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Scored across 135 tools
There are several near-duplicate clusters: ten `util_cb*` tools all do "color by atom with a different carbon color," and `util_rainbow`/`util_chainbow`/`util_ss`/`util_color_by_element`/`util_color_secondary`/`spectrum`/`color` all recolor structures. Rendering/export tools (`ray`, `render`, `draw`, `png`, `mpng`, `turntable`, `print_export`, `print_ribbon_view`) and representation tools (`show`, `as`, `spheroid`, `isomesh`, `isosurface`, `cartoon`) overlap enough that an agent must read long descriptions to choose. Individual descriptions are excellent and often explicitly cross-reference siblings, which rescues some but not all of the boundaries.
At least four conventions coexist: bare PyMOL command names (`as`, `set`, `show`, `hide`, `color`, `turn`, `scene`, `frame`, `clip`), an `util_` prefix group with ad-hoc suffixes (`util_cbam`, `util_cbak`, `util_cbc`, `util_chainbow`), a `_view` suffix group (`ligand_view`, `putty_view`, `qscore_view`), and a `*_report`/`*_info` group. Several names are single vague words (`as`, `set`, `do`-like `draw`, `fab`, `mset`, `mpng`) that give no hint of scope.
135 tools is an order of magnitude beyond what an agent can hold in context for a single server, and many are trivially redundant (ten carbon-color variants, three isosurface/mesh tools, four render paths). The surface should be compressed into parameterized tools (e.g. one `color_by_atom(carbon=...)`, one `render(kind=...)`).
The domain (scripting PyMOL) is covered practically end to end: loading/session, selections, representations, measurements, analysis reports, views/presets, movies, scenes, ray-tracing, and 3D-print export. `execute_pymol_command` provides an explicit escape hatch for whatever the curated set misses. Minor gaps (e.g. no dedicated undo/history, some settings only reachable via `set`/`execute_pymol_command`) are workable.