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MediaWiki extensions manualManual:Extensions
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Release status:Extension status experimental

ImplementationTemplate:Extension#type Media
DescriptionTemplate:Extension#description Enables interactive 3D models of proteins and DNA
Author(s)Template:Extension#username (Emwtalk)
MediaWikiTemplate:Extension#mediawiki 1.19+
LicenseTemplate:Extension#license GPLv2 or later
Download No link

Translate the PDBHandler extension if it is available at translatewiki.net

Check usage and version matrix.

PDBHandler is an extension that allows users to manipulate 3D models of large biological molecules, like proteins and DNA, in wiki pages. Interactive models are included on a page using the same syntax as image files. The extension uses WebGL and GLmol to transform 3D atomic coordinate data in PDB files -- a file format widely used in structural biology -- into graphical models that users can rotate and zoom into in 3D. A WebGL-enabled browser is required to use the interactive feature; a static image of the molecule is shown for browsers that do not support WebGL.

You can try out PDBHandler on Wikimedia Labs at http://pdbhandler.wmflabs.org.

Syntax to embed a model[edit]

Models can be included on a page by using image embedding syntax, e.g. [[File:2A07.pdb]].

Browser support[edit]

PDBHandler's interactive models work on any web browser that supports WebGL, including WebGL-enabled mobile browsers. For browsers that do not support WebGL, a static image of the molecule is shown. Internet Explorer does not support WebGL, and Safari disables WebGL by default.


A few dependencies need to be installed before PDBHandler will work on a MediaWiki deployment. PDBHandler was developed on Ubuntu 12.04 LTS (Precise Pangolin). The server should have installed:

  • PyMOL v0.99 -- this program converts textual PDB files to static PNG images for users with browsers that don't have WebGL enabled. On Ubuntu, running apt-get install pymol should be enough to resolve this dependency.
  • Python 2.7 -- a few PDBHandler scripts are written in Python. Python is also needed to run PyMOL.