Last updated 11 August 2026
Nano Helix (“we”, “our”, “us”) publishes the nanohelix.ai website and a desktop application for macOS and Windows. The application is a molecular viewer built on open-source PyMOL that lets an AI agent you already use — such as Claude Code or Codex — read and control the structure open on your screen.
There are no accounts. The application does not ask you to register, sign in, or provide a name, an email address, or payment details, and it has no way to accept them.
Your structures stay on your disk. Nano Helix opens files locally, the way PyMOL always has. It does not upload structures, filenames, or file contents anywhere.
The agent connection is local. Nano Helix exposes the live scene through a small server bound to 127.0.0.1 (your own machine only), on a port chosen at random each launch, protected by a token generated fresh for that session. Both are written to a file in your home directory readable only by you, and removed when you quit. Nothing accepts connections once the app is closed.
Usage data from the app. The application does not send us analytics, usage statistics, or crash reports. If that changes in a future release we will say so here first, disclose it in the app before anything is sent, and provide a way to switch it off.
This is the part worth reading carefully, because it is the one place your work leaves your machine — and it is not us receiving it.
When you connect an agent, that agent can read your scene: object and chain names, the residues in your selection, and — when it explicitly asks for one — an image of your viewport. Whatever it reads becomes part of its conversation and is therefore sent to its model provider, exactly as anything else you type to that agent would be. Anthropic, OpenAI, or whoever operates the agent you chose handles that data under their own privacy policy and their own retention and training terms, not ours.
Nano Helix is not a party to that exchange and never receives a copy of it. We cannot see your structures, your selections, your commands, or your screenshots. If your work is confidential, the question to answer is what your agent’s provider does with it — connecting an agent to a structure is not privacy-neutral, and we would rather say so plainly than let the local-first architecture imply otherwise.
Nothing is sent automatically. Screenshots are captured only when the agent makes an explicit request for one, and the agent only acts when you ask it to.
nanohelix.ai is separate from the application and does use third-party services:
These services receive the usual information a website visit carries, including your IP address, browser and device type, the pages you view, and the page that referred you. Each acts as an independent controller of that data under its own privacy policy. Blocking third-party scripts in your browser prevents all three without affecting your ability to use the site or download the app.
Mailing list. If you enter your email address in the update form, we store that address and use it only to tell you about new releases. Because there are no accounts, it is the only way we can reach you. We do not sell it or share it for marketing. Ask us and we will delete it.
If you are in the European Economic Area or the United Kingdom, we rely on your consent for website analytics and for the mailing list, and on legitimate interests for keeping the site secure and working. You may withdraw consent at any time.
You have the right to ask what personal data we hold about you, to have it corrected or deleted, to obtain a copy, and to object to processing. In practice we hold very little: unless you have joined the mailing list, we are unlikely to hold anything that identifies you at all. Email us and we will act on the request. You also have the right to complain to your local data protection authority.
Nano Helix is intended for researchers and professionals. We do not knowingly collect personal data from anyone under 16.
If we change what we collect, we will update this page and change the date at the top. Any change that means the application starts sending data it does not send today will be disclosed in the application itself, before it sends anything.
Questions about this policy, or a request about your data: support@nanohelix.ai.
PyMOL is a trademark of Schrödinger, LLC. Terms of use.