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ChimeraX MCP Server

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    Deploy Server
    One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

    TDQS

    A3.5/5.0

    Scored across 39 tools

    Disambiguation4/5

    Most tools have clearly distinct purposes, with descriptive aliases that reduce ambiguity. However, some overlap exists between selection and visualization tools (e.g., hide_atoms vs delete_atoms, multiple surface tools) which could cause minor confusion.

    Naming Consistency5/5

    All tool names follow a consistent verb_noun pattern (e.g., open_structure, show_surface, measure_distance). Variations like align_and_rmsd are still intuitive and fit the pattern.

    Tool Count4/5

    With 39 tools, the server covers a wide range of molecular visualization and analysis tasks, which is appropriate for its domain. While slightly high, each tool serves a distinct purpose and the count is justified.

    Completeness5/5

    The tool surface is comprehensive, covering structure I/O, visualization, selection, measurement, mutagenesis, energy minimization, and animation. There are no obvious gaps for typical molecular modeling workflows.

    Maintenance

    ActivityInactive
    ResponsivenessNo issues

    Resources