Nanome

By: Kota Soda, edited by- Hiloni (04/10/21)

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

https://docs.nanome.ai/

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.