Aakansha's First In-Class Activity

Downloads

Download Nanome

  • Download Nanome from Oculus Store (it is present in the App Lab)

  • You can launch the application but do not do the tutorial as it is part of the class activity

Download UnityMol

  • Download the software from this link by selecting the suitable version and OS. You should download the 1.14 Win64 version on your paperspace

  • Accept the conditions and the software should be downloaded.

  • Launch Steam VR on Oculus

  • Unzip the folder and run the exe file

Download PeppyVR

  • Download the apk file from this link

  • Follow the steps outlined here to sideload this APK file onto your Quest 2

    • Steps to enable Developer mode in the mobile Oculus app -> Menu -> Devices -> select your Quest 2 -> Developer Mode

Class Activity

  • The class activities will be done in pairs. Please upload the screenshots of your activity onto the class board. The pairs are as follows:

    • Eliza, Robert

    • Jacobi, Mandy

    • Cheyenne, Nick

    • Lucia, Alistair

    • Sayan, Maia

    • Beatrice, Shashidhar

    • Amanda, Paul

    • Tongyu, Jennifer

Part 1: UnityMol & PeppyVR (Independent)

UnityMol

  • Compare the VR and 2D version of the software. Which version do you prefer better?

  • You can download any pdb file of your choice on your paperspace machine.

  • Download the software as well on your paperspace machine

  • 2D view: Load the pdb file. In the Utils, Click the Switch VR to turn it off.

  • You can play around with the features to make your visualization of the molecule better. UnityMol offers very little features as compared to Nanome however it is a good tool for visualization and collaboratively discuss.

  • VR view: Click on the Switch VR button again to turn shift to VR mode. Put on your headset and change the features to view better.

  • You can also follow the VR view steps mentioned in the Download UnityMol tab.

  • Screenshot 1: Upload your screenshot of the view you prefer the most for this software.


PeppyVR

  • Select the number of residues you want for the new peptide. I would suggest to select 1 to begin with.

  • In the Quick select, you can select all. this function will select all the residues

  • Click on the sidechains and choose a protein chain to mutate the structure with. You can decide which chain to choose

  • Once you have chosen the sidechain then observe the differences.

  • Screenshot 2: Upload the screenshot of your the mutated molecule on the class board.

Part 2: Nanome

  • Launch the application and begin the tutorial. The aim of the tutorial is to help you gain a basic understanding of protein structures and Nanome features. You and your partner can do the tutorial individually but you can upload the screenshots in pairs.

  • Screenshot 3: You can upload screenshot from any point of the tutorial that you think was the coolest!

  • After the tutorial, sign up for Nanome

  • One partner can create a room while the other partner joins the room.

  • After joining the room, the partners can work together on any activity they prefer!

  • You can either Build a molecule (present in the workspaces), mutate covid-19 molecule or any other fun activity you prefer!

  • Screenshot 4: Upload a screenshot of the activity you did with your partner

Part 3: Google Form

  • Complete the google form and provide your feedback on the three softwares: link