.mkit Files

A .mkit file is Molkit’s native document format. It stores the whole document as JSON, including every structure, annotation and animation, the document settings and the metadata. Save a .mkit file whenever you want to come back to a drawing and keep editing it. To share a finished image, export an SVG or PNG instead.

Saving

Press Ctrl+S or choose File > Save to save the active document.

The first time you save an untitled document, Molkit asks for a filename and then writes a .mkit file. If you are editing text when you save, the edit is committed first so the file includes it.

Save vs Save As

Save (Ctrl+S) writes to the current file. Save As (Ctrl+Shift+S, or File > Save As...) always asks for a name and starts a new file.

How saving works depends on your browser.

Saving in Chrome and Edge

Chrome and Edge let Molkit write directly to a file on disk.

The first save, and every Save As, opens the system’s save dialog.
After that, Ctrl+S writes straight back to the same file with no dialog, and a Saved message confirms it.
If the browser has lost permission to the file, Ctrl+S falls back to the save dialog.

Saving in Firefox and Zen

Firefox and Zen cannot write to a file you opened, so every save is a download.

The first save, and every Save As, opens Molkit’s Save File dialog. Type a name in Filename; .mkit is added for you.
Later Ctrl+S presses download the file again under the same name without asking.
Each save is a new download. Your browser’s download settings decide where it goes, and the browser may add a number to the name if a file with that name is already in the folder. To update the original file, move the downloaded copy over it.
After a save, the tab shows an amber dot instead of no dot. Hover the tab for a reminder that the last save was a download. The dot changes to the unsaved color as soon as you edit again.

The Save File dialog has two options:

Pretty-print JSON (larger file): writes indented, human-readable JSON. The setting is stored in the browser and applies to later saves.
Embed custom fonts in file: shown only when the document uses a font you uploaded. When checked, every uploaded font the document uses is written into the file.

Each save in these browsers also stores a private recovery copy inside the browser. See Tabs, Auto-Save & Recovery.

Fonts in .mkit files

A .mkit file can carry the font files for fonts you uploaded from disk, so the document looks the same on a computer that does not have them.

When you open a file that contains fonts, Molkit installs them in your browser’s font library so they display immediately.
Every later save of that document writes those fonts back into the file, as long as the document still uses them. This applies to Ctrl+S, Save As, and the Firefox download save.
To add fonts you uploaded yourself, use Embed custom fonts in file in the Firefox and Zen Save File dialog. Chrome and Edge saves do not have this option; they keep only the fonts the file arrived with.
If a font cannot be read from the browser’s font library at save time, a warning names it. The file still saves, but other computers will show a default font in its place.

Google fonts are not stored in the file. They load from Google Fonts when the document opens. See Font Management.

Opening

Press Ctrl+O or choose File > Open... to open a .mkit file.

Chrome and Edge show the native file picker; other browsers use a standard file chooser. Opened files load into a new tab, and the view fits to the content. Files with the older .json extension from earlier versions also open.

What a .mkit file contains

The file is a JSON object with a format field set to molkit, a formatVersion field, and a canvas object holding the document. The canvas includes:

Structures: atoms and bonds, with their positions and per-object styling.
Annotations: text, arrows, shapes, brackets, and projections.
Animation states, when present.
Document settings: page setup, color scheme, and structure settings.
Metadata for the document and per-structure metadata.
Embedded fonts, when the file carries any (see above).
A 3D geometry you adopted from an electrostatic potential map, in place of the built one.

Electrostatic potential maps are stored next to the canvas, in a top-level espMaps field. Only the maps of molecules in the document are written, so a map from another open tab never ends up in this file. If a map in a file cannot be read when it opens, Molkit leaves it out with a warning and opens the rest. See Electrostatic Potential Maps.

To keep files small, Molkit drops properties that match their defaults and rounds coordinates to two decimal places on save. Those defaults are restored when the file loads, so nothing is lost.

Version compatibility

The current format version is 2. Molkit reads version 2 files and migrates older files on open (for example, converting legacy textbox annotations and older animation data). If you open a file created by a newer version than your build supports, Molkit warns you that it may not load correctly but still attempts to read it.

Recovery

Saving to a .mkit file is separate from Molkit’s automatic in-browser copy. If the app or browser closes unexpectedly, Molkit restores your open tabs from that copy. See Tabs, Auto-Save & Recovery for how it works and what to do after a crash.