pemsleyCommunity·11 Agent Skills Included

coot

Protein structure model building, refinement, and validation

Automates protein structure model building, real-space refinement, and validation against electron density maps. Detects Ramachandran outliers, bad rotamers, atom clashes, and unmodeled density blobs without manual inspection. Queries PDBe, downloads structures, generates publication figures, and renders interactive per-residue charts.

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npx skills add pemsley/coot --all -g -y

All Skills in This Repository (11)

Pure Emerald Level Indicators

📦 In Repo

pemsley

pdbe-api

Fetch PDBe structure data and search results from within Coot.

coot-essential-api

Document essential Coot API functions available at startup.

coot-unmodelled-blobs

Detect and interpret unmodeled density blobs in Coot electron density maps.

coot-refinement

Refine protein structures in Coot with scripted synchronous workflows and validation checks.

coot-figure-making

Generate publication-quality molecular graphics figures in Coot with color schemes and ribbons.

coot-NCS-reference-guidance

Rebuild NCS-related chains in COOT using reference-guided sequence and coordinate consistency.

coot-rdkit

Convert Coot monomers to RDKit molecules and generate SVG diagrams.

coot-model-building

Automate macromolecular refinement workflows in Coot with checkpoints and validation metrics.

coot-best-practices

Consolidate best practices for using Coot's MCP API in automated workflows.

coot-validation

Validate macromolecular models against density maps using Coot Python APIs.

coot-correlations

Compute per-residue and region-wide density-fit correlations in Coot.

Community

Advanced

Frequently Asked Questions

FAQPage Schema

How to install Coot skills?▼

Run `npx skills add pemsley/coot --all -g -y` in your terminal to install all skills in this suite globally.

What is Coot used for?▼

Coot is a toolkit for macromolecular crystallography used to build, refine, and validate protein structure models against electron density maps.

How to validate a protein structure with Coot?▼

The validation skills check Ramachandran outliers, rotamer scores, density correlations, atom clashes, and unmodeled density blobs, then present results as interactive clickable charts.

Can Coot skills fix model-building errors automatically?▼

Yes. The skills can auto-fit rotamers, flip peptides, extend chains into unmodeled density, and refine residue zones, with checkpoints so changes can be reverted.

Do I need crystallography experience to use these skills?▼

Basic familiarity helps, but the skills guide the agent through standard workflows like validation, refinement, and figure making using plain-English requests.