Abstract
SummaryPrograms such as VMD and PyMOL are excellent tools for analyzing macromolecular structures, but they do not implement many of the advanced rendering techniques common in the film and video-game industries. In contrast, the open-source program Blender is a general-purpose tool for industry-standard rendering/visualization, but its user interface is poorly suited for rigorous scientific analysis. We present BlendMol, a Blender plugin that imports VMD or PyMOL scenes into Blender. BlendMol-generated images are well suited for use in manuscripts, outreach programs, websites and classes.Availability and implementationBlendMol is available free of charge from http://durrantlab.com/blendmol/. It is written in Python.Supplementary information Supplementary data are available at Bioinformatics online.
Highlights
Molecular modeling plays a prominent role in biological and chemical research
Supplementary information: Supplementary data are available at Bioinformatics online
While mathematical analysis is critical, it remains true that many insights come only from visual inspection
Summary
Molecular modeling plays a prominent role in biological and chemical research. While mathematical analysis is critical, it remains true that many insights come only from visual inspection. Programs dedicated to macromolecular visualization and analysis (e.g. VMD and PyMOL) (DeLano, 2002; Humphrey et al, 1996) generate images that are scientifically rigorous and esthetically pleasing. General-purpose modeling programs such as Blender are increasingly popular tools for producing photo-realistic macromolecular images and videos (Johnson and Hertig, 2014). These programs allow users to position macromolecules in their actual microscopic contexts, providing much needed scientific perspective (see, e.g. the June 2, 2017 and May 6, 2016 covers of Science) (Hastie et al, 2017; Stepanek and Pigino, 2016). These files must be separately imported into Blender Both VMD and PyMOL save meshes using camera coordinates rather than the world. The Supplementary Material includes detailed installation instructions (Supplementary Video S1), as well as examples of use
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