cctbx - 2025.8

Release Notes

• Added function to find similar ligands via SMILES with RCSB web services
• Improvements to ligand validation tool (work in progress)
• Initial integration of aspherical structure factors from DiSCaMB

Checksums

SHA256

af10a618c858162609827203c70cbf6167156771250dc9b23ee529cdba6bea70 cctbx-2025.8.tar.gz

- Python
Published by bkpoon 6 months ago

cctbx - 2025.7

Release Notes

• Added _atom_site.auth_atom_id to mmCIF output
• Added calculation of a variable resolution map
• CCTBParser: updated --diff-params to report any incompatible PHIL as unused

Checksums

SHA256

05dc073224ca3ef4e41acf575a2c1a6fd7b157a6c56540bcdf5aec5aa7ccf0e2 cctbx-2025.7.tar.gz 2f55c95fc15ecfed3a5deabd691538f7e4faf9c847ad2b282f0819285f14153a chem_data-2025.7-pyh5490a37_0.conda

- Python
Published by bkpoon 7 months ago

cctbx - 2025.6

Release Notes

• Added ability to remove bonds in geometry restraints manager
• Added forward compatible PDB format for iotbx.cifaspdb
• Improved tool for fixing CaBLAM outliers

Checksums

SHA256

df0a515c00a2726d028c55f613ce81fac6c1904f00928324b4984d893a14a584 cctbx-2025.6.tar.gz b0009b0c2b2f9edfdcf065be3981d83cf5c795115cf0d893465e1985ee922fbf chem_data-2025.6-pyh19cb8ea_0.conda

- Python
Published by bkpoon 8 months ago

cctbx - 2025.5

Release Notes

• Added parameter for user restraints to pdb_interpretation
• Improved barbed wire analysis, including JSON output
• Improved consistency of handling models with hybrid36

Checksums

SHA256

c4fe8f8be5bb984146520b1c285a913ed0f21beab003ad6e79a3f6b9ac2b84c6 cctbx-2025.5.tar.gz ea308e5ea8c6759e72df078dc998ab9fa595205167cd545edfde212c91264e75 chem_data-2025.5-pyh66f2a00_0.conda

- Python
Published by bkpoon 9 months ago

cctbx - 2025.4

• Improved mmCIF compatibility across programs
• Updated amino acid residue parentage
• Updated map preparation so both half-maps and full-maps can be used

- Python
Published by bkpoon 10 months ago

cctbx - 2025.3

• Improved mmCIF compatibility across programs
• Added more intrinsic functions to fable
• CCTBXParser: show PHIL parameters in default help output

- Python
Published by bkpoon 11 months ago

cctbx - 2025.2

• Add peak search to map manager
• Add water renumbering to pdbtools
• Update FSC calculation to use different binning
• Add more searches for RCSB search API
• CCTBXParser: --diff-params flag can proceed with non-local files
• DataManager: fix bug where the default type for Miller arrays may not update correctly

- Python
Published by bkpoon about 1 year ago

cctbx - 2025.1

• Improvements to probe2
• Fix bug where the scattering table was not kept after selecting in xray_structure
• Update for changes in RCSB web API

- Python
Published by bkpoon about 1 year ago

cctbx - 2024.12

• Added consistency checks for mapmodelmanager
• Added tool for finding reference models based on sequence identity

- Python
Published by bkpoon about 1 year ago

cctbx - 2024.11

• Added generalized interface for LBFGS minimizer
• Improved adding of hydrogens near links in Reduce2

- Python
Published by bkpoon over 1 year ago

cctbx - 2024.10

• Added support for Python 3.13
• Improved tools for alternate conformations
• Added option to download maps from the EMDB to iotbx.fetch_pdb
• Fix random selection of atoms to consistently select the same number of atoms

- Python
Published by bkpoon over 1 year ago

cctbx - 2024.9

• Added general minimizer class for LBFGS and LBFGS-B minimizers
• Enabled linking of modified amino acids for cyclic peptides
• Added functions for parsing .geo files

- Python
Published by bkpoon over 1 year ago

cctbx - 2024.8

• Speed improvements to pdb_interpretation
• DataManager: add sanity check for specified resolution limits

- Python
Published by bkpoon over 1 year ago

cctbx - 2024.7

• Speed improvements in NCS search and process non-bonded links
• DataManager: add scoring layer to filter arrays for fmodel

- Python
Published by bkpoon over 1 year ago

cctbx - 2024.6

• Update pdbtools to use targetoutputformat
• Update known residue codes
• Update CCTBXParser to show diff of DataManager scope with --diff-params

