From 7f72c2f622b23eb3cc4cb922cdf5333ff240e334 Mon Sep 17 00:00:00 2001
From: Filip Leonarski <filip.leonarski@psi.ch>
Date: Wed, 2 Sep 2026 15:45:47 +0200
Subject: [PATCH] rugnux: two usage-message lines caught up with the behaviour

--fft-min-unit-cell claimed a crystal below the 10 A floor cannot be
indexed at all; since the default-on short-axis second hypothesis it
can, so the line says so. --model promised 2Fo-Fc/Fo-Fc maps; the maps
have been sigma_A-weighted 2mFo-DFc/mFo-DFc since the rigid-body work,
and the placed model is written beside them.

Co-Authored-By: Claude Opus 5 (1M context) <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_01EFEJG6WBQv8th4UJFNe53N
---
 rugnux/rugnux_cli.cpp | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/rugnux/rugnux_cli.cpp b/rugnux/rugnux_cli.cpp
index d83d204be..91482dde3 100644
--- a/rugnux/rugnux_cli.cpp
+++ b/rugnux/rugnux_cli.cpp
@@ -137,7 +137,7 @@ void print_usage() {
     std::cout << "   -X, --indexing-algorithm <txt>   Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl;
     std::cout << "   -S, --space-group <num|symbol>   Space group number (92) or symbol (P43212) - for indexing and scaling" << std::endl;
     std::cout << "   -C, --unit-cell <cell>           Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl;
-    std::cout << "   --fft-min-unit-cell <num>        Shortest cell axis the FFT search accepts, in A (default: 10). A candidate with a shorter axis is discarded, so a crystal below the default cannot be indexed at all; -C lowers it on its own to cover the cell given" << std::endl;
+    std::cout << "   --fft-min-unit-cell <num>        Shortest cell axis the FFT search accepts, in A (default: 10). A candidate with a shorter axis is discarded, but a de-novo rotation run also tries a second first-pass hypothesis with the floor at 5 A, so a small-molecule cell is indexed without this flag; -C lowers it on its own to cover the cell given" << std::endl;
     std::cout << "   -r, --refine <txt>               Geometry refinement algorithm (none|orientation|beam_and_lattice|flex); flex tries all three per image and keeps whichever indexes the most spots (alias: multi)" << std::endl;
     std::cout << "   --refine-geometry[=N|off]        Stills: extra first pass that bundle-adjusts the shared beam/distance/cell from N strongly-indexed frames (default: 200) then re-indexes (lifts weak-stills indexing). Default ON for stills when a reference cell is given (-C / reference MTZ); =off disables" << std::endl;
     std::cout << "   --index-ice-rings[=on|off]       Index on the spots flagged as sitting on an ice ring too, instead of setting them aside (default: off; no effect without --detect-ice-rings)" << std::endl;
@@ -171,7 +171,7 @@ void print_usage() {
     std::cout << "   --scaling-iterations <num>      Number of scaling iterations with no reference data (default: 3)" << std::endl;
     std::cout << "   -z, --reference-mtz <file>      Reference MTZ file" << std::endl;
     std::cout << "   --reference-column <label>      Reference MTZ column to use (default: auto - F-model, else IMEAN/I, else FP/FOBS/F)" << std::endl;
-    std::cout << "   --model <file>                  After merging, validate vs this atomic model: R-free, 2Fo-Fc/Fo-Fc maps, and - where the merge kept the Bijvoet split - an anomalous difference map with the strongest anomalous scatterers named by the atom they sit on. PDB or mmCIF, gzipped or not, recognised by content rather than by extension" << std::endl;
+    std::cout << "   --model <file>                  After merging, validate vs this atomic model: R-free, sigma_A-weighted 2mFo-DFc/mFo-DFc maps, the model as placed (written beside them), and - where the merge kept the Bijvoet split - an anomalous difference map with the strongest anomalous scatterers named by the atom they sit on. PDB or mmCIF, gzipped or not, recognised by content rather than by extension" << std::endl;
     std::cout << "   --export-unmerged               Write <prefix>_unmerged.mtz, an unmerged MTZ (POINTLESS column layout) of the integrated observations, for aimless / pointless / careless. On by default, whenever there is an output prefix. On a rotation run the partials of each reflection are summed into one full, written at the batch its rocking curve is centred on, with the summed rocking-curve fraction in FRACTIONCALC; an event that caught less of its rocking curve than --min-captured-fraction (or --min-partiality) is not written, exactly as in the merge, since a full is what the reading program is told these rows are. Intensities carry the Lorentz-polarization factor and nothing else: the partiality is not divided out and the per-image scale is not applied at all, since those programs scale the data themselves. Written in --mode mx and --mode scale, and with --no-merge" << std::endl;
     std::cout << "   --no-export-unmerged            Do not write <prefix>_unmerged.mtz. It is the largest file a run produces, so a run whose observations are not going to another scaling program - a regression battery, say - can skip writing it" << std::endl;
     std::cout << "   --export-unmerged-partials      Write <prefix>_unmerged_partials.mtz, the same observations with each partial as its own row (one batch per image) flagged for the reading program to sum, instead of summed here. Off by default and independent of --export-unmerged; both can be written in one run" << std::endl;