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Tool Playbooks

PyMOL

  • reset_workspace, load, select, show, hide, color, camera, measure, distance, label, align, surface, map, scene, object, preset, setting, export, raw_command
  • Best for pocket walkthroughs, named scenes, camera hero frames, synthetic gaussian maps, and ray-traced exports.

ChimeraX

  • reset_workspace, open, close, visibility, select, style, color, camera, measure, distance, label, contacts, align, fit, layout, volume, preset, graphics, cartoon, view, lighting, export, raw_command
  • Best for contact analysis, named-view demos, matchmaker alignments, map fitting, tiled comparisons, AlphaFold review, and polished publication exports.

Guardrails

  • Ask for clarification when chain IDs, residue ranges, filenames, or export paths are ambiguous.
  • Prefer structured tools over raw commands.
  • Confirm destructive actions or overwrites before executing them.
  • Default to the repo-wide demo aesthetic unless the operator explicitly wants a different look.