Detect and interpret unmodeled density blobs in Coot electron density maps.
npx skills add https://github.com/pemsley/coot --skill coot-unmodelled-blobs
Please help me install this Agent Skill. Skill: coot-unmodelled-blobs Source: https://github.com/pemsley/coot/tree/main/mcp/docs/skills/blobs Command: npx skills add https://github.com/pemsley/coot --skill coot-unmodelled-blobs
This Skill helps crystallographers identify and interpret unmodeled density blobs in electron density maps during Coot-based model building.
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.
High-intent search queries and answers about installing and using this skill.
To find unmodelled density blobs in Coot, run a blob search on your electron density map to locate and rank unmodeled regions by blob score. You then inspect nearby atoms and residues to determine if the density represents a missing atom, water, ion, ligand, or an ongoing chain extension.
The best way to extend a chain from an unmodelled density blob is to first confirm the blob lies near the chain terminus. You then use the add_terminal_residue command to extend the chain and refine the added region iteratively to assess changes in the density map.
To cap a completed protein fragment in Coot when no density remains, you add an OXT atom to the terminal residue. This finalizes the fragment structure after iterative chain extension and refinement confirm that all unmodeled density has been successfully resolved.
This Coot blob detection workflow requires no external dependencies beyond your local Coot environment. It directly utilizes built-in scripting access to blob finding, residue inspection, and refinement commands to resolve unmodeled density during model building.
To safely checkpoint your model before resolving density blobs, you create a checkpoint file immediately prior to making any structural changes. This allows you to safely revert if iterative chain extension, residue addition, or refinement produces unfavorable density map changes.
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