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-28902017-09-06successful ci, intel-linux-2.6-x86_64-centos5, intel-linux-2.6-x86_64-centos6, intel-windows, mac-intel-osx-x86_64, intel-windows-x86_64, intel-linux-2.6-centos5 docs; changelog
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
dev-28752017-08-22successful ci, intel-windows, intel-linux-2.6-centos5, mac-intel-osx-x86_64, intel-windows-x86_64, intel-linux-2.6-x86_64-centos5, intel-linux-2.6-x86_64-centos6 docs; changelog
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
dev-28732017-08-20successful ci, intel-windows-x86_64, intel-windows, mac-intel-osx-x86_64, intel-linux-2.6-centos5, intel-linux-2.6-x86_64-centos6, intel-linux-2.6-x86_64-centos5 docs; changelog
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.
User notes for dev-2356: phenix.polder is available. Minor fix in user-provided NCS groups.
User notes for dev-2341: NCS parameters were changed.
User notes for dev-2328: Atoms in input pdb are being sorted by default. This should not affect anything but should make NCS selections nicer.
User notes for dev-2313: NCS-related issues are supposed to be fixed.
User notes for dev-2306: Known bugs exist for NCS, so previous builds should be used.
User notes for dev-2304: Test release for Ensemble Refinement; known bugs exist for Phaser and NCS, so previous builds should be used if you do not need Ensemble Refinement.
User notes for dev-2303: Release for Ensemble Refinement; known bugs exist for Phaser and NCS, so previous builds should be used if you do not need Ensemble Refinement.
User notes for dev-2247: Amber documentation updated to include latest modifications.
User notes for dev-2210: Alpha release of Amber refinement option including GUI support. More complete support of AFITT ligand refinement including a GUI tab.
User notes for dev-2209: More complete support of the AFITT refinement of ligands including a GUI tab.
User notes for dev-2203: Contains an alpha release of Amber refinement option
1.10.1-21552015-10-02successful (no logs found) Official 1.10.1 release; docs; changelog
User notes for 1.10.1-2155: New features include: CDL as the default protein restraints, tools for planning a SAD experiment and scaling/merging SAD data, refactored xtriage GUI, use of intensities in molecular replacement, occupancy refinement mode after MR to automatically prune the model, expanded real space refinement for cryo-EM (and X-ray) data, NCS constraints in refinement, improved rotamer fitting in refinement, improved and consolidated secondary structure restraints, validation of peptide planes, protein backbone validation using Cablam, structure search tool, updated feature enhanced map protocol, TLS analysis tools, new continuous integration build system (BuildBot), and many other new utilities and fixes. Includes a Centos6 installer. Fixes for the following issues: Incorrect location used for heavy atom files when running AutoBuild in certain circumstances; Errors when adding hydrogens to waters in ReadySet; Errors when using GUI helper applications that handle sequences (e.g. Blast search)
User notes for 1.10-2155: User notes for 1.10-2155: New features include: CDL as the default protein restraints, tools for planning a SAD experiment and scaling/merging SAD data, refactored xtriage GUI, use of intensities in molecular replacement, occupancy refinement mode after MR to automatically prune the model, expanded real space refinement for cryo-EM (and X-ray) data, NCS constraints in refinement, improved rotamer fitting in refinement, improved and consolidated secondary structure restraints, validation of peptide planes, protein backbone validation using Cablam, structure search tool, updated feature enhanced map protocol, TLS analysis tools, new continuous integration build system (BuildBot), and many other new utilities and fixes. Includes a Centos6 installer.
User notes for 1.10-2152: User notes for 1.10-2152: New features include: CDL as the default protein restraints, tools for planning a SAD experiment and scaling/merging SAD data, refactored xtriage GUI, use of intensities in molecular replacement, occupancy refinement mode after MR to automatically prune the model, expanded real space refinement for cryo-EM (and X-ray) data, NCS constraints in refinement, improved rotamer fitting in refinement, improved and consolidated secondary structure restraints, validation of peptide planes, protein backbone validation using Cablam, structure search tool, updated feature enhanced map protocol, TLS analysis tools, new continuous integration build system (BuildBot), and many other new utilities and fixes.
User notes for 1.10pre-2135: LINK records in output
User notes for 1.10pre-2131: NCS scope changed.
User notes for 1.10pre-2124: "+" button fixed. phenix.real_space_refine does not shift model and map to zero origin.
User notes for 1.10pre-2120: "Sorry: Bad NCS group selections: Natoms(copy)!=Natoms(reference)" should go away: user-provided NCS selections are corrected automatically.
User notes for 1.10pre-2119: Misc small bug fixes. Tool for TLS validation and analysis: phenix.tls_analysis. Xtriage better shows potential issues with anomalous completeness.
User notes for 1.10pre-2118: NCS constrained refinement bug fix. Switch to new (improved) rotamer fixing in refinement. Enable NCS constrained refinement with twin data.
User notes for 1.10pre-2104: Error "AssertionError : Excessive special position correction:" should go away (I hope).
User notes for 1.10pre-2091: Reference structure restraints in phenix.real_space_refine
User notes for 1.10pre-2090: Bug fix (torsion NCS crash when no groups found automatically)
User notes for dev-2057: Reference model restraints bug fix.
User notes for dev-2056: Reference model restraints bug fix.
User notes for dev-2047: The default for all Rotamer Library activity now uses the Top8000 database.
User notes for dev-2044: Bug fix: using Ramachandran plot restraints for selected residues only.
User notes for dev-2037: Bug fixes in NCS constrained refinement and DNA/RNA specific restraints. Option to specify rigid groups for rigid body refinement in phenix.real_space_refine
User notes for dev-1999: Parameters for secondary structure restraints moved to pdb_interpretation scope. Old parameter files will not be suitable for secondary structure restraints definitions.
User notes for dev-1974: This is the first build after the recent hardware failure.
User notes for dev-1883: This is the initial release of the new buildbot builds and installer. Please treat this release with caution, and be patient if you encounter issues.
User notes for dev-1833: The GUI now incorporates a built-in help browser on Linux platforms (as well as Mac and Windows). This should resolve library-related problems launching Firefox from within Phenix.