| 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 |
| 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 |
