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| Python-based Hierarchical ENvironment for Integrated Xtallography |
This is not the downloads page for current releases.
These installers are provided for historical purposes and for backwards compatibility with third-party software. They are unsupported and not recommended for production use! We do not have the resources to assist with problems encountered using these builds; most bugs will have been fixed in more recent releases.
| Version | Date | Status | Logs | Info |
| 1.14-3260 | 2018-09-11 | successful | 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
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| 1.13-2998 | 2017-12-23 | successful | 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:
| ||||
| 1.12-2829 | 2017-07-07 | successful | 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 | ||||
| 1.11.1-2575 | 2016-10-26 | successful | 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 | ||||
| 1.10.1-2155 | 2015-10-02 | successful | (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) | ||||
| 1.10-2155 | 2015-09-02 | successful | intel-linux-2.6-centos5, intel-linux-2.6-x86_64-centos6, ci, intel-linux-2.6-x86_64-centos5, mac-intel-osx-x86_64-10.9 | offical 1.10 release; docs; changelog |
| 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. | ||||
| 1.9-1692 | 2014-05-07 | successful | cctbx, cci_apps, phaser, phenix, misc | official 1.9 release; docs; changelog |
| User notes for 1.9-1692: New features include: revised and expanded documentation, improved AutoSol performance on weak SAD data, Rosetta refinement, similarity restraints for grouped B-factor refinement, automatic ligand linking, more automated substructure search, new composite omit map tool, "feature-enhanced" map calculation, stand-alone real-space refinement program, command-line MolProbity tool, Ubuntu builds, bug fixes for latest Mac OS, streamlined download of new installers for existing users, and many other new utilities and fixes. | ||||
| 1.8.3-1479 | 2013-09-07 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.8.3 official release; docs; changelog |
| User notes for 1.8.3-1479: New features include: 64-bit Windows 7 installer; improved bulk solvent calculation which eliminates negative peaks in hydrophobic voids; improved local and global real-space refinement; pause/resume of jobs in GUI on Mac and Linux; new commands: phenix.parallel_autobuild, phenix.dynamics; speed improvements in Phaser; and much more. | ||||
| 1.8.2-1309 | 2013-02-27 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.8.2 release; docs; changelog |
| User notes for 1.8.2-1309: New features include phenix.ensemble_refinement (Burnley et al. [2012] elife 1:e00311); improved and consistent hydrogen parameters for both X-ray and neutron refinement and validation; phenix.ligand_pipeline for automated MR, ligand placement, and refinement; mmCIF support added for many applications; visual editing of PDB files with phenix.pdb_editor; (optional) automatic linking for covalent ligands; many improvements to building programs; phenix.maximum_entropy_map; and many more. | ||||
| 1.8.1-1168 | 2012-09-27 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.8.1 official release; docs; changelog |
| User notes for 1.8.1-1168: Primarily a bug fix release. New commands are phenix.erraser for hybrid Rosetta/Phenix RNA refinement; phenix.merging_statistics for calculating R-meas, R-pim, CC1/2, and other useful statistics. Other changes include: improved NCS rotamer correction; split planes in phenix.elbow; apply overall B_cart to individual B-factors (restores pre-1.8 behavior); real-space refinement for twinned structures; keep input occupancies for modified amino acids in Phaser; simplified running of phenix.real_space_correlation; and geometry restraints for more than 400 non-standard amino acids. | ||||
| 1.8-1069 | 2012-06-02 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.8 official release; docs; changelog |
| User notes for 1.8-1069: New features include: much faster bulk solvent and scaling in phenix.refine, validation, and map calculation; TNCS supported by default in SAD phasing in Phaser and AutoSol; NCS restraints now use automatic torsion-angle parameterization by default; phenix.den_refine for DEN refinement; better automatic setup of reference model restraints; new GUIs including phenix.table_one for generating paper content; prototype Windows installer (32-bit only); numerous bug fixes; and much more. | ||||
| 1.7.3-928 | 2011-12-05 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.7.3 official release; docs; changelog |
| User notes for 1.7.3-928: New features include: handling of TNCS in Phaser-MR; MR-Rosetta GUI; TLS group extraction from PDB header; reduced memory use in phenix.refine; automatic anisotropy correction and map sharpening in AutoSol/AutoBuild; validation of model sequence; plus many bug fixes | ||||
| 1.7.2-869 | 2011-09-22 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.7.2 official release; docs; changelog |
| User notes for 1.7.2-869: Highlights: parallelization of weights optimization in phenix.refine (nproc parameter); torsion-space NCS (ncs.type=torsion); improved geometry at low resolution; phenix.cut_out_density for carving regions of map coefficients; phenix.morph_model for model improvement after MR; added HySS GUI; speedup of Phaser/AutoMR rotation function; visualization of reflection data in 3D or 2D (phenix.data_viewer) | ||||
| 1.7.1-743 | 2011-04-27 | successful | cctbx, cci_apps, phaser, phenix, misc | 1.7.1 official release; docs; changelog |
| User notes for 1.7.1-743: New commands: phenix.french_wilson (correction of weak and negative intensities), phenix.reciprocal_space_arrays (model-based phases), phaser.brunett (automated MR pipeline); new GUIs: phenix.phase_and_build, phenix.mtz2map, phenix.french_wilson; phenix.refine: output mtz file with all data and map coefficients (replaces *_map_coeffs.mtz), "top-out" potential for reference model restraints, optional automatic rigid-body and TLS selections; homologous sequences supported in structure comparison GUI; 64-bit Mac installer; graphical installers for Intel Macs; and much more- see changelog for details. | ||||
| 1.7-650 | 2011-01-25 | successful | cctbx, cci_apps, phaser, phenix, misc | Official 1.7 release; docs; changelog |
| User notes for 1.7-650: Highlights include: automatic TLS definitions (phenix.find_tls_groups); Rosetta-assisted molecular replacement for difficult structures (phenix.mr_rosetta); improved real-space refinement (on by default) in phenix.refine; Ramachandran restraints; built-in help browser in GUI on Macs; expanded base-pair support; optional faster translation searches in MR; and much more. | ||||
| 1.6.1-357 | 2010-03-29 | successful | cctbx, cci_apps, phaser, phenix, misc | Official 1.6.1 release; docs; changelog |
| 1.6-289 | 2010-01-20 | successful | cctbx, cci_apps, phaser, phenix, misc | Official 1.6 release; docs; changelog |
| User notes for 1.6-289: New GUIs for AutoMR and Phaser; support for refinement on special positions; C++ version of Resolve | ||||