Model Validation

Why

The atomic models generated from crystallographic experiments should conform to prior knowledge about stereochemistry. This covers a wide range of information, ranging from covalent geometry, through non-bonded interactions, up to known distributions of side chain and main chain conformations in both proteins and nucleic acids. Validation is required to check the consistency of an atomic model with this prior knowledge to identify possible errors in the model. Validation also extends beyond purely geometric measures to include local fit to electron density.

How

The main tool for geometric validation in Phenix is MolProbity. This is tightly integrated with structure refinement such that after running phenix.refine in the GUI a complete set of validation statistics are produced. In combination with the Coot program for visualization of models and electron density it is possible to rapidly check vaidation outliers and make corrections. Validation metrics for local fit to density are also provided in the form of a multi-criterion plot.

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

Common issues

• Outliers versus errors: in most structures there will be a non-zero number of Ramachandran and side chain rotamer outliers. If the electron density, and surrounding chemistry, supports the outlier conformation then it is most probable that this is correct (i.e. an outlier from prior expectations, rather than an error). However, in the absence of supporting density, and/or conflicting local chemistry, it is most probably an error that needs correction.

Related programs

• phenix.model_vs_data: This program assesses the overall quality of an atomic model with respect to the experimental data.

More information about MolProbity