- Python
Published by bkpoon over 1 year ago

cctbx - 2024.5

• Added water picking with alternate conformations
• Removed more unused or not maintained tools in iotbx and mmtbx
• Added check for NaN in ccp4/mrc maps

- Python
Published by bkpoon almost 2 years ago

cctbx - 2024.4

• Added mmtbx.holtongeometryvalidation tool
• Removed unused or not maintained tools in mmtbx
• Fixed bug in PDB remediator for RNA
• Added ability to add water with alternative conformations

- Python
Published by bkpoon almost 2 years ago

cctbx - 2024.3

• Fixed loggraph output in xtriage
• Added initial clashscore2 that uses reduce2 and probe2
• Clean up MolProbity and clashscore code
• Clean up Polder maps code
• Added option to use pyopengl in gltbx if available

- Python
Published by bkpoon almost 2 years ago

cctbx - 2024.2

• Improved handling of writing models in mmCIF or PDB formats
• Speedups to reduce2 and probe2

- Python
Published by bkpoon about 2 years ago

cctbx - 2024.1

• Added checks to see if a model can be outupt in the PDB format
• Added custom scattering factors support to fmodel
• Reogranize fmodel PHIL
• Fixed boost::timer deprecation

- Python
Published by bkpoon about 2 years ago

cctbx - 2023.12

• Fixed bug in modelvssequence
• Updated suitename analysis to ignore DNA
• Fixed bug where mask parameters were not propagated in f_model

- Python
Published by bkpoon about 2 years ago

cctbx - 2023.11

• Initial support for longer alternate locations
• Added some support functions for quantum refinement
• Bug fixes and improvements to cctbx.HKLviewer
• Improved handling of rotable hydrogens

- Python
Published by bkpoon over 2 years ago

cctbx - 2023.10

• Improvements to reduce2
• More improvements for handling long residue names
• Improvments to mosaic bulk solvent model
• Fixed bug in CCTBXParser that did not show one label being parsed
• Added option to customize DataManager PHIL in ProgramTemplate
• Initial support for Python 3.12

- Python
Published by bkpoon over 2 years ago

cctbx - 2023.9

• Added initial support for longer residue names
• Updated lists of modified amino and nucleic acids
• Generalized wilson_plot to neutron and elecron scattering tables

- Python
Published by bkpoon over 2 years ago

cctbx - 2023.8

• Added JSON output to MolProbity structure validation scripts
• Added support for segID when converting between PDB and mmCIF formats
• Fixed bug in CCTBXParser where a file could be processed more than once
• Reorganized restraints based on quantum mechanics

- Python
Published by bkpoon over 2 years ago

cctbx - 2023.7

• Initial support for handling longer residue names in mmCIF
• Improved handling of real-space maps with unexpected metadata for the origin and cell angles
• Improvements to reduce2 and probe2
• Reorganization of quantum mechanical restraints

- Python
Published by bkpoon over 2 years ago

cctbx - 2023.6

• Basic space group check when reading mmCIF
• Fix hybrid36 output in mmCIF
• Updates to lists of modified amino and nucleic acids
• DataManager updates for handling multiple uses (types) for generating fmodel

- Python
Published by bkpoon over 2 years ago

cctbx - 2023.5

• DataManager updates for handling multiple uses (types) of models and Miller arrays
• DataManager updates for handling priority of amplitudes and intensities
• Migration from using any_file when file type is already known
• Start checking atom names of non-standard amino acids

- Python
Published by bkpoon almost 3 years ago

cctbx - 2023.4

• Prevent potenially large memory usage when trying to read reflection data
• CCTBXParser fix to properly re-raise an error when parsing PHIL
• DataManager fix for handling datatypes with parent classes
• Improved water picking
• Improved atom selections to handle more than 10k atoms

- Python
Published by bkpoon almost 3 years ago

cctbx - 2023.3

• Bug fixes for RNA validation
• Improved handling of B and pLDDT values in mmtbx.processpredictedmodel
• Bug fixes for validating C-beta deviations for D-amino acids
• Bug fixes and improvements to cctbx.HKLviewer

- Python
Published by bkpoon almost 3 years ago

cctbx - 2023.2

• Improved modeling of histidine protonation states
• Improved tool for merging models
• Added resolution estimation for map docking (preparemapfor_docking)
• Bug fixes and improvements to cctbx.HKLviewer

- Python
Published by bkpoon about 3 years ago

cctbx - 2023.1

• Enable rounding of occupancies so that the sum is equal to 1
• New tool to validate torsions
• Bug fixes and improvements to cctbx.HKLviewer

