coot-model-building

What problem does it solve?

This Skill consolidates best practices for model-building tools and refinement, guiding researchers to implement robust validation workflows and safe refinements in Coot.

Core Features & Use Cases

• Checkpoint-driven workflow: create and restore named checkpoints to compare alternative refinement strategies.
• Extended residue selection: refine larger regions around a problem residue to maintain context and improve outcomes.
• Spatial-neighbour awareness: include nearby residues to account for non-bonded interactions during refinement.
• Iterative validation: systematically re-check Ramachandran, rotamer, and density metrics after each adjustment.
• Safe navigation: center on residues and manage refinements with undo/restore to prevent irreversible changes.

Quick Start

Start by centering on a problematic residue, create a named checkpoint, perform an initial refinement over a larger region (e.g., ±1-2 neighbors), then evaluate Ramachandran, rotamer, and density metrics and iterate as needed.