> ## Documentation Index > Fetch the complete documentation index at: https://docs.biohub.ai/llms.txt > Use this file to discover all available pages before exploring further. # Troubleshoot Biohub MCP connections and tool errors > Fix common Biohub MCP problems such as HTTP 405, the wrong transport, missing tools, and timeouts, and look up every tool error code and limit. Most connection problems come down to the URL or the transport. Check these first: | Setting | Value | | - | - | | Server URL | `https://biohub.ai/mcp`, with no trailing slash | | Transport | Streamable HTTP, sometimes labeled HTTP | | Authentication | None | ## Common problems ### The browser shows 405 Method Not Allowed That's expected. MCP clients send POST requests to the server, and a browser sends a GET, which the server rejects with `405`. Add the URL to an MCP client instead, as described in [Connect your client](/biohub-mcp/connect-clients). ### The client was added with the wrong transport Biohub MCP uses Streamable HTTP. A client set up with the older SSE transport opens the connection with a GET request, gets `405`, and fails to connect. Remove the entry and add it again with HTTP. In Claude Code: ```bash theme={null} claude mcp remove biohub claude mcp add --transport http biohub https://biohub.ai/mcp ``` If you first added it with `--scope user` or another scope, pass the same scope again. In other clients, choose **Streamable HTTP** or **HTTP** as the server type. ### No tools show up 1. Confirm the URL is exactly `https://biohub.ai/mcp`. 2. Make sure the server is turned on for your chat. In Claude, click **+**, choose **Connectors**, and turn on Biohub. In ChatGPT, choose **Developer mode** from the **+** menu and select Biohub. 3. Refresh the client's server list, or restart the client. 4. Ask your assistant to list the Biohub tools. You should see the seven tools listed in the [Quickstart](/biohub-mcp/quickstart). To check the server itself, list its tools from a terminal with the `curl` command in [Other MCP clients](/biohub-mcp/connect-clients#other-mcp-clients). ### The tool names have a prefix Many clients add the server name to each tool, for example `mcp__biohub__esm_atlas_search_uniprot`. The tools are the same. ### ChatGPT doesn't show Developer mode Developer mode is available on the web for Plus, Pro, Business, Enterprise, and Education accounts. On a workspace plan, ask an admin to allow developer mode. ### The client asks you to sign in Biohub MCP has no sign-in. Choose no authentication, such as **No Authentication** in ChatGPT, and leave any key or token fields empty. In Codex, the auth column of `codex mcp list` reads `Unsupported`, which is expected. ### A call is slow or times out Calls that compute on an ESM Atlas miss take longer, and a structure view took 15 to 25 seconds in our tests. Each call has a 120-second deadline, after which the tool returns `indeterminate`. Some clients stop waiting sooner and report their own timeout. Don't retry an `indeterminate` call automatically, because the work may already have started. Wait a while, then ask once more. [Security and privacy](/biohub-mcp/security#why-some-calls-take-longer) explains which tools compute. ### The structure appears only as an image or text Your client doesn't support MCP Apps, so it can't show the interactive viewer. It shows the text result, and the PNG preview if it displays images. See [What your client shows](/biohub-mcp/structure-viewer#what-your-client-shows). ### The download buttons are disabled Downloads from the viewer need a client that supports file downloads. You can still explore the structure in the viewer. ### The server returns 413 Request Entity Too Large The request body was over 64 KiB, and it was rejected before it reached a tool. The response is an HTML page, not a JSON-RPC error. Send a smaller request. ### A browser-based client gets 403 Forbidden Origin The server rejects requests sent from web pages on other sites. Connect from a desktop app, a CLI, or your own server-side code instead of from browser JavaScript. ## Error codes A failed tool call returns a JSON object with a stable `code` and a readable `message`. Some codes add fields, such as `retry_after_seconds` or `actual_length` and `max_length`. | Code | Meaning | What to do | | - | - | - | | `invalid_input` | An input breaks a type, format, or limit. `Tool arguments do not match the supported schema` means an argument is missing, misnamed, the wrong type, or outside its allowed range, such as `top_k` above 12 or `topk` instead of `top_k`. | Fix the input. `esm_atlas_lookup_accession` doesn't take UniProt accessions, so use `esm_atlas_search_uniprot` for those. | | `not_found` | The accession, cluster, or feature doesn't exist. | Check the identifier. `esm_atlas_get_cluster_info` only works on cluster representatives, such as hits from similarity search. | | `restricted` | ESM Atlas [guardrails](/learn/guides/esm-atlas#guardrails) blocked the request. | Stop, and don't try to work around it. | | `rate_limited` | The ESM Atlas asked callers to slow down. | Wait at least `retry_after_seconds`, which is at most 3,600, and make fewer parallel calls. | | `dependency_unavailable` | The ESM Atlas or an external database is unavailable or sent an unusable response, or a structure is over the viewing limits. | Try again later. If the structure is over the limits, it can't be viewed here. | | `indeterminate` | The deadline passed, or the outcome of a compute step is unknown. | Don't retry automatically. Wait, then ask once more. | | `sequence_too_long_to_fold` | The ESM Atlas has no stored structure, and the sequence is over 700 residues. | Don't trim the sequence to fit, since that would be a different protein. | | `sequence_too_long_for_features` | The ESM Atlas doesn't have the sequence, and it's over 2,048 residues. | Don't trim the sequence to fit. | | `resource_too_large` | The complete result is over 6 MiB. | Ask for fewer results, such as a smaller `top_k` or `size`. | | `internal_error` | An unexpected server failure. Some arrive as a generic error message without a code. | Try once more later. | ## Limits | Limit | Value | | - | - | | Sequence length for most tools | 1 to 4,000 residues | | Sequence length for similarity search | 1 to 2,048 residues | | SAE features computed on a miss | Up to 2,048 residues | | Structure prediction on a miss | Up to 700 residues | | Similarity search `top_k` | 1 to 12, default 10 | | Structures predicted by one similarity search | Up to 6 | | UniProt search `size` | 1 to 6, default 6 | | UniProt query length | 500 characters | | Accession length | 128 characters | | Viewer PDB size | 2 MiB | | Viewer atom count | 20,000 | | Highlighted residues | 32 | | Request body | 64 KiB | | Complete result | 6 MiB | | Tool deadline | 120 seconds | Similarity search can return fewer than `top_k` hits, because the ESM Atlas leaves out matches with a similarity score below 0.5. ## Still stuck? Tell us what happened through the [feedback form](https://info.biohub.org/product-feedback), including your client, the tool name, and the error code.