TorchRef: An open-source PyTorch Framework for Crystallographic Refinement

Macromolecular crystallographic refinement underpins structural biology, yet existing software packages often lack accessible, modular codebases amenable to rapid method development. Here, we introduce TorchRef, a PyTorch-based crystallographic refinement framework that exposes all refinable parameters, atomic coordinates, displacement parameters, occupancies, and scale factors to automatic differentiation. The framework implements FFT-based structure-factor calculations, the French-Wilson treatment of intensities, bulk-solvent modeling with established mask parameters, and stereochemical restraints from the CCP4 Monomer Library. A modular target architecture allows loss functions to be combined, weighted, and extended independently of the core refinement machinery. Validation against 1,000 PDB structures demonstrates that TorchRef-based refinement reproduces a median R-free within 1% of Phenix while maintaining comparable model quality. Structure factor calculation in TorchRef scales readily across multiple CPU cores and is over 100 times faster on modern GPUs than CCTBX. To showcase how modern methods like time-resolved crystallography can benefit from the flexibility that TorchRef provides, we implemented direct refinement of a typical time-resolved model against amplitude differences, a use case currently not explored by classic refinement programs. TorchRef is released under the MIT license with full API documentation and tutorials, providing an accessible platform for developing and testing new crystallographic refinement protocols.