QuickLookProtein

QuickLookProtein is a macOS Quick Look extension to preview protein/3D structure files (PDB, SDF, CIF).

It works in all places where macOS uses Quick Look, e.g. in Finder and Spotlight. In Finder, just select the protein structure file and press Space to open Quick Look.

The rendering of the 3D structure is performed using 3Dmol.js.

The extension is packaged into a main app, whose purpose is to set a few settings used for the display of the 3D models.

I hope this app is useful to you! It is my first Mac OS/Swift app, so I am happy for any feedback! Just open an issue. :-)

Installation

Requirements: QuickLookProtein requires macOS Big Sur (code was built for version 11.0+, but might also require 11.5+, see #2).

Download: The current version can be downloaded under releases.

Installation:

1. After downloading the release, unpack the ZIP file.
2. Move the QuickLookProtein.app to the Applications folder.
3. Open QuickLookProtein.app. If you get a warning that the app could not be verified, follow the steps described here in the section If you want to open an app that hasn’t been notarized or is from an unidentified developer
4. The Quick Look extension should automatically be installed and activated once the main app has been started for the first time. You can check that the extension is activated in System Preferences -> Extensions -> Quick Look.

Features

File types

The following file types are currently supported:

• .PDB
• .CIF
• .SDF

Note that Quick Look extensions depend on the Uniform Type Identifier (UTI) for the association with a file type, and not simply on the file extension. The UTI of a file may change, depending on the applications you have installed that are associated with the given file type. I tried to register the Quick Look extension with some of the commonly used UTIs for the above file types. But in case the extension is not working on your machine, please let me know the UTI of the file you are trying to preview by running the following command in Terminal:

mdls -name kMDItemContentType filename.ext

Settings

The main app allows the customization of the rendering of the 3D structure. Currently, the following settings can be changed:

• Atom display style for each file type (cartoon, line, stick, sphere)
• Rotation speed (no rotation, slow, medium, fast)
• Background color (any color, or transparent)

Note that the cartoon style only works for proteins.

In future releases and depending on user feedback, I might implement additional customizations.

Implementation details

The code is written using Swift 5 in Xcode 13.

The Quick Look extension displays a Webkit view that uses some simple HTML and the 3Dmol.js library to render the 3D structure.

Credits

3Dmol.js is developed by Nicholas Rego and David Koes. See also their publication: Rego & Koes, 3Dmol.js: molecular visualization with WebGL, Bioinformatics, 2015