leonarski_fandClaude Opus 5
cfcb84aece
rugnux gained --model - R-free and 2Fo-Fc/Fo-Fc maps against an atomic model, and with it the resolution of the enantiomorph and of a merohedral indexing ambiguity - without the page ever mentioning it. It was the only option missing; the two lists now agree in both directions, checked against the usage the binary prints. The viewer page still said results are never saved and that no Windows package exists. Both have been false for a while: the Processing panel runs full rugnux jobs on the open dataset, writes _process.h5 and the merged reflections, registers each run as a selectable view so runs can be compared, and can hand out the equivalent command line for a cluster; and the installer is published with every release. The mask menu also loads TIFFs now, and the View menu has layout presets. The writer page documented -R for the root directory, which is the back-compatibility alias for -d, and an HTTP status interface that no longer exists - status reaches the broker over the writer notification socket, and a writer is stopped with a signal. The test page pointed at .gitlab-ci.yml and at jfjoch_offline_process, which is not a binary any more; the CrystFEL fixture pointed at HDF5DatasetWriteTest, which is not either. The broker page linked ../broker/redoc-static.html, which MyST resolved by copying the 700 kB file into _downloads/ rather than using the copy already in _static. Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
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CrystFEL test
This test requires recent version of CrystFEL with Xgandalf indexing algorithm. Tested with CrystFEL 0.10.0.
Generate HDF5 file
To generate HDF5 you need first to compile jfjoch_hdf5_test. From main directory:
mkdir build
cd build
cmake ..
make jfjoch_hdf5_test
Go back to main directory and:
cd tests/crystfel
../../build/tools/jfjoch_hdf5_test ../../tests/test_data/compression_benchmark.h5 -n100 -o writing_test
This will generate HDF5 with protein diffraction data measured with JUNGFRAU 4 Mpixel long time ago.
Analyze with CrystFEL
To process the generated file with CrystFEL, you need to run the following command:
indexamajig -g jf4m.geom -i writing_test.lst -o writing_test.stream --indexing=xgandalf
Hopefully you see the following outcome at the end:
Final: 100 images processed, 100 hits (100.0%), 100 indexable (100.0% of hits, 100.0% overall), 100 crystals.
In case of issues, you can also try providing unit cell information:
indexamajig -g jf4m.geom -i writing_test.lst -o writing_test.stream --indexing=xgandalf -p cell.pdb