DIALS 1.10

Release notes

DIALS 1.10.0 (2018-05-21):

• Faster refinement for hierarchical multiple panel detectors by moving calculations to C++
• Scan-varying refinement of the goniometer setting matrix is now possible
• dials.plot_scan_varying_crystal changed to dials.plot_scan_varying_model. Now plots beam centre drift and error bars on scan-varying unit cell, if these have been recorded (#414)
• Improvements to profile fitting in the presence of negative-valued pixels (#537)
• 'DQE' renamed to 'QE' in across function names and in output data (#544)
• Improved support for Bruker Photon II detectors
• New program dials.cosym: implementation of algorithms described in Gildea, R.J. & Winter, G. (2018). Acta Cryst. D74, https://doi.org/10.1107/S2059798318002978
• dials.reindex: bug fix when dealing with multi-sweep datasets (4027299)
• dials.refine_bravais_settings: bug fix for multi-sweep datasets if experimental models differ between experiments (#554)

xia2 0.5.577:

• pipeline=2d has been marked as deprecated and will be removed at some point in the future

DIALS 1.10.1 (2018-06-16) includes xia2 0.5.580:

• Format fixes for Bruker Photon II images
• dials.show compatibility fixes
• xia2: gracefully handle invalid ranges with image=image_0001.cbf:start:end syntax
• xia2: disable currently unreliable check_indexing_symmetry feature

DIALS 1.10.2 (2018-06-26) includes xia2 0.5.580:

• dials.export_bitmaps: Fix for still images, add output_file parameter
• Remove problematic format class from dxtbx
• Fix installation on newer Ubuntu versions

DIALS 1.10.3 (2018-07-10) includes xia2 0.5.580:

• xia2: fix missing CIF information

DIALS 1.10.4 (2018-07-24) includes xia2 0.5.582:

• dials.report: Fix incorrect y-axis labels in plots
• xia2: Allow image= without range on Windows

DIALS 1.9

Release notes

DIALS 1.9.0 (2018-03-10):

• support for scan-varying beam models
• dials.discover_better_experimental_model has been renamed to dials.search_beam_position (#418)
• fixed crash on Ubuntu 14.04 (#513)
• dials.image_viewer will now work with large Nexus files
• errors when reading files should be more informative

xia2 0.5.540:

• make some processing error messages more informative

DIALS 1.9.1 (2018-04-03) includes xia2 0.5.542:

• Correctly identify Timepix detector images
• dials.image_viewer: Fix issues with mask display, #520
• xia2: use correctly capitalized H5ToXds executable instead of H5ToXDS

DIALS 1.9.2 (2018-04-10) includes xia2 0.5.542:

• fix build issues on Mac, cctbx/cctbx_project#160
• bug fix for h5 files: write template expected by xds

DIALS 1.9.3 (2018-05-08) includes xia2 0.5.546:

• Nexus format files: correctly determine number of images in dataset
• Force scan_varying=False during indexing as indexing only uses static models
• dials.spot_counts_per_image: generate joint .json result file unless told not to.
• xia2: fix HDF5 template issue (xia2/xia2#219)
• xia2: fix processing of .nxs files if a _master.h5 file is present for the same dataset
• xia2: save integrated reflections to DataFiles directory

DIALS 1.8

Release notes

DIALS 1.8.0 (2017-11-02):

• Added option dials.show show_flags=true, for more information about how reflections were classified
• dials.refine: new diagnostic for problematic refinement cases, using the condition number of the Jacobian
• dials.refine: increase default max_iterations for problematic refinement cases
• dials.refine: bug fix for setting smoother parameters for scan-varying refinement
• dials: spot_counts_per_image fixes

xia2 0.5.469:

• respect the number of allocated CPUs on SGE clusters.
• sensible trusted range for Rayonix CCD images with XDS processing
• basic support for Eiger data sets from BioMAX, requires correct goniometer axis to be specified on command line
• can now "see" data with template prefix.nnnn.bz2 etc.
• xia2 / dials / cctbx: correct interpretation of geometry for Rigaku lab source CCD detectors
• xia2 / DIALS: support for Eiger data sets with >1000 sub-files via ulimit
• xia2 / XDS: support for use of "neggia" plugin if in XDS binary directory & processing HDF5 / Eiger data

DIALS 1.8.1 includes xia2 0.5.474 (2017-11-16):

