A paper is not one page and it is not only the draft. Around the draft sit the things you need while writing it: the marked-up manuscript your editor sent back, the journal's guidelines, a sample paper you are matching, the interview transcripts, and the thoughts that outgrew this paper and belong to the next one. An academic who tested MojoPad put a number on it without meaning to — in his own project the draft was eight items out of twenty-eight. The paper is the smallest thing in the workspace.
So MojoPad does not ask you to make a "project". A paper is a folder. Put the sections in it in the order they will be read; put everything else in folders beside it. Nothing is special, which is the point: the same tree, the same pages, the same search.
View ▸ Writing View arranges the app for exactly this job and nothing else. Your folder tree on the left, the section you are writing in the middle, and down the right, about that section:
The strip follows the cursor: move to another section and it is about that section instead.
Everything above this point a dedicated writing app has had for twenty years. This is the part none of them can do — because none of them is also where your reading lives.
As you write, MojoPad reads what is in front of you and offers what else in your wiki belongs beside it — notes, quotations, pages, and the PDFs and books in your library, because their text is read and indexed too. Not by folder, not by tag, not by anything you remembered to file: by meaning. The list changes as you move between sections.
The academic above described the problem before he had seen the answer: "later, when working on another paper, I remember writing notes that could be used, but I cannot remember which app I had written them in." That is the tax every researcher pays for notes spread across apps and folders and years. Here there is nothing to remember, because there was nothing to file.
Click one and it opens beside your draft, not instead of it — in a pane, with your sentence still where you left it. This needs a local embedding model; MojoPad tells you in the strip if one is missing, and nothing leaves your Mac either way.
Panes live inside the one window. Sometimes a page wants to float instead — the translation you are checking, kept in view over whatever else you open. Right-click any page ▸ Open in Small Window, then click the ✎ pen in that window's header: the card becomes a full editor, with the same formatting controls and the same Find and Replace as the main window. The eyeglasses turn it back into a clean reading card.
Each card is its own window, so open as many as you like and put them where you want — across two displays if you have them. Drag one wider and the formatting bar uses the room.
A wide or tall display is for having more in view at once. Right-click any link or page and choose Open Beside: it opens in a pane to the right of the pane you are in, with its own tabs, its own ◀ ▶ and its own ✕. Open as many as the screen fits. (All of what a pane can do is in Panes: several pages side by side, each with its own tabs, in Transclusion and Panes.)
Why the page being written sits on the left. The right is where what you are reading goes. The left is for the page you are writing about the others — a summary, an argument, the narrative that discusses what is standing open beside it. Reading runs left to right, so where a pane sits decides how the whole arrangement reads. View ▶ Open Beside… offers Write in a new page…: type a name nothing matches and the page it makes opens on the left, ready to type in, with the threads starting from it. To put a page that already exists there, open it beside and choose ⋯ ▶ Swap with Pane on the Left and then Draw Threads From This Pane.
Every pane you read has a thread back to your page. Each page open beside yours wears a color of its own, every link to it in the page you are writing is underlined in that color, and a line — a thread — runs from the sentence that mentions it to its pane. It stays for as long as the pane does and moves with your words as you write, so with five panes open you can still see which of them each sentence stands on. Open a pane from a link in the middle of a sentence and its thread draws itself in from those exact words; follow a link to a page that is already in a pane and that pane lights up and its thread draws itself in again, rather than a message leaving you to find it. Threads have a section of their own below — Threads: which column this sentence stands on — with the four ways to draw them and how to turn them off.
How a page opens, everywhere. A wiki link, a row in a database view, a tab, and a page picked out of a list all follow one choice in Settings ▶ Links & Pages: open in the same view, open in a new tab, or open beside the page you are in. The choice holds in every pane. Hold ⌘ while clicking to do the opposite once. Two things sit outside that choice on purpose — under the two tabbed answers a stored paper always gets its own tab, because a document replaces the whole reading surface and following a citation is looking something up rather than leaving; and anything arriving (a clip from your browser, a file imported, a page fetched from a URL) always opens beside what you were reading rather than over it.
The third answer is a reading posture, and it is what to choose if you work from a summary that links to everything it stands on: following a link then adds a pane instead of replacing what you are reading, and its thread ties it to the words you clicked for as long as it stays open. Open four or five and compare them. Holding ⌘ opens the link here instead, over what you are reading.
Sizing them. Panes share the room equally. Drag the line between two panes to make one wider or narrower; a pane you have dragged holds that width while the others give ground around it, and if even they cannot give enough, the row scrolls rather than squeeze it. Double-click the line to share the room equally again.
How many, and what happens when the screen runs out. There is no limit. Panes narrow as you add them, down to a width prose is still readable at, so that with the side panels put away four fit beside your page on a 14-inch laptop and five on a 16-inch one. Past that the row scrolls sideways. The Outline and Page Styles panels stand at the right-hand side of the window, outside every pane, and the panes make room for them.
