Pangur docsHighlights, notes and assistant marks
A highlight is a passage you mark in a source, with a colour and optionally a note and tags. This page explains how to make, find, change and remove highlights, and what to do with the passages an AI assistant marks for you.
A highlight is a passage you mark in a source, with a colour and, if you like, a note and some tags. Highlights are kept with the item they belong to and appear in the PDF viewer, the reading room, your plans and drafts, and in search. An assistant mark is a different thing: it is a passage that an AI assistant connected to Pangur has marked for you to look at. Pangur shows the two side by side without mixing them, and an assistant mark only becomes a highlight of yours when you choose to keep it.
Making a highlight
You can highlight text in the PDF viewer and in the reading room.
- Select the passage. A selection bar appears beside it with Ask, Find work, Highlight, Copy and More.
- Choose Highlight. If the selection is not quite right, choose Adjust selection and select again.
- Choose a colour: Yellow (the default), Red, Green, Blue or Purple.
- If you want, write a Note. Pressing Enter in the note field saves the highlight.
- If you want, choose Tags to add research tags and topics.
- Choose Save highlight. To abandon the highlight, choose Cancel highlight or press Escape.
Pangur records the highlight's place using the page label that the PDF itself carries, such as "p. xiv" or "p. 12". When the PDF has no page labels, the highlight is located by sheet instead ("sheet 12", counting the PDF's sheets), because Pangur will not invent a page number the document does not give.
If the highlight cannot be saved, Pangur tells you why: the library refused it, the request was rate limited, or saving failed on the server. In the last two cases, trying again usually works.
The More menu on the selection bar has Clear selection, and Pin to section when you are working on a draft. The other buttons lead elsewhere: Find work looks up the work that a selected reference describes (References and connections), and Ask asks a question about the passage (Ask a question).
Highlights in the reading room
In the reading room you can highlight the text of any entry whose text comes from a PDF. Pangur works out where your selection in the reflowed text falls on the PDF page, so the highlight appears in the PDF viewer as well. A long selection is saved as several highlights, each covering one page or a page running onto the next, and the note and tags go on the first of them. Highlights already in the PDF are shown in the reflowed text, and a list titled "Highlights in this text" gives keyboard and screen-reader access to them.
Finding and changing your highlights
Choose Annotations in the PDF viewer's toolbar to open the list of highlights and assistant marks in that PDF, with their count. Find in annotations searches the highlighted text, the notes, the page labels and the tags. Choosing a row turns to its page.
Selecting a highlight opens its inspector. There you can change the colour under Highlight colour, add or change the note (Add note or Edit note, then Save note), add or remove tags and topics, or choose Move to trash.
When two people, or two of your own devices, change the same highlight, Pangur merges the changes where it can. If they truly conflict, the second save is refused and you are asked to reload.
Removing a highlight
Choose Move to trash in the highlight's inspector and confirm. The highlight disappears from topics, planning, writing and search, and goes into the project's trash for 30 days. You can bring it back with Undo straight afterwards, or later from the library's Trash, and it returns with its note and its topics (The trash).
Highlights while offline
On the web and in Pangur for Mac, a highlight you make, change or remove while Pangur cannot be reached is shown at once, queued, and sent when the connection returns. This only works for a project that is kept in your browser; for any other project Pangur tells you the change was not saved. Changing a highlight's topics, and keeping or dismissing assistant marks, are not queued and need a connection. On the iPhone and iPad you can highlight items kept on the device while offline. How projects and items come to be kept is explained in Working offline.
Who can highlight
In an organisation's project, a member with the viewer role can see highlights but cannot make, change or remove them, and the inspector's controls are disabled. Owners and editors can highlight (Project members and roles).
Assistant marks
An assistant mark is a passage that an AI assistant connected to Pangur, such as Claude or ChatGPT, has marked in one of your sources, usually with a comment saying why. The assistant makes the mark with the MCP tool mark_passage. Pangur checks that the quoted words actually appear in the source and refuses a mark that misquotes it.
In the PDF viewer, assistant marks are drawn as outlines, whereas your own highlights are filled, and each mark carries a label naming the assistant ("Marked by Claude"). The Annotations panel lists them in a separate section, each row showing who marked the passage and on which page. The Show on page checkbox draws or hides the outlines. It is on by default, and the list shows the marks either way.
Each mark offers two actions. Keep as highlight turns the mark into one of your own highlights, in blue. A mark that Pangur could not place on a page cannot be kept, and says so. Dismiss removes the mark from the list. Pangur keeps a record of dismissed marks, but they are no longer shown in the reader.
Only you can keep or dismiss a mark. The assistant can make marks and read them, but it cannot keep, dismiss, change or remove one. In an organisation's project, members with the viewer role cannot keep or dismiss marks either.
Where a mark appears
Pangur looks for the quoted passage first in the source's text, which gives the mark its page, and then on the PDF page itself, which gives it its outline. If the words are in the text but cannot be found on the page, the mark is listed in the Annotations panel but not drawn. Marks belong to you and to one project, so other members of a shared project do not see the marks your assistant made.
A quote must be between 12 and 2,000 characters long, and a comment can be up to 4,000 characters. What assistants can and cannot do in your library more generally is set out in Assistants and Pangur.
Highlights from the command line
The pangur annotate command makes a highlight from a quotation, for example pangur annotate ATTACHMENT --quote "the words" --comment "why" --colour "#ffd400". This is an ordinary highlight of your own, not an assistant mark. pangur marks ATTACHMENT lists your highlights in a file together with the passages your assistant marked. See The command line.
On the iPhone and iPad
The iPhone and iPad app's PDF reader has the same selection menu, colours, notes, topics, Annotations list and assistant marks, with the same labels (Pangur for iPhone and iPad).
Read a source
Every item opens in a pane whose Read tab shows its files in a viewer suited to each kind. This page explains the tabs, the viewers and their controls, how to find words in a document, and how Pangur remembers where you stopped.
The reading room
The reading room shows one source or a sequence of them as continuous reflowed text. This page explains how to open it, move through a sequence, search it, and set the text size, line width and font you prefer.