• dials: fix build issue on macOS 10.13 (High Sierra), #77
• dials: fix run issues on macOS <10.12
• dials: fix DLS I23 image interpretation
• xia2: Fix ImportError bug on Windows (xia2/xia2#194)
• xia2 / XDS: Fix 'pixel value' issue with recent XDS versions (xia2/xia2#193)
• xia2 / XDS: Refine detector position in second integration round (xia2/xia2#181)

DIALS 1.8.2 includes xia2 0.5.476 (2017-12-05):

• dials: Fix indexing for small molecule data with unit cell <100A^3.
• dials: Improve Eiger file support
• dials: Smargon support for data from DLS I03
• xia2: Fix indexing method fallback

DIALS 1.8.3 includes xia2 0.5.482 (2018-01-16):

• dials.image_viewer: fix crash on Windows
• dials.image_viewer: fix crash when using masks (cctbx/cctbx_project#107)
• dials.stills_process: fix out of memory error when processing large files
• xia2: pipeline=2d support for Rigaku RAXIS detectors (xia2/xia2#200)

DIALS 1.8.4 includes xia2 0.5.487 (2018-01-30):

• dials.image_viewer: Fix crash with "dxtbx Internal Error" (#493)
• dials.stills_process: Validate mask file exists at the start of the program
• xia2: immediately stop when Aimless failed to process data
• xia2: Warn when using XDS with HDF5 files and necessary libraries are missing (xia2/xia2#197)
• Fixed support for DLS I03 full CBF images

DIALS 1.8.5 includes xia2 0.5.492 (2018-02-20):

• allow splitting output of dials.spot_counts_per_image per metric
• xia2: fix crash with .xinfo non-native file line endings
• xia2: add full DIALS paper reference

DIALS 1.7

Release notes

DIALS 1.7.0 (2017-08-18):

• dials.refine: performance improvements for scan-varying refinement
• dials.refine: bug fix for I23's P12M detector
• Better default gain for ADSC CCD detectors
• dials.import: dynamic_shadowing now turned on by default where a goniometer shadow model is available

xia2 0.5.428:

• xia2: dynamic_shadowing now turned on by default where a goniometer shadow model is available
• xia2.html: ensure merging statistics consistent with those reported in text output

DIALS 1.7.1 includes xia2 0.5.432 (2017-09-04):

• dials.show improvements and shoebox stats
• Allow disabling of ice ring filtering in spot finding server
• xia2: Fix dynamic shadowing for pipeline=3d
• xia2.strategy: improve BEST integration

DIALS 1.7.2 includes xia2 0.5.436 (2017-09-19):

• bug fix for DLS I23 images where MultiAxisGoniometer does not exist
• fix map coordinates in dials.image_viewer (#442)
• fix max_cell determination in indexing (#386)
• fix for setting interval widths in scan-varying refinement
• xia2.report: fix multiplicity p

DIALS 1.7.3 includes xia2 0.5.438 (2017-10-03):

• dev.dials.csv: clean up command line help
• xia2 ISPyB interface: use files in DataFiles directory in preference to other locations.
• pytest 3 compatibility fix

DIALS 1.7.4 includes xia2 0.5.442 (2017-10-24):

• fix HDF5 library download location
• support for Smargon goniometer on Soleil PROXIMA-1
• xia2: fix issue with XDS trusted ranges (xia2/xia2#182)
• xia2: allow processing of images with .gz extension (xia2/xia2#184)

DIALS 1.6

Release notes

DIALS 1.6.0 (2017-06-02):

• dials/xia2: dynamic masking of diamond anvil cells for DLS I19-2 high pressure experiments
• JMP improvements to mosaic spread estimate (#342, #119)

xia2 0.5.319:

• xia2: new xia2.html
• xia2 fixed for I23 data with distance != 0; xia2/xia2#124 & friends

DIALS 1.6.1 includes xia2 0.5.325 (2017-06-14):

• dials.image_viewer: respect kernel_size parameter (#354)
• Rayonix TIFF format fixes (#370)
• xia2: XDS compatibility fixes (xia2/xia2#131)
• xia2: Trap non-fatal fatal error (xia2/xia2#115)
• xia2: respect batch_range parameter in resolution determination
• xia2: silence xtriage output

DIALS 1.6.2 includes xia2 0.5.328 (2017-06-20):

