VR examples using ChimeraX

Tom Goddard
November 2, 2017

Here are some virtual reality example data sets that can be viewed with ChimeraX using virtual reality headsets. ChimeraX works with HTC Vive headsets. It will also work with Oculus Rift headsets, but requires using SteamVR since ChimeraX acceses the headset through the Steam virtual reality toolkit.

Install ChimeraX

Install ChimeraX for Windows 10. At our lab we use a high performance Nvidia GTX 1080 graphics card with HTC Vive and Oculus Rift headsets. Be careful -- using less powerful graphics may cause the demonstrations to stutter which can cause motion sickness.

Ribosome antibiotic

Download the ribosome_vr.cxc ChimeraX command file and open it using ChimeraX menu entry File / Open.... This will fetch a molecular structure (4v7s from the Protein DataBank) and X-ray crystallography data from and Electron Density Server public databases. This can take a minute or more (140 Mbytes of data), but the data will be saved in your Downloads directory, so this only has to be done once.

This scene immerses you in an E. coli bacterium ribosome, the giant molecular machine that translates DNA and RNA into proteins in all living things. This scene has an antibiotic telithromycin, consisting of about 40 atoms shown in purple at the center of the ribosome. In the scene, ribbons show RNA, spheres show protein components of the ribosome, and the transparent surface near the ligand shows the experimental X-ray data used to determine this structure. More details.

p97 drug binding

Download and extract the p97.zip archive containing the ChimeraX session file "p97_drug.cxs" and electron microscopy image data and open the session file in ChimeraX. Then type the following command at the bottom of the ChimeraX window to turn on virtual reality headset display:

      vr on
    

This shows a drug that is an inhibitor of the p97 molecular machine (AAA+ ATPase) involved in protein degradation. Single amino acid mutations of the p97 machine cause neuro-degenerative disease. The scene shows just the drug and the parts of p97 immediately adjacent the drug, including the electron microscope imaging seen as a transparent surface. The p97 atomic model is Protein Data Bank entry 5ftj

Molecular Zoo, hands-on small molecules

This molecular VR application allows holding flexible small molecules like water, carbon dioxide, aspirin, caffeine, saturated fat, sulfuric acid, breaking them, reassembling them. It does not use ChimeraX, but instead is a standalone application (built with Unity). Extract it from the zip archive molzoo5.zip and run the application and use the hand controllers, index finger to grab, tractor beam or shoot molecules, and thumb pad to switch modes. Source code and possibly newer releases are available at Github Molecular_Playground.