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Part II: How Virtual Reality Can Help Scientists, Such As Yourself, Better Understand Molecules

Author: Jessie MNGL Suzuki, almost Ph.D. In part one last week, Jesse talked about his first hand experience in using VR in the lab. In today’s post, he talks about setting up VR in the lab.

Hardware

Virtual Reality Rig ­– I recommend purchasing the HTC Vive or Vive Pro. This runs about $1000, inexpensive as lab equipment goes. While there are cheaper headsets on the market, these are not compatible with all molecular viewers and will limit your options.

Computer – The Vive is a “tethered” VR rig, meaning it must plug into a VR-capable computer, either a desktop or laptop. For our set-up we purchased a $3,000 Alienware gaming laptop, optimized for VR graphics, but you can likely use an existing lab computer. Check online to see if a computer is VR-capable before assuming that it is! I recommend getting a GTX 1080 graphics card or above. It is possible to use a lower-powered graphics cards, but poor graphics quality make nausea more likely and reduce the amount of time you can spend inside.

Play Area

You can access virtual reality from a seated or standing orientation. Seated set-ups need less space, but in my experience, most people want to get up and walk around. At minimum, I recommend a roughly 10ft by 10ft play area. We use a shared conference room and just move the big table aside when we want to use VR. The HTC Vive uses two small “lighthouses” which send out a signal used by the headset and hand controllers to orient themselves in space, these can be on tripods or mounted high up on the walls in your play area room. Installation was easy. The lighthouses need to be plugged when in use, so make sure there is an outlet for each one.

I recommend a big screen TV if possible, because it is useful and fun for your lab mates to be able to see what you are viewing. We cast from the laptop to the big screen so that if someone is “co-piloting” on the laptop, they can see what’s going on in VR.

Software

The fanciest, flashiest software is nearly useless if it is not actively supported and maintained. Every time your computer updates, there is the danger of the software no longer working. Unfortunately this is the heartbreaking fate of so many academic software advancements. Other VR programs have flashed and faded, below are the programs I recommend you use and support.

STEAM Gaming Platform – This free platform enables millions of video gamers worldwide to access tens of thousands of video games. It is going to give you access to virtual reality. STEAM is actively supported and maintained.

UCSF ChimeraX – Created and actively maintained by UCSF (2), this molecular viewing program is similar to its older sister Chimera, and competitor PyMol. Unfortunately, it is not compatible with either Chimera or Pymol files, however it has an exciting advantage in that it is VR capable! Also, has warm natural lighting for creating figure-quality images. You can upload a PDB file, change the colors and graphic representation however you want and then with a simple command, “vr on”, you can step into the session. I find this program works best with a co-pilot on the outside, so a lab partner and I will often take turns. One person inside VR with the structure, looking and calling out requests, and the other person sitting at the laptop, writing things down, making changes, typing into the command line. The folks at UCSF have created an excellent page of resources to help folks that are getting started in VR molecule viewing. (3)

Nanome – This is a polished, easy-to-use molecular viewing program. We paid for the $100/year version of Nanome, but there is a perfectly fine free version available. Unlike ChimeraX, Nanome has a virtual floor that lines up with the real floor under your feet, a seemingly small consideration that helps stave off motion sickness. There are fully customizable control panels, third-party software for things like ligand binding dynamics, and a virtual wristwatch with go-go-gadgets and controls. Multiple users can go into a session at the same time (from different headsets), so you and the team from Copenhagen can hold weekly meetings in the presence of your protein of interest. If you are looking to give a potential investor the ol’ razzle dazzle, this is what you want to use. But I actually do most of my VR molecule work in ChimeraX, the workhorse academic program, because you can edit your session in 2D and then just jump into 3D. With Nanome, you have to do everything from inside the VR headset.

I recommend that you try out both programs and try out new programs when they come out. Each program has its strengths and weaknesses, so benefit from what you like best about each. If you use and appreciate a program, make sure to credit, cite and support the creators, so that they can keep maintaining and improving on the software!

Conclusion

As of this writing, it is likely that I have spent more with the spliceosome in virtual reality than any other person on the planet. I have made individual snRNPs the size of a cat, to cradle and consider in my virtual hands. I have expanded full spliceosome assemblies to the size of my four-story lab building to slip between nucleotides, stand side-by-side with the suppressor mutation I discovered (4) and see where it lives. I’ve noticed interactions, context, spacing, blocking, sizing, and mechanics that I could never have seen from the outside. I have sat for hours, in awe and reverence inside the fantastically convoluted core of a machine more ancient than the dinosaurs, more ancient than multicellularity. I guess I could try to keep this secret, keep strolling into conferences with unexplained insight into the physical mechanics of my beloved over-complicated molecular machine, but where’s the fun in that? Knowledge is meant to be shared. Please see it for yourself.

Acknowledgements

Manny Ares, Scott Seiwert, Al Zahler, Susan Strome, Aleta Dunne, UCSC, UCSF

References

(1)        RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences. Burley et al., (2021) Nucleic Acids Research  doi: 10.1093/nar/gkaa1038

(2)        Virtual-reality applications give science a new dimension. Matthews D. Nature. (2018) doi: 10.1038/d41586-018-04997-2.

(3)        UCSF ChimeraX technical support website https://vr.ucsf.edu/

(4)        A Genetic Screen in C. elegans Reveals Roles for KIN17 and PRCC in Maintaining 5’ Splice Site Identity. Suzuki et al., PLoSGenetics (2022) doi: TBD

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