coot-figure-making

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

166|59|Updated Aug 24, 2015

Search Tags:#visualization #PDB #coloring #coot #molecular-graphics #ribbon #publication-figures

Ready to run

npx skills add https://github.com/pemsley/coot --skill coot-figure-making

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: coot-figure-making
Source: https://github.com/pemsley/coot/tree/main/mcp/docs/skills/figure-making
Command: npx skills add https://github.com/pemsley/coot --skill coot-figure-making

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill helps scientists produce publication-quality molecular graphics figures in Coot by providing best-practice workflows for color, ribbons, and representations, reducing trial-and-error and ensuring reproducible visuals.

Core Features & Use Cases

Structured workflows for coloring by secondary structure and custom colors
Ribbon-based representations with user-defined color schemes for clear figures
View and styling presets tailored for publication-quality outputs

Quick Start

Use the Coot Figure-Making Best Practices skill to set up a GFP figure:

Define a color palette for strands, helices, and chromophores using the recommended indices (60, 61, 62).
Assign colors to secondary structure selections and create a ribbon representation.
Hide bonds for a clean silhouette, then center the view and adjust the zoom for publication-quality output.

Frequently Asked Questions about coot-figure-making

High-intent search queries and answers about installing and using this skill.

FAQPage Schema

How do I create publication-quality molecular graphics figures in Coot?▼

To create publication-quality molecular graphics in Coot, use structured workflows for color schemes, ribbons, and representations. This involves assigning custom colors to secondary structures, generating ribbon representations, and hiding bonds for a clean silhouette.

What is the best way to color ribbons by secondary structure in Coot?▼

Coloring ribbons by secondary structure in Coot involves defining a color palette using specific indices and assigning those colors to secondary structure selections. You must reassign all colors when recreating ribbons to ensure accurate visual representation.

Can I use Python-based MCP scripting to automate Coot figure making?▼

Yes, Coot figure making supports Python-based MCP scripting. The workflow requires wrapping multi-line code in functions and documenting steps clearly to ensure reproducible, publication-ready molecular graphics outputs.

Does Coot support custom color schemes for macromolecular structures?▼

Coot supports custom color schemes for macromolecular structures by allowing users to define color palettes with recommended indices. This enables distinct coloring of elements like strands, helices, and chromophores for tailored publication figures.

How do I set up a GFP figure for publication in Coot?▼

To set up a GFP figure in Coot, define a color palette for strands, helices, and chromophores using recommended indices. Assign colors to selections, create a ribbon representation, hide bonds, center the view, and adjust zoom for publication output.