TexMol: interactive visual exploration of large flexible multi-component molecular complexes

While molecular visualization software has advanced over the years, today, most tools still operate on individual molecular structures with limited facility to manipulate large multicomponent complexes. We approach this problem by extending 3D image-based rendering via programmable graphics units, resulting in an order of magnitude speedup over traditional triangle-based rendering. By incorporating a biochemically sensitive level-of-detail hierarchy into our molecular representation, we communicate appropriate volume occupancy and shape while dramatically reducing the visual clutter that normally inhibits higher-level spatial comprehension. Our hierarchical, image based rendering also allows dynamically computed physical properties data (e.g. electrostatics potential) to be mapped onto the molecular surface, tying molecular structure to molecular function. Finally, we present another approach to interactive molecular exploration using volumetric and structural rendering in tandem to discover molecular properties that neither rendering mode alone could reveal. These visualization techniques are realized in a high-performance, interactive molecular exploration tool we call TexMol, short for Texture Molecular viewer.

1 Introduction

While molecular visualization software has developed over the years, today, most tools still operate on individual molecular (protein or RNA - Ribo-nucleic acid) structures and small electron charge and electrostatic potential fields, with little facility to manipulate larger multi-component complexes, integrate geometric and volumetric visual representations, or effectively depict molecular flexibility and dynamics. Few, if any currently used programs allow for or enable interaction with multi-component macromolecules and their atomic level properties, such as reconstructed volumetric maps from tomographic and cryo imaging, that will become common in the next five to ten years. We present TexMol (short for Texture Molecular Viewer), an interactive molecular exploration application created in response to the increasingly demanding visualization needs of the biology community. To efficiently visualize dynamic and flexible structures, TexMol uses a molecular specification file to construct the Flexible Chain Complex (FCC), a robust, dynamic data structure that serves as TexMol's internal representation for molecular structures. The FCC models the flexible joints of a molecule and contains a biochemically-based hierarchy for level-of-detail (LOD) optimizations.