Experimenting with Nanome

HPC Support Staff and Pomona College student Ekeka Abazie reviews the research he’s conducted while using the Virtual Reality environment Nanome, focusing on how the program can visualize and render molecules.

Capture of me using Nanome on the Oculus Tethered Headset

I’ve made one poster presenting my summer computational chemistry research with the chemistry department that I will be presenting on Stover Walk at Pomona College as well as at the SACNAS conference in Honolulu, Hawaii. However, I’m also interested in presenting the work that I did with Nanome while at HPC for the Pomona College summer presentations at Stover Walk. After getting permission from Jorgensen, who is coordinating the poster presentation at Stover Walk, I am now hoping to present two posters—one based on my work with Nanome and another based on my SURP research.

         It was difficult at first to decide what I would present on my poster concerning Nanome. I originally wanted to use Nanome as a research tool with the main focus being on competitive inhibition of the enzyme complex, Succinate Dehydrogenase, of the Citric Acid Cycle. I had previously worked on a similar and more experimentally focused project with resources provided by the Biology department, but this was going to be a different examination that was based more on distances and modeling. After talking to Senior Shklyar [sic], I decided against this and opted for a poster that looked more at the capabilities of Nanome; in other words, focusing more on the VR software. However, after internalizing my conversation with Senior Shklyar even more, I’ve realized that the blog posts that I write concerning Nanome are sufficient to display my work on the project. We already have 3 posters that will be representing HPC, and there will definitely be other opportunities for me to demonstrate my love and commitment to my work at HPC. Nonetheless, I still learned a lot more about Nanome by getting into it with the intent to make a presentation, so I think that deserves some discourse.


Normal Glutamic Acid positioning (healthy patient)

I modeled the mutation of Sickle Cell Anemia using Nanome. Sickle Cell Anemia is caused by a single point mutation at the 6th codon of the β-globin gene which causes GAG which codes for Glutamic Acid to be changed into GUG which codes for Valine. I thought this was a cool undertaking, because for me at the time, it represented a valuable use of VR in education. I’m imagining a genetics class that allows students to mutate sections of DNA and see how that would affect an organism. Imagine a whole class in VR working on mutating DNA molecules, sounds like Ender’s Game to me which is super exciting.

Mutated Valine positioning (sick patient)

I also modeled the binding of Carbon monoxide to myoglobin which causes Carbon Monoxide poisoning. Carbon Monoxide causes reduction of the central metal ion of myoglobin upon binding to Fe2+ turning the complex into Carbonmonoxymyoglobin which can’t perform the normal respiratory functions of the standard oxymyoglobin complex and leads to respiratory difficulty and, possibly, death. Pretty cool health education application in my eyes. It is also worth mentioning the attention to detail in the visualization that Nanome provides for these molecules. It’s astounding.

Normal Oxymyoglobin Fe Complex

Lastly, I learned that Nanome could run a lot of functions which I didn’t expect, such as running a multitude of commands or accept different extensions and attachments to make it easier for the user. I find the addition of extensions and attachments to be the most promising because it seems the most boundary extending for what Nanome could be used for, similar to how games that accept mods can be used for so much more.

Aberrant Carbonmonoxymyoglobin Fe Complex

I also learned how to render unique modified molecules using Nanome. For example, I rendered a modified human Lactate Dehydrogenase where the first 20 amino acids of each chain had been replaced with the GFP (Green Fluorescence Protein) from Aequorea Victoria jellyfish. I wonder what else I thought Nanome couldn’t do that it actually can.

– By Ekeka Abazie

The “How” is Secondary

Kevin Ayala (Pomona College, Computer Science) provides an encouraging insight into his experience working with HPC Support and at the in The Know Lab. Kevin discusses the high standards involved in the projects as well as the opportunities open to minorities who do not have access to such equipment.

Kevin Ayala

I only heard about the lab because I happened to be in the right place at the right time. But as soon as I joined, I knew it was the perfect place for me to be. When Asya gave me the tour, there was a sense of wonder at seeing all the technology that was available, but also at seeing what students like me were already doing with them. It was something I could only describe with the first word that came out of my mouth: “Wow!”

And to be honest, I was a little scared as well. Everyone was already so far ahead, and it seemed like everyone else knew so much. I hadn’t grown up with access to any of this technology, and I felt like I was trying to drink water through a fire hose every time I went to a team meeting. Even now, months later, I know I still have a lot left to learn before I can delve into the industry in any professional way. But I’ve learned something else through my work in the lab, perhaps something more important.

