leonarski_fandClaude Opus 5.5
f81c0c7f0f
- docs/PUBLICATIONS.md: how to cite (Rugnux: bioRxiv 2026 preprint; Jungfraujoch: J. Synchrotron
Rad. 2023 stays primary, J. Appl. Cryst. 2026 for real-time serial / live indexing) and the
paper list (IUCrJ 2023 MAX IV, Struct. Dyn. 2020, TORO J. Appl. Cryst. 2024); linked from the
toctree, ACKNOWLEDGEMENT, README, RUGNUX and JUNGFRAUJOCH pages. All DOIs checked on Crossref.
- Landing page: a Publications band with two typeset title-page cards (Rugnux preprint and the
J. Appl. Cryst. paper, with the 2023 primary reference), nav and footer links; HTML/CSS only, no
logos or images.
- rugnux prints a one-line citation in its startup banner (fits the 78-column console) and the
full reference ("If you find rugnux useful, please cite ...") at the head of _report.txt.
- Files jfjoch_writer writes from Rugnux live mode name both programs: the MTZ files get a
"From Jungfraujoch <version>, data collection" HISTORY record after Rugnux's (and a Rugnux
record where the map tables carry none), the placed/refined model mmCIF get Rugnux
(phasing/refinement) and Jungfraujoch (data collection) in _software. The round-trip tests
expect those additions.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01HVeDQqrMy3Kh9NQw823gEb
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Jungfraujoch
Application to receive and analyse data from the PSI JUNGFRAU and EIGER detectors, together with
rugnux, its program for processing stored diffraction data - rotation and serial, macromolecular
and small-molecule - from images to merged reflections.
All documentation is now placed in docs/ subdirectory and for the current version hosted on Jungfraujoch Read The Docs page.
How to cite
- Jungfraujoch: F. Leonarski et al., "Jungfraujoch: hardware-accelerated data-acquisition system for kilohertz pixel-array X-ray detectors" (2023), J. Synchrotron Rad. 30, 227-234 doi:10.1107/S1600577522010268; for real-time serial crystallography and live indexing feedback also J. Duan et al., "Jungfraujoch: 38 GB s⁻¹ real-time serial crystallography – data acquisition and live indexing feedback" (2026), J. Appl. Cryst. 59, 1668-1677 doi:10.1107/S1600576726008083.
- Rugnux: F. Leonarski and M. Wang, "Rugnux: from diffraction images to structure at synchrotrons and XFELs in one program" (2026), bioRxiv doi:10.64898/2026.10.24.761522.
The full list is in docs/PUBLICATIONS.md.