Getting started and the library
Does Rectoly run on Linux?
Yes. There is a .deb for Ubuntu 22.04, Linux Mint 21, Debian 12 or later, and a .tar.gz for other distributions (64-bit x86). It is the same app as on Windows, so the Windows instructions in this guide apply. Text recognition in scanned PDFs, handwriting search and reading aloud are not available on Linux. You buy it on rectoly.com, as on Windows, and the same account unlocks your other systems too.
More: Using Rectoly on Linux
I can't find a paper
Check that a smart view, collection or tag isn't narrowing the list, and that the search field is empty. The search field matches title, author and year; to find words inside papers or your notes, use Across papers. Papers you just added in Mendeley or Zotero appear after a library sync.
- On Windows the search field also matches DOI and tags.
- Across papers is the second tab at the top of the library column.
- Across papers is the magnifier button in the library's title bar.
More: Browsing and filtering the library, Search
How do I sync the library?
Syncing brings in the papers added or changed in Mendeley or Zotero. Offline, only papers already downloaded can be opened.
- In the library, choose … › Sync, or pull the list down.
- Click Sync above the library. Rectoly also syncs each time it starts.
- In the library, choose ⋯ › Sync changes, or pull the list down.
More: Syncing the library
Where do I organize my library (collections, tags, details)?
Long-press a paper (right-click on Mac) to add it to a collection, mark it read or move it to Trash. Edit tags and bibliographic details in Mendeley or Zotero on your computer; the changes arrive with the next sync.
On a PC you can add papers to collections, mark them read, move them to the Trash, and add PDFs to your library. New collections, tags and details are made and edited in Mendeley Reference Manager or Zotero, and appear here after the next sync.
More: Browsing and filtering the library
How do I delete a paper?
Rectoly goes as far as the Trash and no further. Nothing is removed for good from here, so a paper cannot be lost by a mistaken click — emptying the Trash is always done in Mendeley Reference Manager or Zotero on your computer.
- Long-press a paper (right-click on Mac) and choose Move to Trash. It waits in the Trash view, and you can put it back at any time.
- Right-click a paper and choose Move to Trash. It stays in the Trash view; putting it back, and emptying the Trash, are done in Mendeley Reference Manager or Zotero.
More: Browsing and filtering the library
How do I add a PDF to my library?
After the upload, check the title, authors and year, then press Register. The paper opens right away and reaches your other devices through Mendeley or Zotero. Adding PDFs is included in the purchase.
- In the library, … › Add PDF to Mendeley (Add PDF to Zotero in the Zotero edition), or ⌘⇧M.
- ⋮ above the library › Add PDF to Mendeley… (Add PDF to Zotero… in the Zotero edition), the shortcut (Ctrl+Shift+M in the Mendeley edition, Ctrl+Shift+P in the Zotero edition), or drop a PDF on the library column.
- In the library, ⋯ › Add PDF to Mendeley… (Add PDF to Zotero… in the Zotero edition).
More: Adding a PDF to Mendeley or Zotero
Can I read a PDF without signing in?
Yes. The PDF opens on this device only and isn't added to Mendeley or Zotero. Once opened, you can reopen it free at any time.
- In the library, … › Open a PDF… (⌘O), or drop a PDF on the window. Reopen it from On this device.
- Open file in the top bar (Ctrl+O), or drop a PDF on the window. Reopen it from On this PC in the library.
- Open PDF… on the home screen, or open a PDF from another app. Reopen it from Open papers.
More: Opening a PDF without signing in
It says "File not synced" and won't open
The PDF isn't in Zotero storage, so Rectoly can't download it. Sync the file from Zotero on your computer first. If your attachment files are on a WebDAV server, or ZotFile or ZotMoov moved them into a cloud folder, set that up in settings: see Files on a WebDAV server and Files linked with ZotFile or ZotMoov.
More: Downloading PDFs and reading offline
Can I use my own WebDAV server?
