Video tutorials to accompany the review articleA Guide to the Visual Analysis and Communication of Biomolecular Structural Data
by Graham T. Johnson and Samuel Hertig
To highlight the relationship of the bound ligand to the hydrophobic region of a lipid bilayer, in FIG. 3a we choose to deemphasize the protein and the bilayer by fading them into the color of the background. This can be achieved by carefully selecting coloring and lighting options in the molecular visualization software, or more efficiently by post-processing the default output images during compositing, where results of subtle parameter changes can be immediately perceived in the final context of the labeled figure.
Here we render gray outlines of a transmembrane GPCR using the “Silhouette” feature in Chimera, then paste them together and apply background graphics (bilayer, ECM, and cytoplasm color gradients) using Apple’s Keynote presentation software to maintain a non-destructive workflow that results quickly in an editable slide. Reducing the opacity of the GPCR binding pocket and fading off the jagged top edge helps to clarify that this pocket sits inside the protein. Photo-editing software provides more options to make a slightly cleaner slide, but often this might not be worth the effort for peer communication or for other well-prepared educational audiences.
A Video tutorial will be posted here on September 24, 2014, followed by a printable written tutorial on September 26, 2014.