A paper stands in a pane with its whole reader. Open a PDF, a book, a saved web page, a
picture or a recording beside your page and it reads there the way it reads anywhere: at the zoom
you choose (⌘+ while the pointer is over it), from where you left off, with the marks
in it shown and new ones made, and Find inside it. A narrow pane lays it out more tightly so it
stays readable.
A passage can leave the pane. Copy or drag one out of a paper standing there and it arrives on a board, or in the page you are writing, as a quote that says where it came from: the ↵ beside it reopens the source at the exact page, and the passage stays marked in the document. Clicking that ↵ later jumps to the paper in the pane it is already standing in, rather than rearranging your desk around it.
Papers in panes are what make comparing four or five sources against what you are writing possible. Asking for a page that already has a pane gives you the pane you already have rather than a second copy of the same words.
They come back when you reopen the wiki. Quit with four papers open beside your page and they are there again the next time you open that wiki, each where it stood, in the color it had, with a thread you had hidden still hidden. A page you deleted in the meantime simply does not come back. (A second window on the same wiki opens without them, the way it opens without your tabs.) To keep more than one arrangement, save each as a desk: View ▶ Desks ▶ Save This Setup as a Desk… remembers every pane, its tabs, where it stood and its color, along with your panels, and Go to Desk… puts the whole thing back. Four sources standing against the page you are writing is exactly what a desk is for. A desk saved by an earlier version comes back as panes, in the order its columns stood.
With four or five papers standing in panes beside the page you are writing, reading them is not the hard part. Keeping track is: sentence by sentence, which of those papers is this part of your page talking about? Threads answer that without your asking. Every page open beside yours wears a color, every link to it in your page is underlined in that color, and a thread runs from the sentence to its pane for as long as the pane stays open. In what follows, a column is any pane other than the one the threads start from.
⌃⌘T hides or shows every thread at once.A thread is a connection, not a gesture. There is a thread for every column whose page the page in front of you mentions — by a link to it, a citation of it, or a quote you took from it (the kind with a ↵ back to its source). A link to it counts whichever way you made it: a page link, or a link for this Mac you made with Copy Link to Page or Copy Link to Selected Words — in the paper or on a page — and pasted in, whenever you pasted it, as long as the wiki hasn’t been moved or renamed since you copied it (if it has, copy the link again). Only a link into the wiki you are in counts; a link into another wiki, or one for the web, never draws a thread here. It does not matter how the column was opened: a column opened from the Pages panel or a search result has a thread as soon as your page mentions its page, and loses it when you delete the last mention. Go to another page and the threads follow what that page mentions; a column the new page never names has no line until you come back.
Threads start from the page you are writing. That is one pane, marked ✎ in its bar — the first pane, or the page you made with Write in a new page…. Clicking into a paper to read it, copy from it or mark it gives that pane the keyboard and leaves the threads where they are, so they never jump away while you work. To draw them from another pane, choose ⋯ ▶ Draw Threads From This Pane in its bar, or the same command in the command palette. The colors belong to the pages, not to the panes: a paper keeps its color when you swap panes around.
It follows your words. A thread is drawn from where the sentence is, every time something moves — as you type, as the page scrolls, as a column opens or closes, as the window changes size. Write a paragraph above a link and its thread moves down with it; delete the paragraph and it moves back up.
Which mention the line starts from. A paper cited five times in your summary has one thread, not five, and it starts from one of those mentions: the link you opened the column from, if you opened it from a link, and otherwise the first mention on the page. MojoPad remembers that mention by where it sits in your text, counted from both the top and the bottom of the page, so an edit above it or below it — even pasting in a long passage — leaves the thread on the same sentence. Delete that sentence and the thread moves to the mention nearest where it was; fold it away under a collapsed heading and the thread starts from the first mention that is not folded away until you open the heading again. For a column on the right the line leaves from the end of the mention, and for a column on the left from its beginning — the side that faces the column.
Every mention is underlined in the column's color, in all four styles: the line starts from one of them, and the underlines show you the rest. The underline is drawn over the page rather than added to it, so it is not formatting, your link keeps its own color, and it is gone the moment the column closes.
When the sentence is out of view. Scroll your page until the mention has gone out of sight at the top and its thread does not vanish: it reaches the top edge of your page instead and ends there in a small arrow pointing up, so you can see that the sentence is up there and which column it belongs to. A mention out of sight below gets an arrow pointing down, at the foot of the margin — just above the microphone button, when it is showing there, so no line is drawn across it. And when there are more columns than the window can show and the row has scrolled one out of sight, its thread runs to the edge of the window and ends in an arrow pointing toward it.
Columns on the left get threads just the same, drawn in the margin to the left of your words.
Choose from the ⟋ Threads button in the status bar, or in Settings ▶ Links & Pages ▶ Threads — the same four pictures in the same order.
Pointing picks one out. In Along the edges and Straight across, pointing at a link or at a column draws its thread a little heavier and lets the others step back, which is the quickest way to follow one line among five.