If Zotero on your computer syncs attachment files with WebDAV (Nextcloud, InfiniCLOUD, Jianguoyun and others), open File syncing (WebDAV) in settings, choose WebDAV, enter the same URL, username and password as in Zotero on your computer, and choose Verify Server. /zotero/ is added to the URL automatically. Rectoly then opens PDFs from your WebDAV server, and PDFs you add in the app go there too; Zotero on your computer picks them up at its next sync. Group libraries always use Zotero Storage. Nextcloud, InfiniCLOUD and some others need an app password (connection ID) instead of your sign-in password. Your password is stored encrypted on this device only and sent only to your server.
You can open PDFs stored on a WebDAV server such as Nextcloud or your university's storage. In settings, open WebDAV server, enter the URL, username and password, and choose Test Connection. Then choose Open from WebDAV… in the library menu, browse the server and pick a PDF to open it on this device or add it to Mendeley. Your password is stored encrypted on this device only and sent only to your server.
More: Files on a WebDAV server
I want to open files linked with ZotFile or ZotMoov
If ZotFile or ZotMoov moved your PDFs into a Dropbox or Google Drive folder, those PDFs don't travel with Zotero sync. If the same folder is synced on this device too, open Linked files in settings and choose the folder that Zotero on your computer uses as its Linked Attachment Base Directory. Rectoly finds the PDFs there and opens them, without changing anything in the folder. If a file isn't found, choose Locate… and pick it; Rectoly then finds the other PDFs in that folder as well.
- You can choose Dropbox, Google Drive or OneDrive folders shown in the Files app.
- You can choose the synced Dropbox or Google Drive folder (such as the G: drive).
- If a Google Drive folder can't be chosen, choose a folder synced to the device by an app such as FolderSync, or pick files one by one with Locate….
More: Files linked with ZotFile or ZotMoov
Reading
What is Reading Mode?
Reading Mode rebuilds a two-column paper into one easy column, in reading order. Highlights, sticky notes and handwriting work there too.
- Press the round button at the bottom right (a page icon) or ⌘R. Pinch or use ⌘+ / ⌘− for text size; ⌘⇧R shows the PDF beside it.
- Click Reading in the PDF | Reading switch or press Ctrl+R. Ctrl+= / Ctrl+− change the text size; Ctrl+Shift+R shows the PDF beside it.
- Tap the round button at the bottom right (a book icon). Pinch or use the text size buttons; the side-by-side button at the top shows the PDF beside it.
More: Reading Mode
Handwriting looks shifted in Reading Mode
Reading Mode reflows the text to fit the screen, so handwriting follows the reflowed text rather than a fixed page. After rotating the screen or opening the paper on another device it can look shifted, but the ink is never lost. For marks that must stay exactly in place, write in the PDF view.
More: Reading Mode
How do I use two panes?
The 2 screens button shows the paper twice, so you can keep a figure or the references in view while you read. You can also put a different paper beside it.
- 2 screens at the top left (⌘⇧D). For another paper, open its card in Open papers on the left or right. Drag the border to resize, and choose automatic, side by side or stacked in the reader's settings.
- 2 screens above the paper (Ctrl+Shift+D). For another paper, select it in the library and press Ctrl+Enter. Drag the border to resize; the arrangement button switches automatic, side by side or stacked.
- 2 screens in the top bar. For another paper, long-press it in the library and choose Open in right pane.
More: Two panes and their arrangement
How do I switch between open papers?
The open papers button shows your open papers as cards. Press a card to switch, × to close it, and + to open another paper.
- The stacked-cards button (⌘⇧O), ⌃Tab, or a sideways swipe from the edge of the screen.
- Open papers in the top bar (Ctrl+Shift+A), or Ctrl+Tab.
- The stacked-layers button, or a sideways swipe from the edge of the screen.
More: Open papers and switching
How can I keep a figure beside the text?
Open the figure panel to pin figures and tables beside the text while you read. Step through them with previous and next, or jump to the figure's page.
- The figure panel button at the top left (⌘⇧F).
- The figure panel button in the toolbar (Ctrl+Shift+F).
- The figure panel button in the top bar.
More: Figure panel
What paper does citation [12] refer to?
Press the citation to see its reference card, without scrolling to the reference list. If the paper is in your library you can open it with your notes, and you can open its DOI or arXiv page.
