Coot Structure Validation Best Practices

Overview

When performing structure validation in Coot with both a model and a map, you need to analyze the structure from three complementary perspectives:

1. Model-to-Map Validation: How well does the existing model fit the density?
2. Map-to-Model Validation: Where is there significant density that is NOT explained by the model?
3. Atom Overlap Validation: Are there steric clashes between atoms in the model?

All three perspectives are essential for comprehensive validation.

The Three Types of Validation

Model-to-Map: Finding Problems in Your Model

These functions analyze how well your current model fits the density. They lead you to places in the model that need attention: