We leverage the most cutting-edge computational technologies to develop a virtual reality (VR) system - VRmol - that provides the visualization and analysis of macromolecule structures in an infinite virtual environment on the web. VRmol is natively built with WebVR technology, providing all structural analysis functions in a fully immersive, inspiring virtual environment. It is convenient to use, runs on internet and requires no software downloading and installation. And by connecting to a number of cloud-based genomic and drug databases, it provides an integrative platform to perform advanced structural and translational research. It can be freely accessed online by typing https://VRmol.net in VR-supported browser.
- 08/17/2020: VRmol is back to normal.
- 08/16/2020: Cloud Server migration. Most features are functioning normally except drug docking.
- 07/25/2020: VRmol accepted to Bioinformatics.
- 06/03/2020: Wiki is online.
- 05/18/2020: Upgrade based on the WebXR core API, which supports Chrome(>=81), Microsoft Edge (>=81).
- 02/21/2020:
Special Visfor COVID-19 from Tsinghua Univ.: [Click to Vis], NMDC: [Click to Vis] and West Lake Univ.: [Click to Vis], [Open Conformation], [Closed Conformation] - 05/17/2019: VRmol is back to normal.
- 05/16/2019: The service provider is sufferring of Network Rounte Issue, VRmol server is outage.
- 04/27/2019: VRmol is being on show at Tsinghua's 108th anniversary. News
- 02/27/2019: VRmol is applied in teaching structural biology cource at Tsinghua University.
Tutorials of VRmol can be accessed at here.
VRmol provides two modes:
- VR Mode will guide you to experience VRmol in Virtual Reality environment.
- nonVR Mode will guide you to experience VRmol on the desktop.
- Entering VR Scene [YouTube]
- Loading Structure [YouTube]
- Measurement
- Drag Structure elements
- Structure Editing
- Genome Variations
- Interactive Docking [YouTube]
- Entering VR Scene
- Fragmentation in nonVR mode
- Structure Editing in nonVR mode
- Genome Variations in nonVR mode
- Interactive Docking in nonVR mode
You could practice VRmol with VR device on WebXR supported browsers below:
- Google Chrome(>=81)
- Microsoft Edge (>=81) Download
- Firefox Reality Android standalones and PC in (Q1 2020)
Supported VR devices:
- Windows Mixed Reality*
- HTC Vive*
- Oculus Rift
*: indicates well tested devices.
Operation System:
- Windows 10 (build verion: 1903+)
Also you could practice VRmol without VR device by using WebXR API Emulator extension, download the WebXR API Emulator for your supported browser below:
The source code for the extension is also available.
For Firefox: Solving the problem of
CORS request did not succeedwhen accessing web services (genomic variation, drug docking) by setting below in firefox.
about:config: security.ssl.enable_ocsp_stapling --> False
The framework of VRmol.
A screenshot of structure visualization with stereo view.
You can save a specific structural representation scene by saving operation options setting in VRmol as a URL, like https://vrmol.net/index.html?id=1dfb. And then you can load and share the scene by opening this previously-saved URL in the web browser or embedding it into your own website by using iframe, such as
<iframe src="https://vrmol.net/?id=1dfb" />The options and their data types supported in VRmol are shown in the table below.
| Options | Data Type | Value | Comment |
|---|---|---|---|
| id | String | PDB code | 4 charactors |
| panelShow | Integer | Show:1, Hide:0 | Show menu panel or not |
| mainMode | Integer | LINE:1, DOT:2, BACKBONE:3, SPHERE:4, STICK:5, BALL_AND_ROD:6, TUBE:7, RIBBON_FLAT:8, RIBBON_ELLIPSE:9, RIBBON_RECTANGLE:10, RIBBON_STRIP:11, RIBBON_RAILWAY:12, CARTOON_SSE:13, SURFACE:14 | Main Structure Representation |
| showSurface | Integer | Show:1, Hide:0 | Show surface panel or not |
| surfaceOpc | Float | 0~1 | Transparency of surface |
| surfaceType | Integer | Van der Waals surface:1, solvent excluded surface:2, solvent accessible surface:3, molecular surface:4 | Surface type |
| colorMode | Integer | Element:601, Residue:602, Secondary Structure:603, Chain:604, Representation:605, B-Factor:606, Spectrum:607, Chain Spectrum:608, Hydrophobicity:609 | Color schemes |
| travel | Integer | Show:1, Hide:0 | Enter travel mode or not |
| vmode | String | nonvr, vr | Visualization Mode |
| fragment | String | ['a', 7, 6] | Fragmentation, label the 7th residue with Ball & Rod style |
- Present structure (PDB code:
1MBS) withBall & Rodstyle and hide the menu panel. Try it
<iframe src="https://vrmol.net/index.html?id=1mbs&panelShow=0&mainMode=6" />- Present structure (PDB code:
1DDB) withTubestyle and show its Van der Waals surface with transparency (0.5), and hide the menu panel. Try it
<iframe src="https://vrmol.net/index.html?id=1dfb&panelShow=0&mainMode=7&showSurface=1&surfaceOpc=0.5&surfaceType=1" />- Present structure (PDB code:
1F5X) with the 7th residue labeled withBall & Rodstyle in VR mode. Try it
<iframe src="https://vrmol.net/?id=1f5x&fragment=['a',7,6]&vmode=vr" />- Present structure (PDB code:
2HYY) with surface in VR. Try it
https://vrmol.net/index.html?id=2hyy&panelShow=1&mainMode=13&showSurface=1&surfaceOpc=1&surfaceType=1&colorMode=609&vmode=vr
- Download the code into the apache server web directory
- Set
SERVERURLas your URL (like https://example.com) atlibs/core.js - Start the Speech Recognition service by run:
python3 server/speech/sr.py
- Installation of external tools
- Data files used to build the Database
Server Tools
Paper: Bioinformatics Biorxiv
@article{10.1093/bioinformatics/btaa696,
author = {Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao, Lingyun and Wang, Hong-Wei and Zhang, Qiangfeng Cliff},
title = "{VRmol: an Integrative Web-Based Virtual Reality System to Explore Macromolecular Structure}",
journal = {Bioinformatics},
year = {2020},
month = {08},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btaa696},
url = {https://doi.org/10.1093/bioinformatics/btaa696},
note = {btaa696},
eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaa696/33560033/btaa696.pdf},
}
@article {Xu589366,
author = {Xu, Kui and Liu, Nan and Xu, Jingle and Guo, Chunlong and Zhao, Lingyun and Wang, Hong-wei and Zhang, Qiangfeng Cliff},
title = {VRmol: an Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure},
elocation-id = {589366},
year = {2019},
doi = {10.1101/589366},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2019/03/27/589366.1},
eprint = {https://www.biorxiv.org/content/early/2019/03/27/589366.1.full.pdf},
journal = {bioRxiv}
}
VRmol is developed based on three.js and WebXR with the help of Dawei Zhang and Xun Ran, and we would like to express our special thanks to those open-source projects below.
- https://immersiveweb.dev/#supporttable
- https://www.w3.org/TR/webxr/
- Web3DMol - for PDB file loading and parsing
- GLmol.js - for calculating surface
- Chroma.js - for color handling
- gunzip.min.js - for decompress EM map files
- AutoDock vina - for Docking Drugs in VR scene
- MGLTools - for preparing docking files
- OpenBabel - for convert docking results