Automate PyMOL molecular visualization and basic analysis workflows.
npx skills add https://github.com/ANaka/claudemol --skill pymol-fundamentals
Please help me install this Agent Skill. Skill: pymol-fundamentals Source: https://github.com/ANaka/claudemol/tree/main/claude-plugin/skills/pymol-fundamentals Command: npx skills add https://github.com/ANaka/claudemol --skill pymol-fundamentals
PyMOL workflows can be tedious to coordinate: loading structures, creating representations, applying colors, making selections, and performing measurements across single or multiple structures.
Ask Claude to run the pymol-setup flow and load a structure to begin visualizing in PyMOL.
High-intent search queries and answers about installing and using this skill.
You can automate PyMOL molecular visualization by using deterministic command execution to load PDB or local files, apply representations like cartoons or surfaces, and run measurements across single or multiple structures interactively.
Yes, you can measure binding geometry in PyMOL by making selections and running quick analyses to calculate distances and angles between a protein and its ligand for exploratory visualization.
The best way to apply color schemes and switch representations in PyMOL is through automated workflows that create and toggle cartoon, stick, or surface displays while applying consistent color schemes across structures.
You do not strictly need local PDB files to visualize molecular structures; the workflow supports loading structures directly from PDB databases or local files via the pymol-agent-bridge wrapper.
Yes, you can perform PyMOL analyses across multiple structures in a single interactive session by applying deterministic command execution to coordinate selections, measurements, and visualizations simultaneously.
PyMOL visualization workflow coordination becomes tedious because manually loading structures, creating representations, applying colors, making selections, and performing measurements requires repetitive command execution across structures.
InternScienceRetrieve and download PDB protein structure files by gene name, UniProt ID, or PDB ID.
PharMolixAnalyze protein-ligand interactions in PDB structures with PLIP and generate Markdown reports and 3D visualizations.
ANakaAutomate PyMOL animation and movie creation from structural data.
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