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diff --git a/relnotes-0.10.1 b/relnotes-0.10.1 new file mode 100644 index 00000000..d7388eea --- /dev/null +++ b/relnotes-0.10.1 @@ -0,0 +1,137 @@ +CrystFEL - Data processing for serial crystallography +----------------------------------------------------- + +Release notes for version 0.10.1 + +Copyright © 2012-2022 Deutsches Elektronen-Synchrotron DESY, + a research centre of the Helmholtz Association. + +See AUTHORS as well as the individual source code files for full contributor details. + +CrystFEL is free software: you can redistribute it and/or modify it under the +terms of the GNU General Public License as published by the Free Software +Foundation, either version 3 of the License, or (at your option) any later +version. + +CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY +WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A +PARTICULAR PURPOSE. See the GNU General Public License for more details. + +You should have received a copy of the GNU General Public License along with +CrystFEL. If not, see <http://www.gnu.org/licenses/>. + + +Overview +-------- + +This release is primarily a bug-fixing update to CrystFEL, and there have been +improvements around the entire suite. The most important changes are detailed +below. See the ChangeLog or the Git history for a comprehensive list of all +changes. + + +Graphical user interface +------------------------ + +SLURM jobs started from the GUI will now inherit the entire environment of the +GUI, including the values of 'PATH', 'HDF5_PLUGIN_PATH' and other variables. +This matches the default behaviour of 'sbatch' and should make it easier to set +up the environment correctly. The text entry field entitled 'Search path for +executables' for SLURM jobs has been removed. Simply make sure that any extra +locations (e.g. to find Mosflm, DirAx or XDS) are added to 'PATH' before +starting the GUI, and the SLURM jobs should run correctly. + +Multiple streams can now be imported at once, to create one "result". This is +useful when you want to merge a set of streams inside the GUI, for example if +you've previously used "turbo-index" to split the indexing and integration work +into multiple batches. + +When exporting data to MTZ format, the crystal and project fields of the MTZ +file will now be filled in. The crystal name will be the name of the indexing +run, the project name will be the name of the folder from which the GUI was +started. As before, the dataset name will be the name of the merging run. +See the section 'MTZ and XDS export' below for information about other changes +to reflection data export. + +A new checkbox "Rescan streams when changing frame" has been added to the +"Tools" menu. In certain circumstances, such as when an indexing job is +running, un-ticking this box will make it faster to switch between frames in +the GUI. However, you will need to occasionally run "Rescan streams" to make +sure that the GUI's display is up-to-date. + + +Build system +------------ + +When building with Meson, several dependencies will now automatically be +downloaded and compiled. In this version, this applies to the following +dependencies: FastDiffractionImageProcessing (FDIP), LibCCP4, PinkIndexer, +XGandalf, ZLib and Eigen (Eigen is a dependency of XGandalf and PinkIndexer). +You can disable this feature if you don't want it - see INSTALL.md or the Meson +manual for details. It's also possible to use this feature for a restricted +selection of dependencies. + +Bugs in the detection of certain dependencies (OpenCL and SLURM) have been +fixed. The dependency on ZLib has been made optional, and CrystFEL no longer +depends on 'NCurses' at all. + + +Geometry files +-------------- + +A new field 'mask_edge_pixels' was added to the geometry files. As the name +suggests, you can use this to easily mask the edge pixels of panels. See "man +crystfel_geometry" for details. + +CrystFEL has become more stringent about the contents of geometry files. The +wavelength (or photon energy etc) must be specified, as well as the experiment- +space directions of the fs/ss panel vectors. There is no longer any default +for these. + +The 'detector rail direction' feature, which was broken in version 0.10.0 and +not used at all in practice, has been removed completely. + + +Indexing and integration +------------------------ + +A new option '--data-format' has been added to indexamajig. This is to be used +when receiving data from an online source, such as ZeroMQ. The currently +available values are 'msgpack' and 'hdf5'. Previously, the only possibility +was for online data to be in MessagePack format, but now it can be delivered in +HDF5 format as well. Other formats will be added in future. + +The 'peak pairing' procedure, an important part of the 'prediction refinement' +and resolution estimation calculations, has been changed to use a reciprocal- +space distance cutoff of one third of the smallest inter-Bragg distance. +Previously, a hardcoded distance of ten pixels was used. This change makes the +results almost independent of image binning. + + +MTZ and XDS export +------------------ + +There are now two modes for MTZ export, whether via the GUI or using get_hkl. + +Plain MTZ mode (get_hkl --output-format=mtz, or 'MTZ' in the GUI export +dialog) simply places the reflections into CCP4's definition of the asymmetric +unit and writes the intensity and error estimates into columns I and SIGI +respectively. This mode is the easiest to use for straightforward structure +refinement. + +Bijvoet MTZ mode (get_hkl --output-format=mtz-bij, or 'MTZ, Bijvoet pairs +together' in the GUI export dialog) puts Bijvoet pairs in the same row, under +the columns I(+), SIGI(+), I(-) and SIGI(-). This mode is obviously more +appropriate for experiments involving the anomalous signal. + +Finally, a bug has been fixed in the export to XDS format, where the unit cell +parameters were previously labelled as '!UNIT_CELL_CONSTANT' instead of +'!UNIT_CELL_CONSTANTS'. + + +API changes +----------- + +There was only one change to the libcrystfel API: + +write_to_mtz: Addition of 'crystal_name' and 'project_name' parameters |