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 Indexing algorithm (FFBIDX|FFT|FFTW|Auto|None)" << std::endl; std::cout << " -S, --space-group Space group number (92) or symbol (P43212) - for indexing and scaling" << std::endl; std::cout << " -C, --unit-cell Fix reference unit cell: \"a,b,c,alpha,beta,gamma\"" << std::endl; - std::cout << " --fft-min-unit-cell 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 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 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 Number of scaling iterations with no reference data (default: 3)" << std::endl; std::cout << " -z, --reference-mtz Reference MTZ file" << std::endl; std::cout << " --reference-column