coot-refinement
CommunityBest practices for protein refinement in Coot.
Education & Research#coot#crystallography#protein refinement#rotamer fixing#refinement workflow#density validation#scripted workflows
Authorpemsley
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This skill provides best practices for protein structure refinement and validation within Coot, enabling users to perform high-quality refinements safely and efficiently while avoiding common crashes and inefficiencies.
Core Features & Use Cases
- Safe scripting workflows: guidelines for immediate replacement mode, ensuring synchronous refinement operations.
- Step-by-step refinement strategy: enable, set refinement maps, perform residue/zone refinements, validate density correlation and rotamer fixes.
- Use Case: A user refining residues in chain A between residues 10-20 to improve density fit, with crash avoidance.
Quick Start
Run the recommended initial steps in your Coot scripting environment:
- Enable immediate replacement: coot.set_refinement_immediate_replacement(1)
- Set refinement map using coot.set_imol_refinement_map(imol_map)
- Refine a residue range: coot.refine_zone(imol, chain, start_resno, end_resno, "")
Dependency Matrix
Required Modules
None requiredComponents
Standard package💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: coot-refinement Download link: https://github.com/pemsley/coot/archive/main.zip#coot-refinement Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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