Model Validation


You should validate an atomic model generated from crystallographic experiments by checking if it is consistent with priory knowledge about stereochemistry. This information includes covalent geometry, non-bonded interactions, and known distributions of side chain and main chain conformations in both proteins and nucleic acids. This validation should also extend beyond purely geometric measures to include local fit to electron density.

Validation is performed throughout the structure solution process, which consists of cycles of validation, manual or automated rebuilding, and automated refinement until a satisfactory model is obtained. Useful validation criteria depend on the resolution of the data.


In Phenix, model validation is provided in the comprehensive validation GUI based on the MolProbity tool. This software can be run as a standalone program or automatically as part of phenix.refine. Overall model statistics are presented in a summary chart with local scores reported as plots and as tables listing the outliers on each criterion. The model validation tasks are essentially identical to the MolProbity web service. The validation results are seamlessly integrated with the graphics programs Coot and PyMOL.

How to use the validation tools in the Phenix GUI: Click here

More information about MolProbity

Common issues

Outliers versus errors: In most structures, there will Ramachandran and side chain rotamer outliers. If the electron density and surrounding chemistry supports the outlier conformation, then it is most likely an outlier from prior expectations. In the absence of supporting density and/or conflicting local chemistry, it is probably an error that needs correction.

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