coot-unmodelled-blobs

What problem does it solve?

This Skill helps crystallographers identify and interpret unmodeled density blobs in electron density maps during Coot-based model building.

Core Features & Use Cases

• Blob detection and prioritization: locate unmodeled density regions and rank by blob score to guide inspection.
• Density interpretation workflow: evaluate nearby atoms and residues to determine whether a blob corresponds to an ongoing chain extension, a missing atom, water, ion, or ligand.
• Iterative chain extension workflow: extend chains by adding terminal residues when blobs are near the chain terminus, refining after each addition.
• Decision guidance: determine whether to cap completed fragments with OXT when no density remains.
• Safe checkpointing and refinement: create checkpoints before changes and refine to assess blob changes.

Quick Start

Run a blob search on your map, inspect the biggest blob, determine if it lies near the chain terminus, extend the chain with add_terminal_residue as needed, refine the added region, and finally cap with OXT if no density remains.