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Use when user runs /pymol command to launch PyMOL and establish a controllable session
Install with Codex or Claude Copy this prompt, paste it into Codex, Claude, or another assistant, and let it review the skill page and install it for you.
Based on SOC occupation classification
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.
| name | pymol |
| description | Use when user runs /pymol command to launch PyMOL and establish a controllable session |
| version | 0.1.0 |
Establish a connection to PyMOL for molecular visualization work.
The SessionStart hook runs pymol-agent-bridge status automatically. Read its output:
/pymol-setup first.~/.pymol-agent-bridge/bin/pymol-agent-bridge launch
This connects to an existing PyMOL if running, or launches a new instance.
~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "print('connected')"
All commands go through ~/.pymol-agent-bridge/bin/pymol-agent-bridge exec:
# Fetch a structure
~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "cmd.fetch('1ubq')"
# Multiple commands via heredoc
~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "$(cat <<'PYMOL'
cmd.hide('everything')
cmd.show('cartoon')
cmd.color('spectrum')
cmd.orient()
PYMOL
)"
# Get object names
~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "print(cmd.get_names())"
Always use cmd.ray() then cmd.png() separately:
~/.pymol-agent-bridge/bin/pymol-agent-bridge exec "$(cat <<'PYMOL'
cmd.ray(1200, 900)
cmd.png('/tmp/figure.png')
PYMOL
)"
Never use cmd.png(path, width, height) — causes view corruption.
cmd.reinitialize() unless the user explicitly asks.~/.pymol-agent-bridge/bin/pymol-agent-bridge launch.launch first.