torchref.cli.refine module
Command-line script for LBFGS crystallographic refinement using torchref.
Supports the Bhattacharyya overlap target by default; Gaussian / least-squares
/ maximum-likelihood targets remain available via --xray-mode.
Examples
# Default: Bhattacharyya target, joint XYZ+ADP+scaler LBFGS
torchref.refine -m model.pdb -sf reflections.mtz -o output_dir/
# 10 refinement cycles
torchref.refine -m model.pdb -sf reflections.mtz -o output/ -n 10
# Separated XYZ then ADP cycles
torchref.refine -m model.pdb -sf reflections.mtz -o output/ --mode refine
# Legacy maximum-likelihood target
torchref.refine -m model.pdb -sf reflections.mtz -o output/ --xray-mode ml