![]() Both VMD and PyMOL can export molecular meshes to Blender-compatible file formats. ![]() Then, when preparing a final image, we separately reconstruct the VMD-visualized scene in Blender. We first analyze our molecular structures in VMD. Our past macromolecular-visualization workflow has thus required us to switch between VMD and Blender. Researchers will likely analyze their molecular systems in programs such as VMD or PyMOL regardless. Beyond that, the Blender UI itself, while well suited for visualization, is not convenient for macromolecular analysis. Efforts to implement these features demand a complex, difficult-to-maintain codebase, perhaps explaining why so many previously published molecular-visualization plugins are no longer functional. Given that VMD and PyMOL have been in development for roughly 20 years, independently developed Blender plugins typically lack many of their powerful visualization features. Several Blender plugins can load molecular models independent of any dedicated molecular-visualization program ( Andrei et al., 2012). And universities ranging from Harvard Medical School to the Cleveland Institute of Art teach classes in macromolecular visualization. Companies such as Digizyme and Random42 produce and sell these visualizations. the Jand covers of Science) ( Hastie et al., 2017 Stepanek and Pigino, 2016). These programs allow users to position macromolecules in their actual microscopic contexts, providing much needed scientific perspective (see, e.g. General-purpose modeling programs such as Blender are thus increasingly popular tools for producing photo-realistic macromolecular images and videos ( Johnson and Hertig, 2014). Though popular molecular-visualization programs have impressive rendering engines ( Stone et al., 2013), they cannot yet match Blender ( Fig. 1).Ī green fluorescent protein with a highlighted central helix (Color version of this figure is available at Bioinformatics online.) The free, open-source program Blender implements many industry-standard rendering tools. Advanced rendering techniques such as photo-realistic shadows and lighting can convey subtle but important structural information.īeyond macromolecular visualization, the film and video-game industries have also done much to advance computer graphics in recent years. Poor esthetics are distracting and so impede scientific communication. Artistic considerations are far from frivolous. VMD and PyMOL) ( DeLano, 2002 Humphrey et al., 1996) generate images that are scientifically rigorous and esthetically pleasing. Programs dedicated to macromolecular visualization and analysis (e.g. While mathematical analysis is critical, it remains true that many insights come only from visual inspection. Molecular modeling plays a prominent role in biological and chemical research. ![]()
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