Coot Figure-Making Best Practices

This skill provides guidance for creating publication-quality molecular graphics figures in Coot, with emphasis on custom coloring schemes and ribbon representations.

Critical Rule: Use Function Wrappers

ALWAYS wrap complex multi-line code in functions when using the MCP interface.

Why?

Multi-line code executed directly (without a function wrapper) can corrupt the Python interpreter if any error occurs. Function wrappers provide proper error handling and prevent interpreter crashes.

Pattern

# Step 1: Define the function with run_python_multiline()
def my_figure_function():
    # ... complex code here ...
    return result