pymol
See your molecular structures and inspect their interactions.
What it does
Create molecular structure images, saved PyMOL sessions, and structural measurements for inspection.
When to use it
Use for structure visualization, alignment, distance measurement, binding-site highlighting, confidence coloring, or protein-ligand analysis, not docking, molecular dynamics, or sequence-only analysis.
How to use it
Give it molecular structure files and a visualization or analysis request; it creates a PyMOL script, images, and a saved session in the project and reports measurements.
What you provide
- Your files
What you need · 3
Requires uv installed on the host and available on PATH to run the PyMOL scripts.
The example script declares Python >=3.10 and <3.13.
The scripts depend on pymol-open-source-whl; uv automatically installs declared dependencies when they run.
Access · 1
This skill
pymol-open-source-whl
Installs PyMOL script dependencies