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J Comput Chem. 2018 May 5;39(12):748-755. doi: 10.1002/jcc.25155. Epub 2017 Dec 26.

Pyrite: A blender plugin for visualizing molecular dynamics simulations using industry-standard rendering techniques.

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Department of Biological Sciences, 4200 Fifth Ave, University of Pittsburgh, Pittsburgh, Pennsylvania, 15260.


Molecular dynamics (MD) simulations provide critical insights into many biological mechanisms. Programs such as VMD, Chimera, and PyMOL can produce impressive simulation visualizations, but they lack many advanced rendering algorithms common in the film and video-game industries. In contrast, the modeling program Blender includes such algorithms but cannot import MD-simulation data. MD trajectories often require many gigabytes of memory/disk space, complicating Blender import. We present Pyrite, a Blender plugin that overcomes these limitations. Pyrite allows researchers to visualize MD simulations within Blender, with full access to Blender's cutting-edge rendering techniques. We expect Pyrite-generated images to appeal to students and non-specialists alike. A copy of the plugin is available at, released under the terms of the GNU General Public License Version 3.


Blender; molecular dynamics simulations; molecular visualization; scientific communication


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