Explore Skills

Best Practices for using Coot MCP

coot-unmodelled-blobs

How to handle Unmodelled Density Blobs

coot-rdkit

RDKit molecular manipulation and visualization within Coot's Python environment. Use when working with Coot and need to (1) Create RDKit molecules from Coot monomers, (2) Modify molecular structures (e.g., atom substitution), (3) Generate 2D chemical structure diagrams, (4) Perform cheminformatics operations on ligands or small molecules loaded in Coot.

coot-model-building

Best Practices for Model-Building Tools and Refinement

coot-NCS-reference-guidance

NCS Reference Guidance

coot-refinement

Best practices for protein structure refinement and validation in Coot. Use when performing (1) Residue refinement operations, (2) Model building and fitting, (3) Rotamer fixing, (4) Scripted/automated refinement workflows, (5) Validation and correlation checking.

coot-correlations

Using Density-Fit Correlations in Coot

coot-figure-making

Best practices for creating publication-quality molecular graphics figures in Coot using user-defined colors, ribbons, and molecular representations

pdbe-api

Query the PDBe (Protein Data Bank in Europe) REST API and Solr search API from within Coot to access structure metadata, validation data, revision history, and search capabilities

coot-validation

Comprehensive structure validation combining model-to-map analysis and unmodeled density detection