CHIMERAX VR

@Hiloni (04/05/21)

Description

Chimerax VR is the software that allows display and analysis of molecular structures and density maps.

Tutorials

Instaling Chimerax VR on Oculus Quest 2- link

  • Instructions on how to download and install software on Quest 2

Download and Open Dataset- link

  • Instructions on opening datasets, using command line and downloading data from Chimerax VR

Data Soruces/Format

Data can be loaded through open -> select data -> enter command - vr on.

Chimerax Session-

Supported file formats: ".cxs"

Chimerax Commnd Line files-

Supported file format: ".cxc", enter code directly in command line

Chimerax BILD object-

Supported file format- ". bild", ".bld"

Chimerax Map-

Supported file format- ".cmap", ".cmp"

Density Map-

Supported File format- "*.brix"

Medical Images

Supported formats: "DICOM medical imaging"

Other file formats-

"Amira Mesh (.am), APBS potential(".dx"), AutoDock PDBQT(".pdbqt")

VR Controls

Instructions on how to navigate through ChimeraxVR can be found here.

Environment

Multiple User

Allows multiple user to join using the meeting command and meeting tool. Find more instructions here.

Single User

Allow you to edit and work in your workspace independently.

Communication

Meeting name-

For multiple users collaboration, Meeting is created by one user and other users can join the meeting.

Participant Name and Photo-

A test identifier for individuals with anem to identify other users in the meeting. Also, you can upload an image to represnt participant's headset position.

Pointer-

By default the pointer color of cones is lime in VR, each participant can change color of pointer.

Minimum System Requirements (VR Mode)

OS: Windows 10, MAC and linux(less stable)

GPU: GTX 1080 Ti

CPU: Intel i5-4590

MEMORY: 64 GB

VR Headset: HTC Vive, Vive Pro, Oculus Rift, Samsung, Odyssey and Windows Mixed Reality

Documentation

https://www.cgl.ucsf.edu/chimerax/docs/user/vr.html

Metrics

Accessibility: The estimated time for someone to load and start visualizing data in VR

  • Beginner: No coding or graphics experience | < 2 hour

  • Intermediate: Some coding or graphics experience | < 1 hour

  • Advanced: Both coding and graphics experience | < 30mins

  • Expert: A lot of experience with VR visualization | < 30mins

  • Takeaway:

  • This software provides with multiple features to view your molecular and EM structure in VR, a background in chemistry and biology can come really handy to understand various features and its implementations. Some of the features does face some lag in Virtual reality but it does provide with multiple features to easily understand the data.

  • Power: The engine's power- i.e. how much once can do with this

  • Medium- Although, it provides multiple features- from viewing molecular structures, density maps, medical Images, etc. , it still faces some lag in VR mode while using few features and the usage of the application is limited to biology and chemistry.

Usage: Evaluation of software's use for the following purposes

  • Display and Analysis of Structures

  • Density Maps

  • Medical Image

  • Graphics

  • Viewing of Molecular Structure

Pricing

Personal Use/Academic/Government/Non-profit (Free)

  • Access all the available features and wor collaboratively.

ChimeraX Commercial Licensing-

You will need to get a non-exclusive, nontransferable, 3-year license.

ChimeraX Single User License: $2,000 USD per site

ChimeraX Six User License: $10,000 USD per site

ChimeraX Unlimited User License: $20,000 USD per site

More details about the licensing and cost can be found here.


Limitations

Some of the limitations of using this software can be found here.