- Tap the citation.
- Hover the pointer over the citation.
More: Citation cards
Search doesn't work on a scanned PDF
Scanned pages are read into text on your device when you open the paper ("Scanned text recognized"); then search works. It is free and nothing is sent.
- To highlight scanned text, trace it with the HL Pen.
- Drag to select the recognized text. If nothing is recognized, check Settings › Reader › scanned PDFs for the recognition languages installed in Windows.
- Rectoly on Linux doesn't read scanned text.
The Mendeley edition doesn't read scanned text. Use a PDF that has a text layer.
More: Scanned PDFs
Translation
Can Rectoly translate papers?
Yes. Rectoly translates English papers with a model that runs on your own device. In Reading Mode the translation sits directly under each paragraph, so you can check it against the original as you read, and the PDF page itself can be switched to the translation too. Translation is part of the purchase; there is nothing extra to pay.
- Turn translation on in Settings › Translation and choose your language. The first time, Rectoly offers to download the translation model (about 2.5 GB).
- In Settings › Translation, press Download translation model. Once it is in, a translation appears under each paragraph in Reading Mode.
More: Translation
Does translating send my paper anywhere?
No. The translating is done by the model on the device, and the text of the paper is never sent to Rectoly or to a translation service. The only thing that needs the internet is downloading the model once; after that, translation works offline. When a computer does the work instead, the paragraphs travel over your own network, encrypted with a key only the two paired devices hold.
More: Translation, What stays intact
Which languages can it translate into?
English papers are translated into the languages Rectoly's own interface speaks (19 besides English), and into Vietnamese and Ukrainian as well. On a PC and on Android these are the ones whose quality we have measured; on the iPad and the Mac the rest (Thai among them) are handed to the system translator, with a note saying so. Choose the language in Settings › Translation.
More: Translation language
Can a device with little memory translate?
A device that cannot run the model, or one you would rather not heat up, can hand the work to Rectoly on a Windows or Linux computer on the same network. The computer translates and sends the result back, and the translation is kept with the paper. Without a computer, you can translate with your own API key instead (the paragraphs then go to the provider you choose).
- Translating on a PC needs a 64-bit x86 processor with AVX2 and 8 GB of memory. A Vulkan-capable graphics card makes it quick.
- Translating on the device itself needs roughly 8 GB of memory or more. A device short of memory still reads translated papers through a paired computer.
More: What you need
Annotating
How do I highlight or underline?
Select text, then choose a color and Highlight or Underline. To box a figure or equation, use the area highlight. The eight colors are the same as in Mendeley and Zotero.
- Use HL and Underline in the tools, or H / U.
- Use the color dots, Highlight or Underline in the bar that appears, or H / U.
- Long-press a word, drag the handles, then choose Highlight or Underline.
More: Highlights, underlines and areas
How do sticky notes work?
Choose the sticky note tool and press where the note goes. Press the marker to read, edit or delete the note, and drag it to move it. A highlight can carry a note too.
- Long-pressing an empty spot also adds a sticky note.
- Right-click a highlight to add a note to it.
More: Sticky notes
How do I write by hand?
Turn handwriting on, then write; the eraser removes whole strokes.
- Turn on Ink ON in the status bar (on iPhone, at the top right next to undo). While it's on, highlights and the other tools are paused.
- Choose Pen in the toolbar (P). Dragging with the right button also erases.
- Tap Ink ON in the footer, then choose the Pen in the tool rail.
More: Handwriting
How do I make text and image annotations?
Text annotation places text where you tap; Image annotation boxes a figure. Both sync as Zotero annotations.
- On Windows these annotations are shown, but made on iPad, Android or in Zotero.
More: Text, image and comment annotations
My handwriting from the tablet doesn't appear elsewhere
Handwriting travels with the paper in Mendeley or Zotero. On the tablet, check that you're signed in with the same account, that the paper was opened from the library, and that handwriting sharing is on; then sync the paper's annotations.
- The setting has the same name everywhere: Keep Reading Mode handwriting in Mendeley.
