Molecule Notes vs Capacities

Your thinking, with other people in it.

An outline journal where a [[link]] gathers every mention of a person, book or project on its page, and the people you work with write beside you, live.

Start writing

What Capacities' docs say about collaboration

No, there are no collaborative features in Capacities.

From Capacities docs: Sharing

Capacities is clear about who it's for. Its homepage says: "We build for individuals who think for a living. No collaboration chaos." That's a considered position, not a gap anyone is hiding, and for someone who thinks alone it may be exactly right.

It isn't changing soon, either. The roadmap Capacities published on September 8, 2026 covers reminders for tasks, a more powerful AI assistant, performance, tablet and mobile polish, and design consistency. None of it is collaboration.

We respectfully disagree. A lot of thinking for a living happens with someone else. In Molecule Notes, collaboration is a workspace you invite people to. You write on the same page and see each other's cursors as you type. Comments sit on the bullet they're about. Each person has a role, and a viewer can read without editing. There's no sharing page by page: you share the workspace.

Sharing is a public link.
Content "can currently either be private or shared without any access constraints meaning that everybody you share a link with will have access to your shared content." A shared link is view-only.
Not on the roadmap.
Capacities' September 2026 roadmap has no collaboration item on it.

Molecule Notes and Capacities, side by side
Feature	Molecule Notes	Capacities
Real-time co-editing	Yes: Live, with each other's cursors as you type.	No: "There are no collaborative features in Capacities."
Comments	Yes: Threaded, on the bullet they're about, and resolvable.	No: None. Shared links are view-only.
Sharing and roles	Yes: Invite people to a workspace as owner, admin, member or viewer.	Partly: A view-only link that anyone who has it can open.
Graph of linked pages	Yes: A graph view of the links you make.	Partly: Around one note. "There is no full-space graph."
Object types	No: Pages of bullets and links. No object types.	Yes: Custom object types and layouts.
AI in the app	Yes: Name an agent on a line. It writes what it found below.	Yes: An AI assistant, built in.
Offline	No: Needs a connection to read and write notes.	Partly: Works offline. Full-text search and AI need a connection.
End-to-end encryption	No: No.	No: No, by choice. Their docs explain why.
Apps	Partly: A web app that installs to a home screen. No native apps.	Yes: Windows, macOS, Linux, iOS, Android and the web.
Importing from other apps	Partly: Through MCP, by pointing an AI assistant at an export.	Yes: Guides for Notion, Obsidian, Evernote, Tana and more.
Export	Partly: Any page as Markdown, one page at a time.	Yes: Markdown, with options for media and wikilinks.

Neither of us is local-first

Capacities says it in its own guide for people switching from Obsidian: "Capacities is not local-first. If plain Markdown in a folder is non-negotiable, Obsidian remains the natural choice." We agree with every word of that.

Capacities keeps your notes in the app and hosts them in Europe. It doesn't offer end-to-end encryption, and its docs explain why: it would get in the way of AI features and of integrations like WhatsApp, email, calendars and Readwise.

It does work offline, which is more than we can say. Without a connection, full-text search, search queries and AI wait until you're back online.

Molecule Notes isn't local-first either. Notes are stored as bullets in our database, not as files. There's no end-to-end encryption, and it needs a connection to read or write. What we can offer is a clear way out: any page exports as Markdown, and an AI assistant connected over MCP can read every page you have.

Deciding what a note is

Capacities is built on object types, each with its own page layout. It works best when you decide what kind of thing each note is.

People give up on notes when deciding where each one goes takes longer than writing it. Molecule Notes skips the question. You write on today's page, so every note is dated. When a person, a book or a project matters, type [[ and name it, and every mention gathers on its page under Linked mentions. Nothing needs filing.

The graph view shows the connections you've made between pages. Capacities' graph opens around a single note, and its docs are plain about it: "There is no full-space graph."

When you want help, call an agent by name on a line. It reads your pages and the web, and writes what it found under your line. The rest of the page is still yours. And the MCP server lets the AI assistant you already use read and update your notes.

Getting your notes out of Molecule Notes

Any page exports as Markdown, with Copy as Markdown or Export as Markdown. It's one page at a time; there's no button that exports a whole workspace.

To take everything at once, connect an AI assistant to Molecule's MCP server. It can list your pages and read each one as Markdown, with its bullets and their nesting intact.

Bringing Capacities in

Export from Capacities as Markdown, and choose wikilinks in the export options, so links come out as [[double brackets]].

There's no import screen. Import goes through the MCP server: connect an AI assistant to Molecule Notes and point it at the export folder. It writes pages in bulk, and headings, lists and nesting become bullets. Links point at the page of that name, so Linked mentions build as the pages arrive. A page titled with a calendar day, like 2026-09-13, lands on that day's journal page.

Molecule Notes has no object types or properties, so the structure of your types won't arrive. You keep what you wrote; the schema stays behind.

Running the same import twice appends everything a second time rather than replacing it, so bring your notes in once.

Sources

Comparison verified September 2026.