AI Chat Assistant — POKY Suite Manual

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Overview
API Key Setup
Usage & POKY Context
Privacy & Data

Overview

AI Chat Assistant (command AI) is a chat panel built into POKY that talks directly to POKY LLM, Claude, ChatGPT, or Gemini — not a browser tab to a consumer chat website. A system prompt describing POKY, plus a few live facts pulled from your current session (open spectra, chemical shift lists, the selected view), are automatically included so answers can be grounded in what you're actually looking at.

Access it from Utilities → AI Chat Assistant, or type its command code AI.

💡 POKY LLM needs no setup at all. It's a self-hosted model running on POKY's own server — no API key, no account, no cost, and fully anonymous (nothing about who's asking is sent or logged). It's the default provider for exactly that reason; Claude, ChatGPT, and Gemini remain available if you'd rather use one of those instead.

💡 POKY LLM can query PACSYLLM. Ask a question about real chemical shift or structure statistics — e.g. "What's the general chemical shift for CA for Alanine from IDPs?" — and POKY LLM (only; not Claude/ChatGPT/Gemini) recognizes it as a database question, writes a read-only SQL query against PACSYLLM (Woonghee Lee's protein NMR chemical shift/structure database, correlating BMRB shifts with matched PDB structures), runs it, and grounds its answer in the real numbers returned. See PACSYLLM Database Search for details.

💡 POKY LLM knows PyMOL. Ask it a PyMOL command question, or for a ready-to-run script for a common visualization task — e.g. "give me a PyMOL script to show the binding site around my ligand" or "what does cealign do differently from align?" — and it answers from a curated PyMOL command reference and a set of goal-oriented recipes (binding sites, publication-quality rendering, coloring by chain, etc.), not a generic guess. It also knows the real way to open a structure in PyMOL from POKY itself (s.open_pymol(pdb_path)) and will use that instead of inventing a launcher.

⚠️ Data retention: for privacy and security, each query and response sent to POKY LLM is automatically wiped from the server two weeks after it was made. Nothing you ask it is kept long-term - don't rely on the server retaining a copy of a past conversation.

API Key Setup (Claude / ChatGPT / Gemini)

Chatting through a provider's real API requires an API key from that provider — this is a different, developer-facing credential from your regular claude.ai / chatgpt.com / gemini.google.com login, and it's the only way a third-party desktop application like POKY can actually send and receive messages (there is no public "sign in with your browser session" option for any of these APIs).

💡 Cost: of the three API-based providers, Gemini offers a genuinely free API tier (rate-limited, no credit card required) — a good place to start if you want one of these instead of POKY LLM. Claude and ChatGPT are pay-as-you-go: you'll generally need to add billing in that provider's console before their API will respond. These policies can change, so check each provider's own pricing page if in doubt; POKY shows a short cost note under the provider dropdown as a reminder.

Pick a provider from the dropdown, then click Get API Key... — this opens that provider's key-creation page in your browser.
Create a key there and copy it.
Paste it into the Paste API key field in POKY and click Save Key.

The key is saved locally in a small file (~/.poky_aichat.json) and is only ever sent to that same provider's API — you won't need to re-enter it on this machine.

ℹ️ Why not fully automatic? Anthropic, OpenAI, and Google don't currently offer a public OAuth-style "click Yes, receive an API key" flow for third-party apps — API keys are dashboard-managed secrets you create yourself. (Some first-party CLI tools from these companies do have a browser-login flow, but it's an internal mechanism tied to that specific product, not something a third-party integration can use.) Pasting a copied key once is the closest practical equivalent.

Usage & POKY Context

Type a question and press Enter or click Send. Each provider is called with:

A fixed system prompt establishing that the assistant is helping a POKY NMR software user, and pointing it at the live manual URL (poky.clas.ucdenver.edu/poky_releases/manual).
If "Include live POKY session context..." is checked (the default), a short summary of the current session — open spectra, chemical shift lists, and the currently selected spectrum view — appended to the system prompt.
The same checkbox also triggers a quick manual lookup: your question is matched by keyword against a list of manual pages/topics, and the 1-2 best-matching pages are fetched live from the hosted manual and included as excerpts (with their URLs) — so answers can reflect recently-added or changed pages rather than only what a model was trained on.
The running conversation history from this chat panel, so follow-up questions keep context within the same session.

Clear chat resets the conversation history (and the on-screen transcript) so the next message starts fresh.

ℹ️ Manual lookup is keyword-based, not a full search engine. It matches your question against each page's known topics and fetches the best match(es) live — it isn't a general web search, so very specific or unusually-phrased questions may not match any page. It also requires an internet connection to reach the hosted manual; if that fetch fails for any reason, the chat still proceeds without it.

Privacy & Data

Nothing is sent anywhere until you type a message and click Send. At that point, your message, the fixed system prompt, and (if enabled) the short session-context summary are sent to whichever provider you selected, using your own saved API key — subject to that provider's own terms of use and data-handling policy, not POKY's. No spectra, peak lists, or raw project files are ever transmitted; only the short text summary described above. If manual lookup is enabled, your typed question (only its keywords are used) also results in a plain page fetch to poky.clas.ucdenver.edu to retrieve manual excerpts - that request goes to POKY's own manual server, not to the AI provider.