- Python
Published by bkpoon about 3 years ago

cctbx - 2022.12

• New code for fitting histidine
• DataManager can map scattering table types to data types

- Python
Published by bkpoon about 3 years ago

cctbx - 2022.11

• Improved occupancy handling of multiple conformations so that the sum does not exceed 1
• Improvements to reduce2 and probe2 tools for MolProbity

- Python
Published by bkpoon over 3 years ago

cctbx - 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 from libsvm

- Python
Published by bkpoon over 3 years ago

cctbx - 2022.9

• Improvements to cctbx.HKLviewer for viewing output from xtriage or xtricorder
• Improve stability of preparemapfor_docking
• DataManager models can now have multiple types (e.g. x-ray, neutron, etc.)
• Fix anyreflectionfile_reader when reading "hklf+ins/res" (#787)
• Fix binary and source installers when /usr/bin/python is not available (#788)

- Python
Published by bkpoon over 3 years ago

cctbx - 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

- Python
Published by bkpoon over 3 years ago

cctbx - 2022.7

• Clean up multiple mmtbx tests
• Updated to RCSB API v2 for accessing data

- Python
Published by bkpoon over 3 years ago

cctbx - 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

- Python
Published by bkpoon over 3 years ago

cctbx - 2022.5

• Added function to return fmodel object in DataManager
• Added options for cubic box and soft masking to resolvecryoem
• Updates to tool for preparing maps for docking
• More improvements to cctbx.HKLviewer

- Python
Published by bkpoon almost 4 years ago

cctbx - 2022.4

• Added option to keep unmerged data in DataManager
• Bug fixes for cctbx.HKLviewer
• Improvements to finding water in maps

- Python
Published by bkpoon almost 4 years ago

cctbx - 2022.3

• Added mmtbx.processpredictedmodel command
• Updates and bug fixes to cctbx.HKLviewer
• Added methods for improved handling of heavy hydrogens in model

- Python
Published by bkpoon almost 4 years ago

cctbx - 2022.2

• Added --quiet flag to CCTBXParser to suppress output
• Updates to restraints based on quantum mechanics
• Updates and bug fixes to cctbx.HKLviewer

- Python
Published by bkpoon about 4 years ago

cctbx - 2022.1

• Added option to use legacy bulk solvent mask
• Added option to anyreflectionfile_reader to control averaging of anomalous data columns in MTZ files
• Fix SHELXF formatting where integer values may be interpreted as decimal

- Python
Published by bkpoon about 4 years ago

cctbx - 2021.12

• Initial support for Python 3.10
• Added support for outputting multi-model mmCIF files
• Adjusted mask gridding for bulk solvent

- Python
Published by bkpoon about 4 years ago

cctbx - 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°
• 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

- Python
Published by bkpoon over 4 years ago

cctbx - 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

- Python
Published by bkpoon over 4 years ago

cctbx - 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

- Python
Published by bkpoon over 4 years ago

cctbx - 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

- Python
Published by bkpoon over 4 years ago

cctbx - 2021.7

• Fix pickling error with anomalousprobabilityplot
• 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

- Python
Published by bkpoon over 4 years ago

cctbx - 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)

- Python
Published by bkpoon over 4 years ago

cctbx - 2021.5

• Improved bulk solvent masking with support for multiple regions

- Python
Published by bkpoon almost 5 years ago

cctbx - 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

- Python
Published by bkpoon almost 5 years ago

cctbx - 2021.3

• Initial support for native compilation on Apple Silicon
• Real-space refinement of occupancies and isotropic ADP

• Improvements in mapmodelmanager

  • Split up map and model by NCS groups
  • Create new mapmodelmanager with resampled maps

- Python
Published by bkpoon almost 5 years ago

cctbx - 2021.2

• Improved remediator code for converting PDB version 2 format to version 3
• Add compilation support for Boost 1.72 and 1.74

- Python
Published by bkpoon about 5 years ago

cctbx - 2021.1

• Improvements to cctbx.HKLviewer for displaying reciprocal space data

- Python
Published by bkpoon about 5 years ago

cctbx - 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 mapmodelmanager

  • Better handling of cases when information is missing
  • Calculate the RMSD of matching residues between models

- Python
Published by bkpoon about 5 years ago

cctbx - 2020.11

• Updated API for fetching data from RCSB

- Python
Published by bkpoon about 5 years ago

cctbx - 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

- Python
Published by bkpoon over 5 years ago

cctbx - 2020.9

• Bug fixes and updates for improving conda package

- Python
Published by bkpoon over 5 years ago

cctbx - 2020.8

• First release on GitHub and conda-forge

- Python
Published by bkpoon over 5 years ago