Validate macromolecular models against density maps using Coot Python APIs.
npx skills add https://github.com/pemsley/coot --skill coot-validation
Please help me install this Agent Skill. Skill: coot-validation Source: https://github.com/pemsley/coot/tree/main/mcp/docs/skills/validation Command: npx skills add https://github.com/pemsley/coot --skill coot-validation
Comprehensive validation of macromolecular structures by integrating model-to-map analysis and unmodeled density detection.
Use the coot-validation skill to run a comprehensive validation on the current model and density maps, and report the top issues.
High-intent search queries and answers about installing and using this skill.
Model-to-map validation in Coot cross-checks protein models against density maps to locate unmodeled features like waters or ligands and identify regions requiring refinement. It uses per-residue correlation statistics to assess global fit.
Checking for atom overlaps in a macromolecular structure detects steric clashes and cross-residue packing problems across the molecule. The process evaluates global packing to identify conflicting atoms within the loaded model.
Ramachandran analysis during structure validation scores the backbone dihedral angles of all residues across the molecule. It identifies outliers and geometrically unfavorable conformations using comprehensive molecule scoring APIs.
Yes, comprehensive structure validation in Coot requires a loaded macromolecular model and both electron density and difference maps in the environment. These inputs provide the baseline data needed to detect unmodeled density and packing issues.
Poor model-to-map fit in specific residue ranges indicates areas requiring refinement or alternative conformations. Per-residue correlation statistics pinpoint these mismatches by directly comparing the modeled atoms against the density map.
Yes, finding unmodeled ligands or waters uses difference maps to locate positive density features not accounted for by the current model. This map-to-model discovery guides necessary updates to the protein structure.
pemsleyCompute per-residue and region-wide density-fit correlations in Coot.
pemsleyDetect and interpret unmodeled density blobs in Coot electron density maps.
pemsleyDocument essential Coot API functions available at startup.
carbonscottDetect diffraction rings in X-ray detector images and derive initial beam center and radii.
