phenix

To refine protein structures, this solution integrates AlphaFold predictions for molecular replacement and manages real-space refinement using your cryo-EM data. It orchestrates iterative refinement cycles to build and validate atomic models.

Automating X-ray crystallography workflows involves orchestrating multi-step pipelines for structure determination and iterative refinement. This approach manages cycles with tools like phenix.refine and performs validation using MolProbity for comprehensive quality assessment.

Yes, you can generate visualization scripts for Coot, PyMOL, and ChimeraX directly from refined protein structures. These scripts support manual model inspection and streamline the creation of publication-ready figures.

While real-space refinement is automated, manual model validation is supported. The workflow performs comprehensive automated quality assessments using MolProbity and generates visualization scripts for Coot to aid manual inspection.

AlphaFold integration helps molecular replacement by providing accurate initial predictions for model building and docking. These predictions are seamlessly incorporated into cryo-EM workflows to establish a starting point for real-space refinement.