Extension:PDBHandler

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PDBHandler

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

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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.

Dependencies[edit]

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.