It wasn’t something that anyone said, but rather from feeling the energy in the room at each of those meetings. It was a sense of inspiration, of confidence in our own abilities. It was the feeling of dozens of minds working together, each believing in the changes we were making and the projects we were undertaking. Most important, it was the sense that our inexperience, our lack of knowledge or talent or resources, was not a limitation. It was nothing more than a stepping stone, and we could use it to go wherever we want to go.

“The How is Secondary” became my own little phrase, both to explain the near chaos of the lab and to motivate my own self. It doesn’t mean that “How” wasn’t an important part of what we did, but it did mean that I didn’t have to let it stop me. I slowly became more confident in the idea that I didn’t have to know everything about what I was working with, not yet. I could learn along the way, and perhaps even learn better! I could create my own “wow” moments.

That was a big change for me. I’ve always loved learning, but it’s always served as a means to an end, both a way to get where I was going and a stop sign to keep me from going there until I was ‘ready’. I had always held myself back, waiting until I knew or had enough experience to do what I wanted to do. And that’s not the way the Lab works.

In fact, one of the great things about the Lab, and the reason it’s so successful is because it encourages us to experiment, but holds us to a higher standard when doing so. When I started working with Raspberry Pi’s, I knew nothing about them except that they were small computers. For that matter, I knew nothing about Linux or using Secure Shell to access another system. But I was encouraged to learn about them – to find the resources that I needed. At first, it was terrifying. To know that I might fail, might not know enough to make it work, made me wary of starting my own project. But with each little breakthrough, I grew more confident and more excited. And just last week, I watched in wonder as the 3D printer finally responded to my click on the laptop touchpad.

That little bit of movement was such a relief. I hadn’t let myself believe that I’d done it until I saw it for myself, but man, it felt so good to know that I had done that, from scratch and by learning on the go. I think that bit of confidence that the Lab gives is sometimes underestimated.

One of my favorite things about the Lab, and something I know Asya works very hard on, is the atmosphere of diversity and inclusivity. Part of that is knowing that minorities often don’t have the confidence to work in the field, because we’ve never had the chance to work with or, even be around, these types of technology. There’s a certain feeling of anxiety, worrying that you’ll break or damage something too expensive for you to even look at. But I think that the reason we’ve been so successful in this endeavor is the implicit trust given to us by the idea that we can learn what we need to along the way. That trust inspires confidence and that confidence, in turn, inspires our ideas and our learning to flourish. And that is something I’m profoundly thankful for.

By Kevin Ayala

Impressions of Nanome Curie

Ekeka Abazie uses Nanome to see molecules in a Virtual Reality environment. Here, he discusses his impressions of using Nanome Curie.

Right off the bat, I noticed a reduction in quality from Nanome when using the Oculus S tethered headset and Nanome Curie using the Oculus Quest headset. The best way I can compare it is akin to that of the original version and the lite version where you would find on a lower-tier console, which leads me to question whether it is the platform that is partially to blame.

The graphics quality on Nanome Curie was very pixelated and blocky, making analysis very difficult. Further, there were slow reaction times that added vibrations, making the careful analysis I was able to perform using Nanome on Oculus S challenging. There were also significant delays, and at times, the molecule would be moved very far into the screen which necessitated moving it to myself like I was fishing.

I wasn’t even able to analyze the same molecules as I was with the Oculus S, because many wouldn’t even load properly. For example, when I tried to load graphene from the “Featured” menu, a text box would appear with a green checkmark indicating that the molecule had loaded, and then I would get an error message. For others, that I searched using the database, I would often just start with the error message.

I also noticed that I couldn’t just focus on one molecule and enlarge or work with it. Any changes in size that I made to one molecule would be carried to the other molecule, which, yes, keeps everything to scale, but I imagined that selecting a molecule would allow me to make specific edits to that molecule rather than the entire workspace. This was particularly annoying when I had a 2HBS, a rather large molecule that takes up a lot of space, within the same workspace as a small hexacarbonyl ring. I would have to move 2HBS quite far if I wanted to enlarge the hexacarbonyl and focus on it.

I spoke with Professor O’Leary in the Chemistry Department at Pomona College (I originally came to inquire about any past assignments I could use to test the VR software) about the feasibility of VR for molecule visualization compared to already dominant software in the market like SPARTAN, Chemdraw, or GAUSSIAN. He told me that he didn’t see a need for VR in the market because the present software seemed much more suited for the task and easier to work with. However, he said that he could see how VR would aid in the comprehension of molecule manipulation and in education. He said this would especially be the case if you could input specific files for molecules using a variety of different file extensions. This is something I mentioned in my review of Nanome using Oculus S tethered, and I easily understood how I could upload files for molecules of interest and use it to work with them on that platform. However, on Nanome Curie using the non-tethered Oculus Quest headset, I don’t see how this same file upload process would work.

By Ekeka Abazie