• cctbx algorithmic stability fixes (cctbx/cctbx_project#43)
• dials.export_mtz: improved error messages (#357)
• xia2: Generate .p4p files in small molecule mode (xia2/xia2#134)

DIALS 1.6.3 includes xia2 0.5.337 (2017-07-03):

• Many dials.export fixes, including exports from single images (#388)
• xia2: Make d_min= command line parameter work again (xia2/xia2#136)
• xia2: Avoid crash when running xtriage on centric data (xia2/xia2#139)
• xia2: Move extra multiplicity files away from main directory (xia2/xia2#140)
• xia2: Remove '.bat' from output file names when run on Windows
• xia2: Improvements in HTML report (xia2/xia2#133, xia2/xia2#141)
• xia2: xia2.strategy fixes

DIALS 1.6.4 includes xia2 0.5.340 (2017-07-17):

• dials.reciprocal_lattice_viewer: correctly handle multiple sweeps in single file (#407)
• xia2: image= parameter did not work as expected when including multiple slices from the same dataset (xia2/xia2#138)
• Recognize and drop NaN values in iotbx data plotting (xia2/xia2#142)

DIALS 1.5

Release notes

DIALS 1.5.0 (2017-04-07):

• dxtbx: Converted models into C++. Bug fixes for HDF5/Eiger files to correct a previously inverted axis.
• dials.align_crystal: numerous bug fixes and simplified output
• dials.find_spots: Correctly smooth histogram, #317
• dials.geometry_viewer: display of crystal basis vectors, and added fast, slow, normal vectors to panels in display
• dials.image_viewer: new mask generation tool; performance improvements
• dials.import: full specification of meta data from phil parameters; can now import data with different detector etc into same file
• dials.index: improvements to nearest neighbour analysis used in max_cell estimation (optionally choose between linear and logarithmic histogram binning)
• dials.reciprocal_lattice_viewer: reciprocal unit cell display
• dials.refine: equal shift constraints
• dials.rl_png: fix crash
• All dials programs: no longer attempt to read from STDIN when run on a terminal (#326), generic performance improvements (#292)

xia2 0.5.270:

• xia2.report:
  • use merged intensities for calculating second moment statistics
  • include xtriage report;
  • include analysis of distribution of multiplicity in reciprocal space
  • add plots of completeness and multiplicity vs resolution
  • optionally choose cc_half_method=sigma_tau
• xia2.multi_crystal_analysis: add stereographic projection plots for crystal orientation analysis
• xia2.ispyb_xml: fix for HDF5 files

DIALS 1.5.1 includes xia2 0.5.277 (2017-04-24):

• dxtbx: fixes for DLS I04 full CBF images
• dials.find_spots: add hot_mask_prefix option
• dials.generate_mask: add optional output.datablock parameter
• dials.import: fix geometry scan image_range override (#337)
• xia2: run dials.generate_mask in DIALS pipeline
• xia2: avoid occasional pointless crash in small molecule mode (xia2/xia2#115)

DIALS 1.4

Release notes

DIALS 1.4.0 (2016-11-29):

• dials.refine now determines outlier rejection block width automatically (#158)
• Correctly take into account the goniometer setting rotation
• New commands dials.goniometer_calibration, dials.align_crystal, dials.geometry_viewer and dials.shadow_plot
• Support for dynamic goniometer shadow masking, requires beamline-specific modifications to detector Format class (dynamic_shadowing=True)
• dials.image_viewer: new parameter show_mask=True (displays the pixels that are masked out on each image)
• dials.image_viewer now stays on image when window loses focus (#220)
• dials.image_viewer: improvements for multi-panel detectors (see also #55)
• dials.index max_cell estimation improvements
• dials.refine_bravais_settings: recommend suitable settings

xia2 0.5.152:

• xia2 -quick is now faster & deprecated (use fast_mode=true)
• xia2.cif and .mmcif now land in DataFiles directory and contain more entries (xia2/xia2#66, xia2/xia2#67, xia2/xia2#69) including those from the new dxtbx detector database (xia2/xia2#78)
• When run in small molecule mode (xia2.small_molecule or small_molecule=True) SHELXT input files are generated in DataFiles (xia2/xia2#62)
• absorption surface map and merging statistics table are generated in the LogFiles directory (xia2/xia2#63, xia2/xia2#74)
• New parameter xds.correct.air to override the AIR= parameter in XDS correct step
• New parameter xds.defpix.value_range_for_trusted_detector_pixels
• pipeline=dials: now runs scan-static refinement before scan-varying refinement
• pipeline=dials: support index.method=auto
• pipeline=dials: optional scaling with XSCALE (scaler=xdsa)
• Add ability to override experimental geometry on the command line (xia2/xia2#87)
• Support for dynamic goniometer shadow masking in DIALS and XDS pipelines (dynamic_shadowing=True)
• xia2.report now plots cc1/2 and cc_anom critical values

