Model. The atomic models derived from cryo-EM reconstructions 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.

Model to data fit. A perfectly good model from stereochemistry prospection may not describe (fit) the experimental data (3D reconstruction) sufficeintly well or at all. Therefore it is important to validate how well the atomic model described the experimental information.

Data. The quality of experimental data, such as the resolution or amount noise defines the quality of derived models. For example, a higher-resolution data is likely to yield a more accurate atomic model than a lower-resolution date. It is vital then to learn about data quality as much as possible to have correct expectations about corresponding models as well as to use correct model building and refinement procedures appropriate for the data at hand.


Comprehensive validation (cryo-EM) is one stop program in Phenix that validates model, data and model-to-data fit. Minimal input to Comprehensive validation is a map (mrc, ccp4 or related format) or an atomic model in PDB or mmCIF format. However, providing the map, model and two half-maps is desirable. For geometric validation Phenix uses MolProbity, which is fully integrated into into the packadge, and Coot that is enabled to communicate validation results.

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

Common issues

Related programs

These three command line programs are the main drivers of the Comprehensive validation (cryo-EM) tool in Phenix GUI: