DIALS 3.17.0

2023-11-03:

Features

• Circular dependencies have been removed between DIALS and cctbx.xfel by using the new serialtbx. (#2404)
• dials.import: Enable use of an image range selection when importing a still sequence. (#2490)
• dials.estimate_resolution: Improved CC½ fitting by using a weighted tanh fit. (#2499)
• dials.find_spots and dials.integrate now accept exclude_images_multiple=N, which will be expanded to the appropriate exclude_images= definition that excludes every Nth image from the data set. This is intended for the sitation where a scan of diffraction images is regularly interrupted by calibration images. (#2511)
• dials.ssx_integrate: Add mosaicity_max_limit= setting, to control what mosaicity limit is considered unphysically large. (#2518)
• dials.ssx_integrate: Add max_cell_volume_change_fraction= parameter to catch highly divergent cell refinements (#2521)
• dxtbx: Add nxmx_writer, a tool for converting any data dxtbx can read to NeXus data. (cctbx/dxtbx#615)
• dxtbx: Remove circular dependencies between dxtbx and cctbx.xfel, by using the new serialtbx. (cctbx/dxtbx#627)
• dxtbx: Set the beam probe to electron in both FormatNXmxED and FormatSER. (cctbx/dxtbx#661)
• xia2.ssx: Enable slicing a subset of images/templates using <filename>:start:end syntax. (xia2/xia2#740)
• xia2.ssx_reduce: Improved workflow for resolving indexing ambiguity. (xia2/xia2#761)
• xia2.ssx: Add starting_geometry= option, to set an initial geometry for further geometry refinement. (xia2/xia2#763)
• xia2.cluster_analysis: Add run_cluster_identification= option to toggle cluster identification analysis. (xia2/xia2#767)

Bugfixes

• dials.cosym: Fix handling of refinement weights, for sparse data with a low number of common reflections. This improves the handling of serial still data. (#2503)
• dials.reflection_viewer: Fix a wsPython-related type error. (#2506)
• dials.sequence_to_stills: Now works with statically-refined experiments. (#2516)
• dials.sequence_to_stills: Generate identifiers for the split experiments. (#2517)
• dials.sequence_to_stills: No longer crashes when operating on a scan that does not start at image 1. (#2520)
• dials.symmetry: Print reindexed unit cell in log output. (#2523)
• dials.index: Correctly index multiple sweeps for multi-sweep indexed input. (#2534)
• dials.ssx_integrate: Fix bug in foreground mask calculation, affects datasets where wavelength is much bigger or smaller than 1 Å. (#2535)
• dials.index: Fix lattice counting when indexing with >1 sweep and >1 lattice (#2539)
• dials.cosym/dials.scale: Handle potential quasi_normalisation failures (for serial data). (#2540)
• Bootstrap --cmake: Fix configuration when CCP4 is already loaded. Previously, this could cause a failure as it tried to resolve the CCP4 copy of HDF5 in order to determine version. (#2544)
• dxtbx.image_average: Better handle detector gain and pixel data type. (cctbx/dxtbx#660)
• dxtbx: Beam.probe is no longer reset if any geometrical override is provided at import. (cctbx/dxtbx#661)
• dxtbx: Pilatus 4: Do not invert module size that is correctly written in master file. (cctbx/dxtbx#663)
• dxtbx.plot_detector_models: Use noninteractive matpotlib backend, if using the pdf_file= option. (cctbx/dxtbx#664)
• xia2.multiplex: Automatically extend r_free flags for clusters and filtered datasets. (xia2/xia2#747)
• xia2.ssx_reduce: Improve data selection for indexing ambiguity resolution. (xia2/xia2#760)
• xia2.cluster_analysis: Fixed bug where interesting clusters were not identified, due to inconsistency in file paths. (xia2/xia2#764)
• xia2.multiplex: Fix duplicate-batch-offsets crash for multi-lattice data. (xia2/xia2#765)
• xia2.multiplex: Exit cleanly when supplied with still-shot data. (xia2/xia2#766)
• xia2.ssx_reduce: Fix test for potential accidental indexing ambiguities for non-MX space groups. (xia2/xia2#768)

For a more complete list of changes and fixed bugs check the dials, dxtbx and xia2 changelogs.