DIALS 1.4.1 (2016-12-14):

• Various small bug fixes (#268)
• New command dials.two_theta_offset tells the offset of the two theta axis given two experiment .jsons

xia2 0.5.161:

• Resolution cut-off was too conservative (xia2/xia2@45df7e4)
• Updated cctbx loggraph parser to run with new versions of AIMLESS (dials/cctbx@7bf8540)
• Various smaller bug fixes (xia2/xia2#89)

DIALS 1.4.2 (2017-01-16):

• Fix "Mark centers of mass" in dials.image_viewer (#278)

xia2 0.5.170:

• Fix xia2 html report for sweeps containing a number of images that is not a multiple of 60
• Fix to correctly apply reindexing operations
• Observe d_min and d_max parameters when running in small molecule mode

DIALS 1.4.3 (2017-01-31):

• dials.align_crystal and dials.stereographic_projection now write json files
• dials.image_viewer fixes (#262, #284)
• dials.export bugfix for BEST output with rhombohedral space groups
• improved nearest-neighbour indexing logic

xia2 0.5.175:

• Fix image epoch crashes (xia2/xia2#90)
• Make HTML reports more responsive (xia2/xia2#98)

DIALS 1.4.4 (2017-02-09):

• dials.export format=json
• fix labels and ranges in dials.report plots

xia2 0.5.179:

• fix incorrect anomalous completeness statistics
• bug fix for pipeline=dials scaler=xdsa combination
• putative bug fix for resetting refiners when combined with multi-sweep indexing
• fix for integrate_p1=True reintegrate_correct_lattice=False when lattices are eliminated

DIALS 1.4.5 (2017-03-02):

• fix dials.reciprocal_lattice_viewer crash (#313)

DIALS 1.3

Release notes

DIALS 1.3.0 (2016-07-29):

• Improved support for processing compressed images (#79)
• More efficient parallel processing in dials.find_spots (#150)
• dials.image_viewer is now more responsive to parameter changes (#166), and can display resolution ellipses when detector is at 2theta angle > 0 (#66). Image annotations work for summed images (#107).
• The distl spotfinding webserver has been updated to the most recent versions of apache and mod_python, and expanded to support the dials spotfinder, including native support for Eiger HDF5 data from Dectris. Some documentation is available.
• dials.two_theta_refine provides a refinement of the unit cell parameters against the 2theta angles of indexed reflections.

xia2 0.5.45:

• xia2 version 0.5 includes a major overhaul of the available command line parameters (xia2/xia2#42). xia2 is moving away from switch-like command line parameters (eg. -3dii) to PHIL format parameters (eg. pipeline=3dii) - the same command line parameter format used in DIALS. Deprecation warnings are given for the most used commands, including all pipeline commands. Run xia2 without any parameters to get a very brief overview of available parameters.
• Unit cell sizes are obtained via 2theta refinement, and reported with estimated standard deviations when possible (xia2/xia2#28). The command xia2.get_unit_cell_errors will be removed in the future.
• Bruker CCD images (.sfrm) are now supported. It may be necessary to set a suitable gain value as command line parameter (eg. gain=10)
• xia2 generates a crystallographic information file (xia2.cif) by default (xia2/xia2#27)
• Small molecule processing now uses multi sweep indexer by default when possible (xia2/xia2#37). High resolution data are no longer cut off when running small molecule processing. To return to previous behaviour, use keep_all_reflections=false (xia2/xia2#30). xia2.small_molecule is a new shortcut for xia2 small_molecule=true.
• Spotfinding results are displayed for XDS pipeline processing (xia2/xia2#20)

DIALS 1.3.1 (2016-08-01):

• Fix dials.find_spots shoebox=false (#186)

DIALS 1.3.2 includes xia2 0.5.48 (2016-08-10) :

• Fix Rigaku Saturn SN457 image header parsing
• xia2 supports -atom and -failover command line options with deprecation warnings

