Nanome
By: Kota Soda, edited by- Hiloni (04/10/21), edited by Mohammed Akel (Spring 2023)
Description
Nanome is a VR data visualization software specializing in displaying molecular data at the nanoscopic level.
Tutorials
Installing Nanome on Oculus Quest 2
Instructions on how to download and install software on Quest 2
Data Soruces/Format
Data can be loaded through the load menu.
MD Trajectory
Supported file formats: .PDB, .PSE, .DCD, .GRO, .XTC, .TRR.
Click on "files" and select the folder containing the trajectories. Then press load. Play the trajectory by launching the "Frame" menu.
Molecules/Structures
Supported file formats: .pdb, .cif, .mmcif, .sdf, .mol, .xyz, .mol2, .ccp4, .dsn6, .dcd, .gro, .pqr, .trr, .xtc, .psf, .pse, .nanome, .png, .jpg, .jpeg, .pdf
Databases
Supported databases: RCSB, Drugbank, Pubchem
VR Controls
Instructions on how to navigate through Nanome can be found here.
Environment
Public Rooms
A room where anybody is free to join. Available to Personal Use users.
Private Rooms
A room with a password set to prevent other people from joining. Only available to Academic and Enterprise.
Single User Rooms
Offline mode which no one else can join. Only available to Academic and Enterprise.
Communication
In Game Voice Chat
A built in voice chat feature that allows users to converse with each other. The speaker icon next to a user's username lights up when a user is talking.
Laser Pointer
A laser pointer can be used by a user to point at specific things.
Collaborative Model Manipulation
The same model can be manipulated by multiple users. The collaboration works in Presenter Mode. So, only one person is allowed to make changes to the model, while others can view. The presenter Mode keeps on changing the presenter every 2 minutes to encourage collaboration.
Collaborative pointer
In collaborative mode, you can see other people's wrist movement to figure out what part they are editing. However, wyou are unable to see laser pointer of another user.
For paid version-
Teleport other users to you
This feature allows you to select a member in the room and teleport them near your position.
Give Presenter
This feature allows you to make some other member presenter.
Get Presenter
This feature allows you to be the presenter and manipulate the model.
Minimum System Requirements (VR Mode)
OS: Windows 10
GPU: NVIDIA GTX 780/AMD R9 290
CPU: Intel i5-4590
MEMORY: 4GB+ RAM
VR Headset: Oculus Rift S, Oculus Rift, HTC Cosmos, HTC Vive Pro, Valve Index, WMR/HP Reverb G2
Documentation
Metrics
Accessibility: The estimated time for someone to load and start visualizing data in VR
Beginner: No coding or graphics experience | < 1 hour
Intermediate: Some coding or graphics experience | < 1 mins
Advanced: Both coding and graphics experience | < 30mins
Expert: A lot of experience with VR visualization | < 30mins
Takeaway: Although the download process was fairly simple through SideQuest, a background in chemistry and biology is a must in order to fully take advantage of the features in the software.
Power: The engine's power - i.e. how much one can do with this
High - Although the usage for this is limited to biology/chemistry, this VR application leads the industry in collaborative VR applications for bio/chem research.
Usage: Evaluation of software's use for the following purposes
Molecular Dynamics Simulation
Create-your-own-molecule
Electron Density Mapping
Molecular editing
Molecular viewing
Size measuring
Pricing
Personal Use (Free)
Join Host public workspaces
Load up to 2 molecules at a time
Basic molecular viewing/editing features
Load up to 2 molecules at a time
Academic (Single license, $199/yr)
Everything in personal
Load from PubChem, Drugbank, personal computer
Save VR workspaces
Private rooms
Export in PDB SDF format
Play PDF trajectory animations
Multi SDF Ligand Support
Electron Density Map Support
Unlimited molecules
Commercial ($5k+/yr)
Everything in Academic
Nanome hosted collaboration support
Nanome hosted plugin support
Nanome hosted plugin server
Plugin integration support
Enterprise (Custom)
Private server deployment
Offline mode
Internal database integration
Custom development
Avatars
Each member is represnted by an Avatar.
Avatars can be edited - Choose different color for Avatar or Choose hair style.
