Improved quadric surface impostors for large bio-molecular visualization

Abstract

The shape of biomolecules, such as proteins, may be represented using different representations like space-fill, ballstick, backbone, or secondary structures. The secondary structure of proteins, comprising of sheet-like, helix-like and loops structures, represent a higher level abstraction of its structure. With ever increasing sizes of protein structure data produced by high resolution x-ray crystallography and cryo-electron microscopy, biologists often rely on visualizations to better understand the overall structure of proteins. In this paper, we present a unified framework for accelerating the rendering of various representations of these structure using GPUs. The framework first produces "impostor primitives", which are simple linear element approximations of quadric objects, such as spheres, cylinders, and helices. Next, the rasterizations of the impostors are corrected to produce pixel-precise renderings of the quadric objects. We incorporate this framework into a bio-molecular visualization tool proteinvis to demonstrate quantitative and qualitative performance gains over earlier approaches for rendering various representations of proteins.

iRASPA: GPU-accelerated visualization software for materials scientists

“…Despite this, drawing spheres using imposters is 1 or 2 orders of magnitude faster than drawing it is using many individual triangles or using tesselation shaders. Many imposter algorithms have been developed for spheres, ellipsoids, cylinders, cones, and helixes [17,93,[96][97][98][99], generic quadratic [100], cubic and quadratic [101], piecewise algebraic surfaces [102], and compound imposters [103]. Note that a small angle of view can lead to large numerical errors [99].…”

Immersive virtual reality in computational chemistry: Applications to the analysis of QM and MM data

“…To obtain an interactive visualization of a large number of spheres and cylinders, resulting from the “all atoms” representation of complex molecular structures, we have developed a set of GPU shaders (A “ shader ” is a program running on the Graphics Processing Unit (GPU), which allows the programmer to define a specific algorithm for drawing the objects it is applied to) implementing a technique known as “ GPU‐based ray‐casting of quadric surfaces .” This method has been first introduced by Gumhold to render a large number of ellipsoids representing symmetric tensor fields, and later generalized by Toledo and Lévy so to ray‐cast any quadric surface on the GPU. This technique provides very good results (both in terms of performance and image quality) when applied to molecular visualization and, according to Kozlíková et al in a recent survey on the subject, it still represents the state of the art. A brief discussion on the implementation of this method, with specific reference to Caffeine, can be found in Appendix A.…”

Advanced inspection techniques for molecular simulations

“…Despite using impostors did not require precomputation and it improved the performance, the visual quality was not as good as the one provided by the 3D geometry. As similar technique was used by Bagur et al [BSN12] (see Figure 2.6). They also used procedural impostors to represented the secondary structures, but, although the visual quality of the method was better than Bajaj et al's, they still had visual artifacts in the joints of the secondary structures with the rest of the protein backbone.…”