2023.2 ====== * Improved modeling of histidine protonation states * Improved tool for merging models * Added resolution estimation for map docking (prepare_map_for_docking) * Bug fixes and improvements to cctbx.HKLviewer 2023.1 ====== * Enable rounding of occupancies in the ouput files so that the sum is equal to 1 * Improved mmCIF support with twinning information and fixes in _pdbx_struct_oper_list handling * New tool to validate torsions * Bug fixes and improvements to cctbx.HKLviewer 2022.12 ======= * New code for fitting histidine * DataManager can map scattering table types to data types 2022.11 ======= * Improved occupancy handling of multiple conformations so that the sum does not exceed 1 * Improvements to reduce2 and probe2 tools for MolProbity 2022.10 ======= * Added array selection via data labels to CCTBXParser * Match partial labels to full labels in data file * Combine multiple label selections via the command line * Allow mosaic buil solvent model to have initial values * Fix bug where atoms may be missing in a super-sphere * Bug fixes and improvements to cctbx.HKLviewer * Switch to using libsvm-official for Python interface to libsvm 2022.9 ====== * Improvements to cctbx.HKLviewer for viewing output from xtriage or xtricorder * Improve stability of prepare_map_for_docking * DataManager models can now have multiple types (e.g. x-ray, neutron, etc.) * Fix any_reflection_file_reader when reading "hklf+ins/res" (#787) * Fix binary and source installers when /usr/bin/python is not available (#788) 2022.8 ====== * Update to handle new PAE format from AlphaFold * CCTBXParser can parse DataManager PHIL parameters and provide more information about ambiguous parameters * Initial support for density dependent restraints * Bug fixes and updates for cctbx.HKLviewer 2022.7 ====== * Clean up multiple mmtbx tests * Updated to RCSB API v2 for accessing data 2022.6 ====== * Added --dry-run flag to CCTBXParser to validate inputs * Bug fixes for cctbx.HKLviewer * Updates to reduce2 and probe2 * Updates to restraints based on quantum mechanics 2022.5 ====== * Added function to return fmodel object in DataManager * Added options for cubic box and soft masking to resolve_cryo_em * Updates to tool for preparing maps for docking * More improvements to cctbx.HKLviewer 2022.4 ====== * Added option to keep unmerged data in DataManager * Bug fixes for cctbx.HKLviewer * Improvements to finding water in maps 2022.3 ====== * Added mmtbx.process_predicted_model command * Updates and bug fixes to cctbx.HKLviewer * Added methods for improved handling of heavy hydrogens in model 2022.2 ====== * Added --quiet flag to CCTBXParser to suppress output * Updates to restraints based on quantum mechanics * Updates and bug fixes to cctbx.HKLviewer 2022.1 ====== * Added option to use legacy bulk solvent mask * Added option to any_reflection_file_reader to control averaging of anomalous data columns in MTZ files * Fix SHELXF formatting where integer values may be interpreted as decimal 2021.12 ======= * Initial support for Python 3.10 * Added support for outputting multi-model mmCIF files * Adjusted mask gridding for bulk solvent 2021.11 ======= * Added right-handed nucleic acids for DNA * Improved handling of different unit cells in MTZ file * Avoid division by zero when rotating 0 degrees * Added option to ignore secondary strucure annotations when reading models through the DataManager * Initial support for restraints based on quantum mechanics * Improved consistency of binning by d_star_sq 2021.10 ======= * Initial migration of MolProbity functionality (probe and reduce) to mmtbx * Initial tool for likelihood-based map preparation for docking * Improvements to ADP refinement for real-space 2021.9 ====== * Improved structure factor calculation at ultra-low resolution * Improved processing of prediced models * Added diffBragg to simtbx for modeling pixels in stills to improve structure factors * Added suitename to mmtbx for classifying RNA 2021.8 ====== * Added tools for processing predicted models based on the error estimate * Updated list of modified amino and nucleic acids * Better handling of sequence files with empty sequences 2021.7 ====== * Fix pickling error with anomalous_probability_plot * Fix bug in reading data CIF file with paired data and sigma arrays of different sizes * Added functions for retrieving H-bond types and Van der Waals radii to the model manager class * Sequence validation will only use protein or nucleic acid residues for alignment 2021.6 ====== * More improvements to bulk solvent masking for multiple regions * Updates to ensemble refinement * Enable conversion of some numpy types into flex types instead of requiring that the types match (e.g. int to float is now supported) 2021.5 ====== * Improved bulk solvent masking with support for multiple regions 2021.4 ====== * Improved parsing of reciprocal space data in CIF * CCTBXParser can handle intermixed arguments for Python >= 3.7 * Consolidate management of conda depenencies with conda-devenv 2021.3 ====== * Initial support for native compilation on Apple Silicon * Real-space refinement of occupancies and isotropic ADP * Improvements in map_model_manager * Split up map and model by NCS groups * Create new map_model_manager with resampled maps 2021.2 ====== * Improved remediator code for converting PDB version 2 format to version 3 * Add compilation support for Boost 1.72 and 1.74 2021.1 ====== * Improvements to cctbx.HKLviewer for displaying reciprocal space data 2020.12 ======= * BIOMT/MTRIX matrices in model reading * Added option to loosen handling of improper matrices in DataManager * Make behavior conistent between mmCIF and PDB formats * Improvements to map_model_manager * Better handling of cases when information is missing * Calculate the RMSD of matching residues between models 2020.11 ======= * Updated API for fetching data from RCSB 2020.10 ======= * Added basic ``flex`` arrays for fixed width integer types (`#533 `_) * Signed types (``int8``, ``int16``, ``int32``, ``int64``) * Unsigned types (``uint8``, ``uint16``, ``uint32``, ``uint64``) * Additional functions may be wrapped in the future to support these types * Improved building of downstream software with ``cctbx`` conda package * In some cases, the location of ``annlib`` is not found properly 2020.8 ====== * First release on GitHub and conda-forge