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A guide to the visual analysis and communication of biomolecular structural data

Abstract

Biologists regularly face an increasingly difficult task — to effectively communicate bigger and more complex structural data using an ever-expanding suite of visualization tools. Whether presenting results to peers or educating an outreach audience, a scientist can achieve maximal impact with minimal production time by systematically identifying an audience's needs, planning solutions from a variety of visual communication techniques and then applying the most appropriate software tools. A guide to available resources that range from software tools to professional illustrators can help researchers to generate better figures and presentations tailored to any audience's needs, and enable artistically inclined scientists to create captivating outreach imagery.

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Figure 1: The spectrum of biomolecular visualization.
Figure 2: Visualization tools for specific audience needs.
Figure 3: Three general steps to produce effective visuals in any medium.

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Acknowledgements

The authors thank E. Meng for editing, and G. Bhabha for inspiration and assistance with DHFR. S.H. acknowledges funding from a postdoctoral fellowship by the Swiss National Science Foundation, and G.J. from a QB3@UCSF (University of California, San Francisco) Fellowship.

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Correspondence to Graham T. Johnson.

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PowerPoint slides

Supplementary information

Supplementary information S1 (movie)

A molecular dynamics simulation of two fibronectin domains in the context of an entire fibronectin fiber. Molecular viewers such as VMD (Humphrey, W., Dalke, A. & Schulten, K. VMD: visual molecular dynamics. J. Mol. Graph. 14, 33–38, 27–28 (1996)), UCSF Chimera (Pettersen, E. F. et al. UCSF Chimera — a visualization system for exploratory research and analysis. J. Comput. Chem. 25, 1605–1612 (2004)), PMV (Sanner, M.F. Python: a programming language for software integration and development. J. Mol. Graph. Model. 17, 57–61 (1999)), and PyMOL (DeLano, W. L. The PyMOL molecular graphics system. DeLano Scientific [online], (2002)) can export movies displaying the atomic motions of molecular dynamics (MD) trajectories, but the camera move¬ment, lighting and visual effects options are relatively limited. 3D animation software, such as Autodesk Maya and 2D compositing software such as Adobe After Effects, were used in tandem here to provide more extensive camera, lighting, and effects capabilities. Experimental data (demonstrated here for electron microscopy), geometric shapes, and labels can also be imported or created easily in these packages to provide context for biomolecular structures. The task of visualizing MD trajectories for narrative-driven outreach pro¬jects can now be achieved using Bioblender, ePMV (the embedded Python Molecular Viewer; Johnson, G. T., Autin, L., Goodsell, D. S., Sanner, M. F. & Olson, A. J. ePMV embeds molecular modeling into professional animation software environments. Structure 19, 293–303 (2011)), and mMaya (the Molecular Maya Toolkit), how¬ever, this movie was initially created at an earlier time using the fol¬lowing method: 1) create the surface and ribbon representations for the entire trajectory from a steered MD simulation using VMD; 2) export these geometries frame by frame from VMD as .obj files (a universal 3D file format) using a short TCL script (Tool Command Language); 3) import the.obj files into Autodesk Maya using a short custom MEL (Maya Embedded Language) script; 4) import 3D geometric shapes reconstructed from transmission electron micro¬graphs of a fibronectin fiber (created with Bitplane Imaris) and wrap the shape with a texture that references an image file from a scan¬ning electron micrograph; 5) modify textures, transparency, lighting and camera movements to convey the planned message; 6) render the movie to a Quicktime file; 7) composite text and sound into the movie using Adobe After Effects and export the file shown here as a composited Quicktime movie. Created by Samuel Hertig ©2012, http://www.samhertig.ch. Production time: approximately 40 hours after studying introductory tutorials for Autodesk Maya. (MP4 28200 kb)

Supplementary information S2 (movie)

Kinesin motor proteins pull organelles along microtubule tracks. This narrated movie describes a complex sequence of molecular interactions that enable the motor protein kinesin to move proces¬sively (that is, to “walk”) along microtubule protofilament tracks and efficiently move organelle cargo across great distances along a cell’s cytoskeleton. The movie was created to accompany and enhance a summarizing figure in a review article (Vale, R. D. & Milligan, R. A. The way things move: looking under the hood of molecular motor proteins. Science 288, 88–95 (2000)) that uses arrows to show the key steps of motion. Initial models were constructed as detailed molecu¬lar surfaces from a Protein Data Bank (PDB) file comprised of a kinesin dimer bound to the tubulin dimer subunits of a microtubule. This atomic structure contains starting and ending states of micro¬tubule-bound kinesin derived from electron microscopy. Using the 3D animation software Maxon Cinema 4D, the surface models were rigged with a character animation skeleton (ubiquitous in 3D anima¬tion software), which defines a simplified joint network at the highly flexible bonds along the kinesin neck-linker domains to constrain bond or domain angles and to reduce steric collisions as the motions of the protein are animated. The surface representation is tethered to the joint network and moves like skin to follow the atomically based joints. Because no details of the path between the two states of the “front” and “back” motor heads were available in the structure, the animator worked in close collaboration with the authors Ronald Milligan (of the Scripps Research Institute) and Ronald Vale (of the University of California, San Francisco) to generate detailed motion paths as plausible hypotheses, using the constrained joint model as a virtual molecular puppet. The path models were iteratively evolved to satisfy all of the input and analysis from diverse experi¬mental data. The detailed molecular surfaces were replaced with simpler coarse molecular surfaces to focus the audience’s attention on the general motion of the motors and the specific motion of the neck-linker domains. A narration for the movie was later written by Peter Walter (UCSF), recorded by Julie Theriot (UCSF) and com¬posited by Johnson with new labels and sound from Mike Morales (Garland Science) to repurpose the original movie into the teach¬ing movie (shown here) for the textbook Molecular Biology of the Cell (Alberts, B. et al. Molecular Biology of the Cell 4th edn (Garland Science, 2002)), aimed at undergraduate biology students. Created by Graham T. Johnson (2000), research and production time: approximately 38 hours over a six-week period. View additional molecular movie examples at https://youtube.com/user/grahamj21. © 2002 from Molecular Biology of the Cell, 4th Edition by Alberts et al. Reproduced by permission of Garland Science/Taylor & Francis LLC. (MOV 4381 kb)

