| 1.17rc4-3626 | 2019-09-12 | successful |
intel-windows-x86_64, ci, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6 |
docs; changelog |
| 1.17rc2-3619 | 2019-09-05 | successful |
ci, intel-windows-x86_64, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6 |
docs; changelog |
| User notes for 1.17rc2-3619: Release Candidate 3, even though it's labeled rc2 |
| 1.17rc2-3612 | 2019-08-29 | successful |
ci, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6, intel-windows-x86_64 |
docs; changelog |
| 1.17rc1-3605 | 2019-08-22 | successful |
ci, intel-linux-2.6-x86_64-centos6, mac-intel-osx-x86_64, intel-windows-x86_64 |
docs; changelog |
| 1.16-3549 | 2019-06-27 | successful |
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
|
| 1.15.2-3472 | 2019-04-11 | successful |
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
|
| 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
- 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
|
| 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:
- 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
|
| 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 |
