Abstract
The modeling of large biomolecular assemblies relies on an efficient rendering of their hierarchical architecture across a wide range of spatial level of detail. We describe a paradigm shift currently under way in computer graphics towards the use of more realistic global illumination models, and we apply the so-called ambient occlusion approach to our open-source multi-scale modeling program, Sculptor. While there are many other higher quality global illumination approaches going all the way up to full GPU-accelerated ray tracing, they do not provide size-specificity of the features they shade. Ambient occlusion is an aspect of global lighting that offers great visual benefits and powerful user customization. By estimating how other molecular shape features affect the reception of light at some surface point, it effectively simulates indirect shadowing. This effect occurs between molecular surfaces that are close to each other, or in pockets such as protein or ligand binding sites. By adding ambient occlusion, large macromolecular systems look much more natural, and the perception of characteristic surface features is strongly enhanced. In this work, we present a real-time implementation of screen space ambient occlusion that delivers realistic cues about tunable spatial scale characteristics of macromolecular architecture. Heretofore, the visualization of large biomolecular systems, comprising e.g. hundreds of thousands of atoms or Mega-Dalton size electron microscopy maps, did not take into account the length scales of interest or the spatial resolution of the data. Our approach has been uniquely customized with shading that is tuned for pockets and cavities of a user-defined size, making it useful for visualizing molecular features at multiple scales of interest. This is a feature that none of the conventional ambient occlusion approaches provide. Actual Sculptor screen shots illustrate how our implementation supports the size-dependent rendering of molecular surface features.
Highlights
Multi-scale molecular modeling is concerned with the computational integration and interpretation of spatio-temporal biophysical data from various experimental origins [1,2,3]
We present an implementation of screen space ambient occlusion (SSAO), which supports the visualization and modeling of multi-scale biophysical data, such as atomic structures and 3D density maps, at multiple scales of interest
The ever-growing size of macromolecular assemblies presents a formidable challenge to molecular modeling programs
Summary
Multi-scale molecular modeling is concerned with the computational integration and interpretation of spatio-temporal biophysical data from various experimental origins [1,2,3]. The unifying goal of these efforts was to observe and to account for functional architecture and dynamics in native environments (solution or vitreous ice) or in silico and to reconstruct and interpret the 3D shapes of large biomolecular assemblies across multiple spatial or time scales. Such large structures are visualized at the atomic level; volumetric 3D maps have become increasingly common [8]. Availability and quality of rendering were mainly driven by the development of more advanced hardware. When OpenGL emerged as a common interface for 3D graphics programming, it eventually resulted in a widespread support of hardware acceleration available in commodity computers
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