MediaWiki Extension PDBHandler

This extension generates 2D/3D previews and thumbnailes for uploaded the PDB: Protein Data Bank files.

Install

Pre-requisites

This extension requires the following tools to be installed first:

• PyMOL
• ImageMagick

Setup

To install this extension, add the following to LocalSettings.php.

// enable image uploads and setup ImageMagick, if you haven't already configured yet.
$wgEnableUploads = true;
$wgUseImageMagick = true;
$wgImageMagickConvertCommand = "/usr/bin/convert";

// load extention
wfLoadExtension("PDBHandler");

Optional settings

• $wgPyMOLCommand
  • pymol command path.
  • default: "/usr/bin/pymol"
• $wgPDBHandlerUseWebGL
  • enables to use the WebGL 3D viewer based on the GLmol.
  • default: true
• $wgPDBHandlerCacheDirectory
  • cache directory to store rasterized PDB images generated by the pymol command.
  • default: "${wgUploadDirectory}/pdbhandler"

Syntax to embed a PDB file

The PDB files can be included on a page by using image embedding syntax, e.g.

[[File:2A07.pdb]]

License

This software is licensed under the GNU General Public License 2.0 or later.

Authors

• Yoshihiro Okumura
• Emw (Original Author)

Usage examples

• https://bsd.neuroinf.jp/ : Brain Science Dictionary project in Japanese.