leonarski_fandClaude Opus 4.8
abbee2d4dc
Datasets may be confidential; sample names and measured unit cells committed to the repo can leak outside the group working on them. Scrub existing occurrences and add a "No sample identities in the repository" section to CLAUDE.md (forbidden: sample/dataset names, internal codes, measured cells tied to a sample; fine: space group / lattice / twinning descriptors). - Comments: replace internal dataset codes and protein names with the crystallographic situation they illustrate (centred vs pseudo-symmetric, holohedral, cubic, F-cubic/hexagonal, ...). - Docs: same, in the analysis/writer/stream references and example configs. - Tests: rename sample-named identifiers, TEST_CASE names, file prefixes and asserted labels to neutral crystallographic names (e.g. tetragonal_uc); behaviour unchanged. Reduce the CrystFEL reference PDB to a bare CRYST1 cell file (cell.pdb) and rename the reference data file. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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 HDFDatasetWriteTest. From main directory:
mkdir build
cd build
cmake3 ..
make HDF5DatasetWriteTest
Go back to main directory and:
cd crystfel
HDF5DATASET_WRITE_TEST_SWMR=1 ../build/tests/HDF5DatasetWriteTest ../tests/test_data/compression_benchmark.h5 100
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