 Changes
  • 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.

User notes for 1.20-4459:

1.20 Changes

  • 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.

User notes for 1.20rc4-4425: macOS installers fail to create app bundle (Phenix icon that launches GUI) due to missing dependency.
1.19.2-41582021-02-25successful ci, intel-windows-x86_64, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6 Official 1.19.2 release; docs; changelog
User notes for 1.19.2-4158:

1.19.2 Changes

  • Avoid GUI crash when running validation after phenix.real_space_refine
  • Other bug fixes
1.19.1 Changes
  • phenix.real_space_refine
    • Fix bug in restoring previous jobs
    • Clarify NCS options
1.19 Changes
  • 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

User notes for 1.19.1-4122:

1.19.1 Changes

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

User notes for 1.19-4092:

1.19 Changes

  • 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

User notes for dev-3973: phenix.real_space_refine has undergone changes and the GUI has not been updated yet.
1.18.2-38742020-05-17successful ci, intel-windows-x86_64, intel-linux-2.6-x86_64-centos6, mac-intel-osx-x86_64 Official 1.18.2 release; 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 [email protected] 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
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
 
 
ValueError		 Python 3.11.10: /home/cciadmin/.conda/envs/httpd/bin/python
Sat Jun 21 22:00:35 2025

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /home/cciadmin/html/phenix-online.org/phenix/download/nightly_builds.cgi in <module>
      4 sys.path.append("/home/cciadmin/html/phenix-online.org/phenix_dev/installer/web")
      5 import phenix_download
      6 
      7 if __name__ == "__main__" :
=>    8   phenix_download.run(allow_download=False)
phenix_download = <module 'phenix_download' from '/home/cciadmin/h...org/phenix_dev/installer/web/phenix_download.py'>, phenix_download.run = <function run>, allow_download undefined
 /home/cciadmin/html/phenix-online.org/phenix_dev/installer/web/phenix_download.py in run(allow_download=False, admin_mode=False, page_type='nightly')
    156     print("""<p><font color="red"><b>%s</b></font></p>""" % error)
    157   if version is None :
=>  158     display_index_page(base_uri=base_uri,
=>  159                        allow_download=allow_download,
=>  160                        show_source=show_source,
global display_index_page = <function display_index_page>, base_uri = '/download/phenix/nightly/', allow_download = False, show_source = False, show_all = True, show_retired = False, admin_mode = False, force_refresh = False
 /home/cciadmin/html/phenix-online.org/phenix_dev/installer/web/phenix_download.py in display_index_page(base_uri='/download/phenix/nightly/', allow_download=False, show_source=False, show_retired=False, show_all=True, admin_mode=False, force_refresh=False)
    373     build_logs = "(no logs found)"
    374     if tag is not None :
=>  375       build_logs = ", ".join(get_log_links(tag=tag, version=row['version']))
    376     link = version
    377     if status not in ["started", "failed"] :
build_logs = '(no logs found)', ", ".join = <built-in method join of str object>, global get_log_links = <function get_log_links>, tag = 'buildbot', version = 'None', row = {'availability': 'hidden', 'build_date': datetime.datetime(2017, 11, 9, 22, 6, 59), 'build_info': '', 'build_status': 'started', 'build_tag': 'buildbot', 'developer_notes': None, 'error_count': None, 'released_by': '', 'user_notes': None, 'version': 'None', ...}
 /home/cciadmin/html/phenix-online.org/phenix_dev/installer/web/phenix_download.py in get_log_links(tag='buildbot', version='None')
    900   modules = ["cctbx", "cci_apps", "phaser", "phenix", "misc"]
    901   links = [ link % (app, tag, app) for app in modules ]
=>  902   if is_phenix2(version):
    903     links = []
    904   return links
global is_phenix2 = <function is_phenix2>, version = 'None'
 /home/cciadmin/html/phenix-online.org/phenix_dev/installer/web/phenix_download.py in is_phenix2(version='None', build_number=5555)
   1041 
   1042 def is_phenix2(version, build_number=5555):
=> 1043   bn = get_build_number(version)
   1044   if bn is not None and bn >= build_number and not version.startswith('dev'):
   1045     return True
bn undefined, global get_build_number = <function get_build_number>, version = 'None'
 /home/cciadmin/html/phenix-online.org/phenix_dev/installer/web/phenix_download.py in get_build_number(version='None')
   1037   if version == 'release' or version == 'nightly':
   1038     return None
=> 1039   build_number = int(version.split('-')[-1])
   1040   return build_number
   1041 
build_number undefined, builtin int = <class 'int'>, version = 'None', version.split = <built-in method split of str object>

ValueError: invalid literal for int() with base 10: 'None'
      add_note = <built-in method add_note of ValueError object>
      args = ("invalid literal for int() with base 10: 'None'",)
      with_traceback = <built-in method with_traceback of ValueError object>