File Menu

The File menu contains commands useful for opening, importing, and exporting molecules.

New Ctrl+N

Create a new molecule document.

Open Ctrl+O

Open a file containing molecule information from a file browser.

Open Recent

Display a list of the 10 most recent files opened.

Close Ctrl+W

Close the current window.

Save Ctrl+S

Save the current molecule.

Save As… Ctrl+Shift+S

Save the current molecule as a CJSON (.cjson) or CML (.cml) file.

Import

See Import

Export

See Export

Quit Ctrl+Q

Close Avogadro 2

Import Menu

The Import menu contains commands useful for importing molecules to the current document, such as downloading a molecule by name, fetching it from the Protein Data Bank (PDB), or importing a crystal structure.

Download by Name

Load a molecule by its common name.

Note

This is most likely to work for common molecules such as caffeine, and is not guaranteed to work for every molecule name.

Fetch from PDB

Download a PDB entry by its identifier.

Crystal

Import a crystal structure from those provided by Avogadro.

Export Menu

Export the current molecule as chemical file format or as a graphic.

Molecule

Open a file dialog to select a format to save the current molecule to.

Graphics

Open a file dialog to save the current screen as a PNG.

3DMol HTML Snippet

Automatically generate HTML to render the molecule in a web browser.

SVG

Export a 2D rendering of the current molecule as a scalable vector graphic (SVG).

PLY Render

Export a 3D render of the current molecule in a format readable by CAD software such as Blender.

POV-Ray Render

Export a 3D render of the current molecule in a format readable by POV-Ray.

VRML Render

Export a 3D render of the current molecule in a format readable by CAD software.