diff options
Diffstat (limited to 'relnotes-0.10.1')
| -rw-r--r-- | relnotes-0.10.1 | 137 |
1 files changed, 0 insertions, 137 deletions
diff --git a/relnotes-0.10.1 b/relnotes-0.10.1 deleted file mode 100644 index d7388eea..00000000 --- a/relnotes-0.10.1 +++ /dev/null @@ -1,137 +0,0 @@ -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 |