Molecular Visualization on the Holodeck

Abstract

Can virtual reality be useful for visualizing and analyzing molecular structures and three-dimensional (3D) microscopy? Uses we are exploring include studies of drug binding to proteins and the effects of mutations, building accurate atomic models in electron microscopy and x-ray density maps, understanding how immune system cells move using 3D light microscopy, and teaching schoolchildren about biomolecules that are the machinery of life. Virtual reality (VR) offers immersive display with a wide field of view and head tracking for better perception of molecular architectures and uses 6-degree-of-freedom hand controllers for simple manipulation of 3D data. Conventional computer displays with trackpad, mouse and keyboard excel at two-dimensional tasks such as writing and studying research literature, uses for which VR technology is at present far inferior. Adding VR to the conventional computing environment could improve 3D capabilities if new user-interface problems can be solved. We have developed three VR applications: ChimeraX for analyzing molecular structures and electron and light microscopy data, AltPDB for collaborative discussions around atomic models, and Molecular Zoo for teaching young students characteristics of biomolecules. Investigations over three decades have produced an extensive literature evaluating the potential of VR in research and education. Consumer VR headsets are now affordable to researchers and educators, allowing direct tests of whether the technology is valuable in these areas. We survey here advantages and disadvantages of VR for molecular biology in the context of affordable and dramatically more powerful VR and graphics hardware than has been available in the past.

Keywords: AltPDB; ChimeraX; Molecular Zoo; microscopy; virtual reality.

Figure 1:

Beta-amyloid fibril consisting of stacked anti-parallel beta strands. A single amino acid mutation favors anti-parallel fibril formation. The mutation can be manually reversed in VR and energy-minimized to explore how residue repacking may disrupt the fibril.

Figure 2:

ChimeraX user interface. Mouse modes, toolbar buttons and other controls can be used with hand controllers on this floating panel in the VR scene. A 3D optical microscopy time series of a crawling neutrophil is shown along with interface elements specific to this type of data in the lower right.

Figure 3:

Measuring and tracking features in 3D lightsheet microscopy. Measurement of deflection of a collagen filament over a 5-second interval as a crawling neutrophil passes it (left). Manually marked path of motion of a T-cell protrusion over a 15-second interval (right).

Figure 4:

Antibiotic telithromycin (purple) bound at the catalytic center of E. coli ribosome with antibiotic resistance methylation site on ribosomal RNA shown in yellow and X-ray density shown as a transparent surface. Level-of-detail tuning allows viewing complex scenes such as this in VR rendered at 90 frames per second.

Figure 5:

ChimeraX VR meeting command shows each party as a postage-stamp head with customizable image and cone hands for pointing (left). AltPDB allows VR participants to discuss Protein Data Bank structures with custom human avatars, control molecule styles, and browse web pages within a popup pane (right).

Figure 6:

Molecular Zoo educational application depicts fully flexible models in a large space. A tractor beam (blue) activated with hand controllers brings out-of-reach molecules to the VR user’s hand.