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

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Graphics QuickLookProtein
Overview

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. :-)

Demonstration of the Quick Look extension in Finder

Screenshot of the main app

Installation

Requirements: QuickLookProtein requires macOS Big Sur (version 11.0+).

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. 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.

Screenshot of 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 (default values in bold):

  • Atom display style (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 12.5.

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

Comments
  • Does not open cif files

    Does not open cif files

    Hi there, firstly I wanted to say this sounds like a great quicklook extension!

    I tried to open a .cif file on my computer but it seems the plugin does not register. I should mention that I had CrystalMaker installed and it would seem that quicklook is defaulting to that program, even though it doesn't have a specific quicklook extension (as far as I am aware).

    For the file in question:

    >>> mdls -name kMDItemContentType GaAs_mp-2534_computed.ci:

kMDItemContentType = "com.crystalmaker.crystalmaker.cif"

    The file itself is from MaterialsProject: https://materialsproject.org/materials/mp-2534/

    If you have any suggestions I would love to give this app a try!

    opened by harripj 4
  • Can't get extension to work

    Can't get extension to work

    After downloading and installing the Quick Look Protein extension it doesn't appear when using the MacOS Quick Look feature.

    OS details:

    macOS Big Sur
version: 11.5.2

    Checking the Uniform Type Identifier I get the following:

    mdls -name kMDItemContentType 1xhz.pdb
kMDItemContentType = "dyn.ah62d4rv4ge81a3dc"
    opened by glass-w 4
  • Default viewing mode based on filetype

    Default viewing mode based on filetype

    Love this plugin! I've noticed that for CIF files, which are usually small molecules, they don't display correctly in "Ribbon" format. Likewise, PDB files, which are usually proteins, are tough to interpret on anything other than ribbon mode. Would it be possible to set a default for each file type… e.g. "stick" for CIF files and "ribbon" for PDB files?

    opened by jgassens 3
  • Big Sur 11.5+ required?

    Big Sur 11.5+ required?

    Hello. Thanks for creating nice Quick Look extension. I tried to run this on Big Sur 11.0, but it did not work properly. It closed immediately when I ran it. After the OS upgrade to Big Sur 11.5, it works fine. This may require Big Sur 11.5+.

    opened by mariota20 1
  • Suggested new features

    Suggested new features

    Hi,

    I'm not very familiar with how a project like this is put together, and how everything works, but a few features that would be useful or just nice for chemists such as myself might be:

    • The option to manually change atom colours using the settings app you already have.
    • Can more file types be used? For example a .res file (I can provide examples of these if needed).
    • For .cif files that contain disordered components, is it possible to filter so only PART0 and PART1 are shown? And could this selection be changed in the settings app?

    Thanks for this wonderful project.

    opened by ConradGoodwin 1
Releases(v1.4)
Owner
Jethro Hemmann
Postdoc in the area of microbiology and biochemistry at HKI Jena.
Jethro Hemmann
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