SketchBio: a scientist's 3D interface for molecular modeling and animation

Instant Construction and Visualization of Crowded Biological Environments

We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.

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

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 http://durrantlab.com/pyrite/, released under the terms of the GNU General Public License Version 3. © 2017 Wiley Periodicals, Inc.

PyMOL mControl: Manipulating molecular visualization with mobile devices

Viewing and manipulating three-dimensional (3D) structures in molecular graphics software are essential tasks for researchers and students to understand the functions of molecules. Currently, the way to manipulate a 3D molecular object is mainly based on mouse-and-keyboard control that is usually difficult and tedious to learn. While gesture-based and touch-based interactions are increasingly popular in interactive software systems, their suitability in handling molecular graphics has not yet been sufficiently explored. Here, we designed the gesture-based and touch-based interaction methods to manipulate virtual objects in PyMOL utilizing the motion and touch sensors in a mobile device. Three fundamental viewing controls-zooming, translation and rotation-and frequently used functions were implemented. Results from a pilot user study reveal that task performances on viewing controls using a mobile device are slightly reduced as compared to mouse-and-keyboard method. However, it is considered to be more suitable for oral presentations and equally suitable for education scenarios such as school classes. Overall, PyMOL mControl provides an alternative way to manipulate objects in molecular graphic software with new user experiences. The software is freely available at http://cbbio.cis.umac.mo/mcontrol.html. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):76-83, 2017.