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N283T

chimerax-mcp-plus

by N283T

chimerax_start

Start ChimeraX with REST API enabled for MCP server control. Set port, GUI mode, and wait time to initiate a managed session.

Instructions

Start ChimeraX with REST API enabled.

AI clients should use this tool instead of launching ChimeraX directly from a shell, so the MCP server can enable and track REST control.

Args: port: Port for REST API (default: 63269) nogui: Run without GUI (default: False) wait_seconds: Seconds to wait for startup (default: 15) background: If True, return immediately and let ChimeraX start in background. Use chimerax_status to check if ready. (default: False) include_version: If True, run the ChimeraX version command once after connecting and include it in the response. Defaults to False to avoid writing version checks to the ChimeraX Log.

Returns: Status of the startup attempt.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
portNo
noguiNo
backgroundNo
wait_secondsNo
include_versionNo

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault

No arguments

Behavior5/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations, the description fully carries the behavioral burden. It discloses that the tool enables and tracks REST control, supports background startup with immediate return, and explains why include_version defaults to false: "to avoid writing version checks to the ChimeraX Log." This goes beyond a simple 'start' command and covers side effects and state implications.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with an introductory purpose sentence, a clear Args list, and a Returns note. Every sentence adds value; no filler or redundant content. The parameter explanations are necessary and appropriately detailed for the tool's complexity.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool has 5 parameters, no annotations, and an output schema, the description covers all necessary aspects: purpose, usage context, parameter semantics, background behavior, and return status. It also references a sibling tool for follow-up status checks. The presence of an output schema reduces the need to detail return values, but the description still provides a sufficient summary: "Status of the startup attempt."

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters5/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 0%, so the description is the sole source of parameter meaning. The Args section meticulously explains each of the 5 parameters, including defaults, behavioral impact (e.g., "If True, return immediately and let ChimeraX start in background"), and rationale for defaults (e.g., include_version). This fully compensates for the schema's lack of descriptions.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description starts with a specific verb and resource: "Start ChimeraX with REST API enabled." It clearly distinguishes from siblings like chimerax_stop and chimerax_status by explaining the unique purpose of launching the application and enabling REST control. The additional note about the MCP server tracking REST control reinforces the tool's distinctive role.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines5/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description explicitly provides usage guidance: "AI clients should use this tool instead of launching ChimeraX directly from a shell, so the MCP server can enable and track REST control." It also mentions an alternative follow-up path with "Use chimerax_status to check if ready" for background startup, which helps the agent choose the correct sequence of tools.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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