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VRmol: An Integrative Cloud-Based Virtual Reality System to Explore Macromolecular Structure
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README.md


VRmol: Virtual Reality for Molecular Structures

Introduction

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.

Demo

News

  • 05/17/2019: VRmol is return 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 from Tsinghua
  • 02/27/2019: VRmol is applied in teaching structural biology cource at Tsinghua University.

Documentation

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.

Video Tutorials

VR Device requirements

VR devices such as HTC Vive, Oculus Rift, and Microsoft Mix Reality are well-supported by VRmol. More details can be seen at documentation.

Framework

The framework of VRmol.

Screenshot

A screenshot of structure visualization with stereo view.

Sharing by URL

URL Options

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/index.html?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 desktop, vr Visualization Mode
fragment String ['a', 7, 6] Fragmentation, label the 7th residue with Ball & Rod style

Examples for API

  1. Present structure (PDB code:1MBS) with Ball & Rod style and hide the menu panel. Try it
<iframe src="https://vrmol.net/index.html?id=1mbs&panelShow=0&mainMode=6" />
  1. Present structure (PDB code:1DDB) with Tube style 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"  />
  1. Present structure (PDB code:1F5X) with the 7th residue labeled with Ball & Rod style in VR mode. Try it
<iframe src="https://vrmol.net/?id=1f5x&fragment=['a',7,6]&vmode=vr"  />
  1. 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

Deploy VRmol on your own server Using VRmol API Services

  • Download the code into the apache server web directory
  • Set SERVERURL as your URL (like https://example.com) at libs/core.js
  • Start the Speech Recognition service by run:
    python3 server/speech/sr.py

If you deploy VRmol in your local server with a prefix URL http://localhost or you do not have a setting of https, you should delete the .htaccess file. While without setting https, you would not access the Speech Recognition function.

Setup VRmol API Services on your own server

Server Tools

  • Linux/Windows/macOS Apache
  • Integretive tool for Linux LAMP
  • Integretive tool for Windowns WAMP

Release Versions

Citation

Paper: Biorxiv

@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}
}

Acknowledgments

VRmol is developed based on three.js and WebVR, and we would like to express our special thanks to those open-source projects below.

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