Aakansha's First In-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:
Part 1: UnityMol & PeppyVR (Independent)
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.
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