Validation (cryo-EM)


There is a long path from the initial idea about a molecule to the final atomic model and its interpretation. This path comprises many steps stretched over time, including obtaining samples, acquiring data, analyzing the data, building an atomic model, and refining the model to better represent the data. Errors can occur in each of these steps, so validation procedures should be implemented in each of them.

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


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

** Cut these last two? They were listed as 2 of 3 command line programs that were main drivers of the comprehensive validation tool. But I don't see the files/pages. **