1.19-4092 | 2020-12-21 | successful |
ci, mac-intel-osx-x86_64, intel-linux-2.6-x86_64-centos6, intel-windows-x86_64 |
Official 1.19 release; docs; changelog |
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
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1.18.2-3874 | 2020-05-17 | successful |
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
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
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1.17.1-3660 | 2019-10-16 | successful |
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
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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
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