Try them on your own columns before you choose. A picture of a style is a guess at how it will look over your papers, and your papers are right there. So with the ⟋ Threads picker open, point at a picture and your columns are redrawn that way — even while threads are switched off — and move the pointer off the pictures, or close the picker, and what you had comes back; nothing has changed. Click a picture to keep it. From the keyboard, the arrow keys move between the pictures and try each one, and Return or Space keeps it. Choosing a style also turns threads on if they were off. The picker shows the four in a row when the window has room and two by two when it does not, and Esc, a click anywhere outside it, or the button again closes it. The ⟋ Threads button is in the status bar whenever a column is open.
When a column is opened from a link, its thread waits until the column has finished sliding into place and then draws itself in from the words you clicked, so you can watch which column those words just put there. In Color only the dashed line appears for a moment and fades, leaving the colors; in Quiet it draws in at full strength and settles to its faint self a couple of seconds later. With Reduce motion on in your Mac's Accessibility settings nothing draws itself in or fades: the thread is simply there, and in Color only the line appears for the same moment and goes. A column opened from a list, or brought back when you reopen the wiki, has its thread from the start with no drawing in.
⌃⌘T), the Show switch in the
⟋ Threads picker, Show / Hide Threads in the command palette, or the checkbox under
Settings ▶ Links & Pages ▶ Threads. They are all one switch, and each shows
what the others set. With threads off, the header stripes and dots go too, and the ⟋
Threads button stays in the status bar and says Threads off, so the way back is where you
left it.Nothing about the page — a color is how you tell one column from another. There are six, given out in order as columns open: blue, green, plum, ochre, teal and rose. A new column takes the first one no open column is wearing and keeps it until it closes, so its color never changes under you while you work. It skips a color your theme already draws its links or its accent in, while another is free — an underline in the same blue as the link above it would tell you nothing — so in some themes the first column is green rather than blue. It wears it in four places: the stripe along the top of its bar, the dot in its bar, the underline under every link to it in your page, and its thread. On a dark page the same six are drawn a little brighter.
A column keeps its color when you reopen the wiki and when you go back to a desk, so "the green one" is still the green one tomorrow. The one exception is a color another open column is already wearing at that moment — two columns in one color would defeat the point — and then it takes the first free color instead.
Why does a column have no thread? It is one of five reasons:
⌃⌘T.What if I open more than six columns? The colors start over from blue, so past six, two columns share a color. The lines still go to the right place — in Along the edges and Straight across each ends in its own column, and in the other two, pointing at a link shows which column it belongs to. Close a column and the next one you open takes its color.
Does any of this change my page? No. Nothing is written into your page: the underlines, the margin bars and the lines are all drawn over the window, beside the page rather than in it. Your links keep their own color, the page you save is exactly what you wrote, and an export, a share or a printed page shows none of it — Print Page leaves the columns off the paper too.
Will it slow down typing in a long page? No. The lines are redrawn as the screen refreshes and never more often, and on a very long page MojoPad looks for the mentions again only when you pause, while the lines go on following your words in between. With no column open, none of this runs at all.
A column that did not come back is usually the right answer — its page was deleted in the meantime — but from the outside it looks exactly like columns going missing. So Help ▸ Save Diagnostic Report… has a line in its Rendering section beginning Columns and threads this session. It counts the times reopening the wiki or going to a desk put back fewer columns than were saved, the times a column could not have back the color it had because another open column was wearing it, and the times a column had to share a color because more than six were open. The line of render failures above it counts threads too: a thread that fails to draw is put away until the next moment something moves, so without that count it would be the quietest failure there is. Both are counts only, never a page's name or a word of it, so the report stays something you can send.
Everything a paper needs is here, though it is taught in the Properties chapter because a reference is a page with properties on it. In short: File ▸ Import ▸ Import References (BibTeX)… brings a library over from your reference manager; Format ▸ Cite a Source… drops a citation where the caret is; Insert Reference List puts a bibliography at the end that keeps itself in step with what you have cited; and Caption This Picture or Table plus Refer to a Figure or Table… number your figures and keep the cross-references right when you move them. See Citing as you write and A reference list that keeps itself under Properties.
Compile walks the folder in order, so the binder order is the paper's order: front matter first, sections in the middle, references and any closing abstract last. Depth decides heading level. See Compiling a Long Document.
Things that must not appear in the output have three ways out, and it is worth knowing which is which:
Compile writes a new page in the wiki, a PDF, a Word file, Markdown, or plain text. For a paper the PDF is the one that matters, and Settings ▸ Exporting ▸ Paper sets page size, margins, line spacing, typeface and page numbers so it comes out looking like a paper rather than a printed web page.
Which file you send depends on where you are in the process, and the order surprises people who have only ever submitted once. A paper goes out for peer review as a Word file — usually through the journal's own submission system, sometimes still as an email attachment — and it must meet the submission and formatting guidelines or it is rejected before anyone reads it. Review is normally blind, so that copy has to be stripped of your name and your affiliation. Only at the very end, once the reviewers' changes are agreed, does the editor want a ready-for-print PDF — a page they can send straight to the printers, which is increasingly the author's job rather than the publisher's.
So both matter, at different moments: Word is what gets you read, and the PDF is what gets you printed. Set the paper up once and Compile produces either.