Validation (cryo-EM)

Why

Many steps are involved to get from the initial idea about a molecule to the final atomic model and its interpretation. Errors can occur in each of these steps, so validation procedures are necessary to ensure that the atomic models are sensical and fit the experimental data.

In particular, validation addresses data, model, and model-versus-data quality:

How

Comprehensive validation (cryo-EM) is a one-stop program in Phenix that validates model, data, and model-versus-data fit. The minimal input is a map (in MRC, CCP4, or related format) and an atomic model (in PDB or mmCIF format). However, providing a map, model, and two half-maps is desirable.

For geometric validation, Phenix uses MolProbity, which is fully integrated into the Comprehensive validation (cryo-EM) package. The graphics programs Coot and PyMOL are also fully integrated, enabling communication of the validation results.

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

Common issues

Related programs