Extension:PDBHandler

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
Models can be included on a page by using image embedding syntax, e.g.   .

Browser support
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.

Dependencies
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.