- On iPad and Mac this one switch covers handwriting written on PDF pages and in Reading Mode. With it off, handwriting stays on your devices (shared through iCloud if you turn that on).
- Handwriting on PDF pages always syncs to Zotero; for Reading Mode handwriting, turn on Keep Reading Mode handwriting in Zotero.
More: Sharing handwriting between tablets and PCs
My annotations won't send, or show a conflict
Annotations that couldn't be sent stay on the device and are retried automatically; press the paper's sync button to send them now. If the same annotation changed somewhere else too, it becomes a conflict: press the conflict and choose which version to keep.
More: Annotation sync, unsent and conflicts
How do I undo a mistake?
Undo with the undo button or ⌘Z / Ctrl+Z. To go back further, open the change history and restore an earlier version.
- … › Change history.
- The History tab in the side panel.
More: Undo and change history
Finding and writing
How do I search all my papers at once?
Use Across papers to search the full text and notes of every paper. Full text can be found in every paper whose PDF is on this device. If results are missing, rebuild the index under Settings › Troubleshooting.
- Across papers is the second tab at the top of the library column.
- Across papers is the magnifier button in the library's title bar.
- On Windows and Mac, Across papers is included in the purchase.
More: Search
Can I search my handwriting?
Yes. With Settings › General › Handwriting search on, your handwriting is read into text on the device and appears under "Handwriting" in search.
- It needs iPadOS or macOS 27 or later.
- If nothing is recognized, add the handwriting language in Windows settings.
- Rectoly on Linux has no handwriting search.
- On Windows and Mac, handwriting search is included in the purchase.
- It needs Google Play services. Handwriting written in Reading Mode isn't included.
More: Handwriting search
What are research themes?
A research theme is a note for one piece of work that collects quotes and highlights with their sources. Select text and choose Send to theme (⌘⇧N / Ctrl+Shift+N). You can jump back from any quote to its place in the paper, and export the theme to Markdown or Word, with a reference list in your citation style.
- Open it with the light bulb at the top left (⌘⇧T).
- Open it with Research theme in the top bar.
- Open it with the light bulb in the reader's top bar (under ⋮ on a phone).
- Export › Zotero note makes the theme a note in Zotero, and the two stay in step both ways: edits made to the note in Zotero come back into the theme, and if both were edited, nothing is overwritten — a new note is made. When sending, you can also tag the cited papers with the theme's name and put them in a collection of that name.
- Export › Organize in Mendeley… tags the papers the theme cites with its name, puts them in a collection of that name, or both.
More: Research themes
Can I see my manuscript beside the paper?
Yes. Open your Word (or other) document beside the paper; the view updates every time you save it in Word.
- … › Open a document beside the paper…, or drop the document on the reader.
- Open file (Ctrl+O) and choose the document, or drop it on the window.
- ⋮ › Open a document beside the paper… in the reader, or drop the document on the reader.
More: A document beside the paper
How do I copy with a citation, BibTeX or a citation key?
Select text and choose Copy with page (⌘⇧C / Ctrl+Shift+C) to copy it as “quote” (p. 5), or Copy with citation (⌘⌥C / Ctrl+Alt+C) to copy it with its source in your citation style: APA, Chicago, Harvard, MLA, IEEE, Vancouver, Nature or GB/T 7714. Choose the style and the citation key format (Pandoc, Obsidian, LaTeX and others) in settings.
- Copy BibTeX or the citation key by long-pressing a paper in the library, or from … in the reader.
- Copy BibTeX or the citation key from the export menu.
- Copy BibTeX or the citation key by long-pressing a paper in the library, or from ⋮ in the reader.
More: Copy with page, BibTeX, citation keys
Can I use my highlights in Obsidian?
Yes. Choose a Notes folder in settings, for example inside your Obsidian vault. Rectoly keeps one citationkey.md per paper with its highlights and notes, and only rewrites the part between its marker lines.
More: Notes folder
Can I extract figures and tables, or compare many papers?
You can export figures as PNG and tables as CSV, for one paper or many. The section comparison table puts the abstracts, methods, results and conclusions of many papers in one table, one row per paper. Both are included in the purchase.
