Simple First Zettelkasten on Protolyst

You can get started with your first Zettelkasten on Protolyst. This Zettelkasten is built around just 2 types of note; fleeting and permanent.
See our blog for more info on Zettelkasten and this ‘simple’ first Zettelkasten.

Create your Account and Build Along with this Guide

Capturing Fleeting Notes for your First Zettelkasten #

Your Fleeting Notes are captured as Atoms on Protolyst.

You can create fleeting notes in 2 ways;

1 Capturing directly from Sources

Upload or import your Sources and as you read through, highlight the sections of text, and select ‘Capture Atom’. This lifts the text out of the page and stores it as an Atom in your workspace.

Image shows some text highlighted with a floating Capture Atom button. Highlight text to Capture it as an Atom on Protolyts. Atoms are your fleeting notes in your first Zettelkasten system
Capture a Fleeting Note (Atom) on Protolyst by highlighting text and selecting Capture Atom

You can add your initial thoughts into the Atom box – think of it like adding an annotation.

The Atom box showing text captured as an Atom and space to add your own ideas and annotations alongside it into your fleeting note
To add your annotations to your Fleeting Note, type in the Box that appears after clicking ‘Capture Atom’


Saving Atoms, creates a list of individual Atoms that you can access as a list alongside your source, and they are searchable and viewable anywhere else in your workspace.

Captruing fleeting notes from an article in Protolyst. On the left side the article is displayed with several highlights visible. On the right there is a list of all these highlights aka fleeting notes
An article imported into Protolyst on the left, the Fleeting Notes (atoms) captured from the article displaying down the right.

We’ve added a YouTube transcription tool (in Beta) to help you take notes on videos too!

2 Adding Manually

You can also add Atoms without highlighting text. Create a Page for your Source, and then use the ‘Add Atom’ button to manually type in your Fleeting Notes and save them as Atoms

Manual creation of Atoms. In a Protolyst Page, there's a plus button displaying 2 options; New Atom and Import Atoms from a Page. Selecting New Atom will allow you to add an atom without highlighting text
In the Atoms Menu, select the Add Atom Plus Icon and then select New Atom. This will give you a box to add your Fleeting Note into.

Creating Permanent Notes #

You can browse through all the Fleeting Notes captured from a source to select the ones you want to make into Permanent Notes

To create a Permanent Note, add a new Notes Page into your workspace and then drag your Fleeting Note (Atom) into the page.

Drag and drop a Fleeting Note into a Notes Page to add it into a Permanent Note

Once added in, a Numbered Citation appears, which links you back to the exact location in your source if you ever want to go back to it.

Best practice for Permanent Notes is to add a Title and express the key idea in your own words.

Connecting your Permanent Notes #

As you add more Notes into your system, you can capture the relationships between the different ideas you have added into your Zettelkasten, by linking your Notes together.

To link a Note, you open the Page Properties Menu, select Add a Page and Choose Link a Page. You then select the Page you want to link to from the list of Pages in your workspace.

The Locations of the Pages Menu, Add Page Button and Link a Page options to connect your Permanent Notes together

You can add as many connections as you like by repeating the Link Page process. Once Linked, each page will list in the Pages Menu for quick navigation to the related notes.

The Links between your Permanent Note are bidirectional – they work in both directions so you’ll be able to view the connection between 2 notes from either of the connected notes.

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