pymol-mcp has 8 well-defined tools with consistent naming (verb-first: load_, fetch_, list_, get_, reset_, render_, run_), clear descriptions (average ~150 chars), and proper parameter schemas. However, several critical issues prevent a higher score: (1) Missing output schema documentation, the return types are inferred from code but not formally documented in tool descriptions, (2) Insufficient error guidance, most error paths lack recovery instructions for LLMs, (3) Parameters lack explicit constraints for numeric ranges and enum values in descriptions, (4) No mention of parameter relationships or dependencies, (5) The opt-in code execution tools (run_pml, run_python) lack proper permissions/scope documentation despite being extremely sensitive. Tool naming is solid (load_structure, fetch_pdb, list_objects, render_image follow verb_noun patterns), and descriptions clearly state purpose and prerequisites. Parameters have types but many lack detailed format/constraint guidance in descriptions.

• Add formal output schema documentation to every tool description. Format: 'Returns a JSON object with fields: {field1: type, field2: type, ...}'. Example for load_structure: 'Returns {object: string, n_atoms: int, n_states: int, objects: list[string]}'.
• For run_pml and run_python, add permission/scope declarations to descriptions: 'Requires permission: exec:pymol (admin-only). Risk: IRREVERSIBLE. May execute arbitrary code via prompt injection, validate all inputs.' Include rate-limiting guidance.
• Update error-prone tools (load_structure, fetch_pdb, get_object_info) with recovery hints: 'If file not found, verify path is absolute. If PDB fetch times out (120s), network may be unavailable or code invalid, verify with RCSB website. If object not found, call list_objects() to see available objects.'
• For render_image, add ray_style guidance: 'pymolwiki_outline (default): black outline, publication-quality; pymolwiki_bw: grayscale, simple; pymolwiki_color: colored atoms, publication-style. Default recommended for most uses.'
• Restate numeric constraints in parameter descriptions. E.g., 'width: Image width in pixels (16-2000, default 800)' instead of only in schema.
• Add confirmation pattern to reset_session: 'This operation irreversibly clears all objects, selections, and settings. Confirm action before executing to prevent accidental data loss.'
• For code execution tools, add explicit input sanitization note: 'PyMOL command strings are subject to prompt injection if derived from untrusted sources (e.g., file names, user input). Validate and escape all dynamic input before passing to this tool.'