From 7a60cb6a2f792f2928f2c509cc930dc91fc7f037 Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Tue, 10 Nov 2026 19:36:08 +0100 Subject: [PATCH] README: bring back the serial stills example at SACLA as its own short walk-through Co-Authored-By: Claude Opus 5.5 Claude-Session: https://claude.ai/code/session_01HVeDQsU5a8AJUdJPgWevAK --- README.md | 37 +++++++++++++++++++++++++++++++++++-- 1 file changed, 35 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index dda9ee5ca..76fae72e6 100644 --- a/README.md +++ b/README.md @@ -145,14 +145,47 @@ deposited structure (`https://files.rcsb.org/download/4NWV.cif`). | [4NWV](https://www.rcsb.org/structure/4NWV) | SBGrid Data Bank [10.15785/sbgrid/9](https://doi.org/10.15785/sbgrid/9) | marCCD frames, 16.8 GB; a 400 A cell | 390 s | | [9V3D](https://www.rcsb.org/structure/9V3D) | CXIDB [236](https://cxidb.org/id-236.html), [10.11577/3014306](https://doi.org/10.11577/3014306) | MPCCD, Cheetah-SACLA HDF5; files `run157084-0..2.h5`, 10.1 GB | 35 s | -Serial stills are given the known cell and space group and all the files of the run: +### Serial stills: lysozyme at SACLA + +Serial data go through the same program. A dataset without a goniometer axis is taken as stills; +give it the known cell and space group. The example is one run of a tape-drive experiment at SACLA +BL2 (CXIDB 236): three of its hit files. The files carry the detector's panel layout, so no geometry +file is needed. ``` +mkdir -p sacla236 +for f in run157084-0 run157084-1 run157084-2; do + curl -L -C - -o sacla236/$f.h5 https://cxidb.org/data/236/Data/lyso01-apo-bigXtal/$f.h5 +done curl -L -O https://files.rcsb.org/download/9V3D.pdb rugnux -o sacla236 -C 79.45,79.45,38.15,90,90,90 -S P43212 --model 9V3D.pdb sacla236/run157084-*.h5 ``` -It indexes 95 % of the 2424 frames, merges to 1.7 A and refines the model to an R-free of 0.17. +It takes about 35 s and ends with + +``` + Result WARNINGS: Merged to 1.69 A in P 43 21 2. 2 conditions need + attention: MODEL_FREE_SET, OVERLOADS. + Space group P 43 21 2 + Unit cell 79.343 79.343 38.121 90.000 90.000 90.000 + Resolution 1.69 A written; the CC1/2 fall-off is fitted at 1.72 A + Completeness 100.0 % to 1.79 A; 98.4 % over the full written range + Signal I/sigma 12.8 CC1/2 0.978 + Files sacla236.cif sacla236.hkl sacla236.mtz sacla236_blobs.json + sacla236_log.txt sacla236_maps.mtz sacla236_model.cif + sacla236_model.pdb sacla236_module_placement.json + sacla236_modules.h5 sacla236_plot.txt sacla236_refined_maps.mtz + sacla236_refined_model.cif sacla236_refined_model.pdb + sacla236_report.txt sacla236_unmerged.mtz + Wall time 34.64 s +``` + +Both warnings are expected here. The deposited model was refined against these reflections, so the +free set drawn by this run is not truly free. A few percent of the reflections hold a saturated +pixel. About 95 % of the 2424 frames are indexed and the refined model has an R-free of about 0.17. +For serial data `sacla236_report.txt` gives `R_SPLIT` and `CC_HALF_SPLIT` (one half of the frames +against the other) in place of R_meas. `sacla236_module_placement.json` records where each panel +was placed. ## Your own data