RUGNUX: a model run also refines the model it placed; the model can be
given as an input; only the unmerged MTZ is written by default; the
_process.h5 is not a default output; a short "when a run fails" note.
TUTORIAL: the .ins, the refined model/maps/blobs, the log and _modules.h5
in the output list; the report is not written with -o ""; stills: -X Auto
picks ffbidx with a cell, a run over several files.
FORMATS: the XFEL stills formats and model/reference inputs told by content.
CALIBRATION: -C and -S as the calibrant. INSTALL: the CPU path runs every
indexer and the refinement. MODEL_AND_REFERENCE: the refined model is
written as .pdb too.
Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_015CeEGgpKdfkCTJb3YNMJcu
(cherry picked from commit 0062d72b95e996438ddc65dc343b526c84daa7fb)
leonarski_f
c3c5a32a0d