DIALS 1.3.3 includes xia2 0.5.50 (2016-08-23):

• xia2 supports -ispyb_xml_out command line option with deprecation warning

DIALS 1.3.4 includes xia2 0.5.53 (2016-09-15):

• xia2 fixes to take space group reindexing operation into account when refining unit cells

DIALS 1.3.5 includes xia2 0.5.57 (2016-09-22):

• fix image overlays when summing multiple images
• xia2 fix crash with xinfo files when only high resolution limit is defined
• xia2 fix command line in ISPyB xml output and set default xml filename

Installation

Installers for Linux, MacOS X and MacOS X 10.6 as well as a source file distribution are available below.

Alternatively you can compile DIALS 1.3 from scratch by running

$ wget https://raw.githubusercontent.com/dials/cctbx/dials-1.3/libtbx/auto_build/bootstrap.py
$ python bootstrap.py --builder=dials hot update base build

DIALS 1.2

Release notes

DIALS 1.2.0 (2016-05-05):

• Support for EIGER data
• Outlier rejection for centroid refinement now in blocks
• dials.discover_better_experimental_model now uses random subset of reflections from entire scan

xia2 0.4.0.335:

• Support for EIGER data in -dials and -3d pipelines (latter requires H5ToXDS)
• xia2.html report automatically generated after successful completion of xia2
• DIALS pipeline now includes DIALS beam centre search
• xia2.to_shelx can use output of xia2.get_unit_cell_errors and generate cif file
• Improved processing of chemical crystallography data

DIALS 1.2.1 (2016-05-06):

• Fix bitshuffle plugin (#133)

DIALS 1.2.2 includes xia2 0.4.0.338 (2016-05-09):

• bug fixes if passing space_group but not unit_cell to xia2 -dials
• correct theta angles in .cif file generated by xia2.to_shelx
• fix issues when building with older versions of Python <2.6

DIALS 1.2.3 includes xia2 0.4.0.340 (2016-05-16):

• Accept relative paths for HDF5 files in xia2

DIALS 1.2.4 includes xia2 0.4.0.342 (2016-05-23):

• Fix indexing/refinement crash
• Fix typo in xia2 xml output

DIALS 1.2.5 includes xia2 0.4.0.345 (2016-06-09):

• improve display for dials.image_viewer with sum_images (#107)
• add cursor control, improved display for dials.reciprocal_lattice_viewer (#142, #145)
• reduce dials.refine log verbosity
• xia2 warns on missing wavelength in xinfo file
• xia2.get_unit_cell_errors erroneous constraint for unit cell error estimates relaxed

DIALS 1.2.6 includes xia2 0.4.0.345 (2016-07-05):

• fix ice ring filtering for blank images

Installation

Installers for Linux, MacOS X and MacOS X 10.6 as well as a source file distribution are available below.

Alternatively you can compile DIALS 1.2 from scratch by running

$ wget https://raw.githubusercontent.com/dials/cctbx/dials-1.2/libtbx/auto_build/bootstrap.py
$ python bootstrap.py --builder=dials hot update base build

DIALS 1.1

Release notes

Amongst many other improvements

• unit cell restraints are now available in dials.refine. These are particularly intended for use for multi-crystal joint refinement tasks. Cells may either be restrained to a known target, or groups of cells to their mean or median values.
• reciprocal lattice viewer runs much more smoothly
• xia2 now offers improved small molecule support, including a multi sweep indexer (use multiple_sweep_indexing=True), and the option to estimate unit cell uncertainties with xia2.get_unit_cell_errors

DIALS 1.1.1:
Let xia2 calculate merging statistics using cctbx. Increase speed of sorting flex tables.

DIALS 1.1.2:
Updates in cctbx and xia2 for improved EIGER support.

DIALS 1.1.3:
Fix compilation issues with recent MacOS X update. Fixed xia2.html. Fix colour issues in dials.reciprocal_lattice_viewer on Windows machines.

DIALS 1.1.4:
Fix incorrect DQE calculations. Improvements on xia2.html.

Installation

Installers for Linux, MacOS X and MacOS X 10.6 as well as a source file distribution are available below.

Alternatively you can compile DIALS 1.1 from scratch by running

$ wget https://raw.githubusercontent.com/xia2/cctbx/dials-1.1/libtbx/auto_build/bootstrap.py
$ python bootstrap.py --builder=dials hot update base build