More: Exporting figures and tables, Section comparison table
What are "Similar passages in other papers"?
It finds paragraphs in your other papers with similar wording or topic to the one you selected. They are not necessarily making the same claim. Everything runs on your device, with a language model on the device and an index of your papers that Rectoly builds there.
More: Similar passages in other papers
What does the AI do with my notes and papers?
Two things. Organize with AI, in Across papers, groups your own notes in the collection you choose (comments, sticky notes and text boxes) by topic and saves them as a research theme. The AI writes only the headings; your notes stay as you wrote them. Paper cards… writes out, for each paper, the research question, method, data, findings and the limitations the authors state, from the paper's own text, into a literature review table. Every sentence carries its page, and a sentence the text does not support is dropped.
Both run on your device with the same model as translation, and nothing is sent anywhere. Only when you have chosen Your own API key in the settings does the provider you picked do the work. Both are included in the purchase.
More: Organizing your notes with AI, Paper cards and the literature review table
Can I use the AI with my own API key?
Yes. In Settings › AI, under Where AI runs, choose Your own API key, then pick a provider (OpenAI, Anthropic, Google Gemini, DeepSeek, OpenRouter, any OpenAI-compatible service, or Ollama or LM Studio on your own network) and enter the key. Translation, Organize with AI and paper cards then run with that provider, on devices that cannot run the model too.
Your text goes from the device straight to the provider, not through Rectoly's server. Before you start, the app shows what is sent and asks for your agreement, and the first time you translate a paper you see an estimate of how much will be sent and confirm it. Papers you have not opened are never sent. The key is stored on that device only, and the provider bills you. Where the settings have no AI, in some regions and stores, the key cannot be used.
More: AI settings and your own API key
Data, purchase and more
What stays free after the trial?
Reading the PDFs and annotations already on your device, exporting them, reopening PDFs you have opened before, and everything inside the sample paper stay free. New syncs, downloads, annotating, Reading Mode and the other paid features need the purchase. One purchase covers Windows, Linux, Mac, iPad and Android; the Mendeley and Zotero editions are sold separately.
More: Trial and purchase
How do I use my purchase on another device?
Sign in with the same Mendeley or Zotero account. The purchase is normally unlocked automatically when Rectoly starts; if it isn't, press Restore purchases under Settings › Purchase.
- To use the purchase with other accounts signed in on the same PC, use Use this purchase with other accounts in Settings › Purchase.
More: Trial and purchase
How do I move to another device or keep a backup?
Annotations that sync to Mendeley or Zotero arrive when you sign in with the same account on the new device. For handwriting and anything kept only on the device, export an archive under Settings › Data and import it on the new device.
- iCloud backup also keeps a copy (handwriting only when you turn it on).
More: Archives: export and import, iCloud backup
Can I use several accounts?
Yes. Add another account and switch between them; unsent annotations are sent before switching.
- Use the account at the bottom of the library sidebar, then Add account.
- Use Settings › Accounts › Add account.
More: Signing in and accounts
Which keyboard shortcuts are there?
- Hold ⌘ to see them. Change the keys in Settings › FAQ › Keyboard shortcuts.
- Press F1 to see them. Change the keys in Settings › Shortcuts.
- With a keyboard, see them in Settings › FAQ › Keyboard shortcuts, and change the keys there. The volume keys turn the page.
Mouse side buttons can be used as shortcuts too.
More: Keyboard shortcuts
What do the icons mean?
The What the icons mean page describes every button for your system, with where it is and what it does.
- Settings › Help › What the icons mean also lists the main icons.
More: What the icons mean
Where does my data go?
Paper analysis, search indexes, similar passages, translation and reading handwriting or scanned text all happen on your device. Only anonymous usage statistics leave it, and only if you allow them (Settings › General › Privacy). Text goes to an AI service only if you choose Your own API key in the settings yourself.
More: Your data
Something's wrong. How do I contact you?
Choose Send diagnostic data under Settings › Troubleshooting, add what happened, on which paper and when, and send. No email is needed. You decide whether to send it, and it never contains your PDFs.
More: Troubleshooting