YASARA View - molecular graphics for all devices - from smartphones to workstations.

Elmar Krieger,Gert Vriend

doi:10.1093/bioinformatics/btu426

Abstract

Summary: Today's graphics processing units (GPUs) compose the scene from individual triangles. As about 320 triangles are needed to approximate a single sphere—an atom—in a convincing way, visualizing larger proteins with atomic details requires tens of millions of triangles, far too many for smooth interactive frame rates. We describe a new approach to solve this ‘molecular graphics problem’, which shares the work between GPU and multiple CPU cores, generates high-quality results with perfectly round spheres, shadows and ambient lighting and requires only OpenGL 1.0 functionality, without any pixel shader Z-buffer access (a feature which is missing in most mobile devices).Availability and implementation: YASARA View, a molecular modeling program built around the visualization algorithm described here, is freely available (including commercial use) for Linux, MacOS, Windows and Android (Intel) from www.YASARA.org.Contact: elmar@yasara.orgSupplementary information: Supplementary data are available at Bioinformatics online.

Highlights

1 INTRODUCTION In 1966, Cyrus Levinthal pioneered molecular graphics at the Massachusetts Institute of Technology, when he set up the first interactive wire-frame display of a protein on a monochrome oscilloscope (Levinthal, 1966)
Molecular graphics has made tremendous progress, mostly thanks to the video game industry, which induced the rise of graphics processing units (GPUs)
The general idea is very simple and has been used ever since texture mapping became part of 3D graphics: if an object is too complex it is replaced with ‘impostors’, i.e. fewer triangles that have precalculated textures attached, which make them look like the original object

Summary

Introduction

The logical solution would be to adjust the pixel Z-values on the fly during rendering (with a so-called ‘pixel shader’), but this approach is either slow (because the hardware can no longer perform an early Z-test to discard pixels) or not supported at all (e.g. mobile devices based on OpenGL ES lack this feature, and PowerVR GPUs do not even have a Z-buffer). (2) For each atom i, the CPU creates a temporary Z-buffer that includes atom i and all the more distant atoms k, which can influence the shape of atom i by intersection, i.e. those atoms whose sphere image touches atom i and who are closer along Z than their own radius Rk. The atoms k could be found quickly with a neighbor search grid, but it turns out that the trivial approach to just look at covalently bound atoms is good enough.

Results

Conclusion