claudemol

Use when working with PyMOL for molecular visualization tasks including loading structures, creating representations, coloring, selections, and basic analysis.

Use when connecting Claude to PyMOL, troubleshooting socket errors, or setting up the PyMOL integration for the first time

Use when setting up, configuring, running, or inspecting La-Proteina protein generation tasks including unconditional design and motif scaffolding. Helps build configs and visualize outputs through PyMOL.

Use when setting up, configuring, running, or inspecting Proteina-Complexa protein binder design, ligand binder design, AME motif scaffolding, or monomer motif scaffolding. Helps build configs, select targets, and visualize outputs through PyMOL.

Use when validating protein designs with AlphaFold2/AlphaFold3/ESMFold predictions, coloring by pLDDT or pAE, computing self-consistency RMSD, or screening design candidates through PyMOL.

Use when comparing multiple protein designs, ranking design candidates, tracking design iterations, overlaying before/after structures, or performing batch visual QC through PyMOL.

Use when analyzing protein-protein or protein-ligand interfaces in designed complexes, computing buried surface area, identifying hotspot contacts, or characterizing binding interfaces through PyMOL.

Use when visualizing ProteinMPNN or LigandMPNN sequence design results, inspecting designed vs. fixed residues, viewing per-position confidence, or analyzing sequence design outputs through PyMOL.

RFD3 Interactive Config Builder with PyMOL

Use when inspecting RFdiffusion/RFdiffusion2/RFdiffusion3 outputs, viewing diffusion trajectories, tiling scaffold candidates, or performing visual QC on generated backbones through PyMOL.

Use when visualizing antibodies, Fab fragments, CDR loops, epitopes, paratopes, or antibody-antigen complexes through PyMOL.

Use when visualizing protein-ligand binding sites, drug binding pockets, active sites, or protein-small molecule interactions through PyMOL.

Collection of useful PyMOL patterns and commands that don't fit into specific workflow skills. Use as reference for edge cases and less common operations.

Use when creating movies, animations, rotations, or morphing sequences in PyMOL.

Use when visualizing protein structures, showing secondary structure, coloring by B-factor, creating surface representations, or generating basic structural figures through PyMOL.

Use when creating publication-quality molecular figures with proper styling, ray tracing, and export settings through PyMOL.

Use when user runs /pymol command to launch PyMOL and establish a controllable session

Use when comparing protein structures, aligning molecules, calculating RMSD, or visualizing structural differences through PyMOL.

This skill should be used when the user asks to "create a skill", "build a skill", "develop a skill for Claude Code", or mentions "skill structure", "SKILL.md", or "progressive disclosure".