Supplementary information S3 (movie)

The molecular machine ATP synthase works like a turbine to generate ATP. The molecular machine ATP synthase works like a turbine to gener¬ate ATP. This narrated movie combines several styles of molecular representations with other graphical structure metaphors to describe how the molecular machine ATP synthase converts the energy stored in a proton gradient into chemical energy stored in molecules of ATP. The movie was generated using the 3D animation software Maxon Cinema 4D (C4D) before molecular plugins such as ePMV existed, via the following approach: 1) the animator worked in heavy collaboration with the narration author Peter Walter (UCSF) to simultaneously develop a storyboard and a narration script; 2) several PDB files were assembled from fragments of ATP synthase structures to generate a near complete model in a molecular viewer and exported in a universal 3D file format, VRML, as ribbon rep¬resentations; 3) the ribbon models were imported into C4D, and simplified “skins” were modeled over the ribbons to create visually clean molecular surfaces that emphasize global structural relation¬ships rather than atomic details; 4) background elements, missing fragments of the molecule, and nucleotide icons were generated in C4D to match icons used in the textbook Molecular Biology of the Cell (Alberts, B. et al. Molecular Biology of the Cell 4th edn (Garland Science, 2002)) and added to the animation scene file; 5) two cop¬ies of the F1 ATPase subunits were duplicated and superimposed onto the first subunit to overlay all three states of motion that were captured in the asymmetric crystal structure, offset 120º by the molecular shaft domain; 6) one copy of the alpha-beta dimer (dark green and light green) was rigged with character animation joints and then morphed at the hinges of the atomic structure to generate three “target” states that changed shape relative to the programmed motion of the rotating shaft; this approach enabled a single joint rig to control both the ribbon structure and the overlying surface model to save time and effort; 7) the rigged model was animated to match the storyboard while working in an iterative cycle with the script author to ensure that no errors were introduced; 8) textures, lights and camera motions were refined and several short raw movie clips were exported as a Quicktime files; 9) the labels, narration and other sound, transitions and effects were composited in Adobe After Effects and the final movies was exported as the Quicktime file shown here. Created by Graham T. Johnson (2001), research and production time: approximately 48 hours over a four-week period. View additional molecular movie examples at https://youtube.com/user/grahamj21. © 2002 from Molecular Biology of the Cell, 4th Edition by Alberts et al. Reproduced by permission of Garland Science/Taylor & Francis LLC. (MOV 14993 kb)

Supplementary information S4 (movie)

Molecular details of odor detection by the olfactory system. This movie was originally generated as a 2D animation using Macromedia Flash (now Adobe Flash) to augment a static figure on olfaction from the textbook Cell Biology (Pollard, T.D., Earnshaw, W. C., Johnson, G. T. Electronic Image Collection for Cell Biology (W. B. Saunders, Philadelphia, 2002); Pollard, T.D., Earnshaw, W., Lippincott- Schwartz, J. Cell Biology 2e (Elsevier, New York, 2007)) (FIG. 29–1 in the first edition, 27–1 in the second edition of the book). The textbook figure, which shows a signal transduction mechanism with more than ten distinct physical molecular interactions, is compli¬cated for teachers to present and for students to understand. This and several of the other figures in the textbook were thus animated with a relatively fast method compared to 3D animation using Flash, which enables objects such as 2D images of molecules to move around programmatically, rather than presenting 30 full frames of pixel-based images for every second of motion as in a Quicktime movie file (thus saving a great deal of storage space). The original. swf Flash file for this figure takes 0.361 MB of storage space and plays with a high visual quality compared to the 31.8 MB required for the Quicktime file it has since been converted into; however, fewer web browsers and small devices support Flash and bandwidth limita¬tions of the internet are less of a concern today. The same approach could be emulated in slide presentation software or in Adobe After Effects with the following steps: 1) generate a layered illustration, in this case using a combination of molecular representations rendered from molecular viewers and geometric shapes drawn by hand in Adobe Photoshop and informed by molecular or microscope refer¬ence images; 2) import each molecule as a distinct object into After Effects, PowerPoint, Keynote, or similar software that supports animated motion paths and effects; 3) time the motion of sequen¬tial or simultaneous interactions and labels to convey the signaling transduction mechanism by replacing the interaction arrows of the original figure with physical motions and interactions; 4) add some context for the molecular details of the mechanism by first showing a micrograph and then zooming in to the cellular or molecular scales to present the complete animation shown here. Created by Graham T. Johnson (2001), research and production time: approximately 6 hours to produce the original illustration and 2 hours to produce the animation. (MOV 31053 kb)

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Johnson, G., Hertig, S. A guide to the visual analysis and communication of biomolecular structural data. Nat Rev Mol Cell Biol 15, 690–698 (2014). https://doi.org/10.1038/nrm3874

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