From c570b9f3a8988ebc6f1c343ebe3ca6bd077305dc Mon Sep 17 00:00:00 2001 From: Filip Leonarski Date: Tue, 25 Aug 2026 07:29:49 +0200 Subject: [PATCH] rugnux docs: say which pass-1 files stopped being written, and which did not "Only the refined pass is written" is true of the merged files and false of the process file: with --no-merge or --write-process-h5 each pass writes its own, so _01_process.h5 is still there beside _process.h5. Name the four files that did go, and the one that did not. Co-Authored-By: Claude Opus 5 (1M context) Claude-Session: https://claude.ai/code/session_01Y5XisyYxmF8mUEQjzpMRe2 --- docs/RUGNUX.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/docs/RUGNUX.md b/docs/RUGNUX.md index 054bc6e6..c15b6e3e 100644 --- a/docs/RUGNUX.md +++ b/docs/RUGNUX.md @@ -335,10 +335,12 @@ By default a rotation run also **post-refines the geometry** in a second pass: t integrates and merges at the header geometry, then the detector distance + beam centre and the crystal cell / rotation-axis are refined against the merged fulls (cross-validated, and committed only for a small < 1 % move, with the gauge-weak beam centre restrained toward the header), and the second pass -re-indexes de novo and re-integrates at the refined geometry. Only the refined pass is written, as -the canonical `_*` output; the header-geometry pass merges only to choose the space group and -to judge the refined pass against, and writes no merged files of its own. Disable it with -`--rotation-no-postrefine`. +re-indexes de novo and re-integrates at the refined geometry. The refined pass is the canonical +`_*` output; the header-geometry pass merges only to choose the space group and to judge the +refined pass against, and writes no merged files of its own — no `_01.mtz`, `.cif`, `.hkl` or +`_01_image.dat`. (Where a process file is asked for at all, with `--no-merge` or +`--write-process-h5`, each pass still writes its own, so `_01_process.h5` appears beside +`_process.h5`.) Disable it with `--rotation-no-postrefine`. After the per-frame scale-fulls step, rotation scaling applies three **correction surfaces**, **on by default** (`--no-scaling-corrections` disables all):