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ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

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durrantlab/protein-vr

1.0.7
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ProteinVR 1.0.7

Introduction

ProteinVR is an open-source web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. The molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

ProteinVR is made possible thanks to support from the University of Pittsburgh (Center for Research Computing; Innovation in Education Award) and the National Institutes of Health (R01GM132353). It is released under the terms of the BSD-3-Clause license. If you use ProteinVR in your research, please cite: "Cassidy, K. C., Šefčík, J., Raghav, Y., Chang, A., & Durrant, J. D. (2020). ProteinVR: Web-based molecular visualization in virtual reality. PLoS computational biology, 16(3), e1007747."

Most users will wish to simply access the already compiled, publicly available ProteinVR web app at http://durrantlab.com/pvr/. This code repository is designed to help developers.

Repository Contents

  • src/: The ProteinVR source files. You cannot use these files directly. They must be compiled.
  • utils/, package.json, package-lock.json, tsconfig.json: Files used to compile the contents of the src/ directory to the dist/ directory.
  • CHANGES.md, CONTRIBUTORS.md, README.md: Documentation files.

If you wish to run ProteinVR on your own web server, simply download the latest proteinvr_web_app.zip file from the Releases page.

Description of Use

Loading Screen

Figure 1

Figure 1: An illustration of a ProteinVR scene with the default NanoKid molecule visualized. Several buttons are available from the main screen. A) Load a new molecule and environment. B) Provide help. C) Enter follow-the-leader mode. D) View in full screen. E) Enter VR mode.

When users first open ProteinVR, the application displays the default molecule (NanoKid, Figure 1). After a few seconds, a simple popup form appears where users can type the PDB ID or URL of the molecular model they wish to visualize. The same form also allows users to indicate the 3D environment in which to place the molecular model, as well as whether the molecule should cast shadows. After clicking the "Load Molecule" button, NanoKid is replaced with the desired molecular structure.

2D Menu

Several buttons appear on the right of the screen that are only accessible when not in VR mode (Figure 1A-E). The first allows users to load a new molecule and environment; the second opens this help system; the third generates a sharable URL that others can use to mirror the ProteinVR scene on their own devices (see "Leader Mode" below); and the fourth and fifth put ProteinVR into full-screen and VR mode, respectively.

3D Menu

All other ProteinVR functionality is accessible through the in-world 3D menu system (Figure 2). ProteinVR places a simple button at the user's feet with the text "Show Menu" (Figure 2A). Users on laptop/desktop computers can click this button using a mouse or keyboard (space bar); users on mobile devices without VR headsets can simply tap their screens; and users with VR headsets can pull the VR-headset or VR-controller trigger button.

Once clicked, a hierarchical 3D menu appears, embedded in the 3D scene itself. At the top-most level, this menu is divided into two broad categories (Figure 2B-C). The "Rotate" submenu allows users to rotate the molecule about the X, Y, or Z axis. The "Styles" submenu contains further submenus that allow users to change how the molecule is displayed, both in terms of the molecular representation (e.g., cartoon, sphere, stick, surface) and the color (e.g., white, color by element, etc.) (Figure 2D-F). "Styles > Components" applies these changes to common, pre-defined molecular components (e.g., proteins, ligands, nucleic acids, water molecules). "Styles > Selections" applies changes to the model using characteristics specific to the loaded molecule itself (e.g., specific residues, elements, chains, etc.). And "Styles > Remove Existing" allows users to remove previously specified representations/colors (Figure 2G).

Figure 2

Figure 2: A schematic of the menu buttons available from within the 3D environment. A) Open the menu system (located at the user's feet). B) Access the "Rotate" submenu. C) Access the "Styles" submenu. D) Change the style of common, pre-defined molecular components. E) Change the style of selected atoms specific to the loaded molecule itself. F) Remove previously specified styles. G) Change the representation and/or color of the selected atoms/components.

URL Tracking

ProteinVR makes it easy to save molecular scenes with custom visualizations such as these. Every time a molecular representation is loaded, rotated, or otherwise altered, ProteinVR updates the browser URL to track the change. Copying the URL at any point into a new browser tab--even on a different device--recreates the exact same ProteinVR scene.

Display Modes

To accommodate a broad range of devices, ProteinVR runs in four modes: VR mode, device-orientation mode, desktop mode, and leader mode. In all four, ProteinVR uses video-game-style navigation. Objects reside at fixed positions in a 3D environment, and the camera moves (or teleports) to different locations in the scene.

VR Mode

Description and Navigation

Users who wish to view ProteinVR scenes through a VR headset (e.g., an Oculus Rift, Oculus Go, HTC Vive, or Google-Cardboard compatible viewer) must navigate to the ProteinVR web app via a browser that supports the WebVR api. VR mode provides a fully immersive experience wherein users can view their molecular structures in stereoscopic 3D. The 3D environments are particularly useful in VR mode, as they improve the sense of realism and immersion. By allowing viewers to orient themselves spatially, 3D environments may also reduce VR sickness, which occurs when users perceive a disconnect between the 3D scene presented to the eyes and the movement/orientation of the head. To enter VR mode, users must first attach a VR headset as well as any hand controllers. They then click the VR button in the main ProteinVR screen.

In VR mode, users can look about the scene by physically moving their heads. Some VR headsets also allow users to navigate to nearby locations by physically moving about the room. Teleportation navigation enables movement to distant points in the virtual world. A simple navigation sphere indicates the current teleport destination. When using a VR headset that lacks hand controllers (e.g., Google Cardboard), this sphere appears on the object immediately in front of the user's gaze. When using a headset with hand controllers (e.g., the HTC Vive, Oculus Rift, or Oculus Go), the sphere appears at the location where the user is pointing. To teleport to the location of the sphere, the user simply presses the VR-headset button, the VR-controller trigger (Figure 3A), the keyboard space bar, or the mouse click button.

VR controllers with trackpads enable more fine-grained movements (Figure 3B). To slowly move forward or backward in the direction of the navigation sphere, users can simply press the top or bottom of the trackpad. To rotate left or right without having to rotate the head (e.g., to reset the view), users can press the left and right side of the trackpad, respectively.

Figure 3

Figure 3: An illustration of the VR-controller buttons that enable navigation in VR mode.

Caveats

We have tested VR-mode on multiple operating-system, web-browser, and VR-headset setups. In some cases, it is necessary to explicitly enable the WebVR application programming interface (API) and/or browser access to the device-orientation sensors. We have also found that WebVR access to the VR controllers can be finicky. We recommend turning on the controllers before entering VR. On VR systems that have multiple controllers (e.g., one for each hand), we also recommend turning on all controllers, even though teleportation navigation requires only one. VR technology is rapidly evolving; a web search can reveal the steps necessary (if any) to fully enable VR in a given browser of choice.

Windows

We have verified that VR mode works well on Windows 10. We currently recommend the Firefox web browser, which provides a stable WebVR implementation that is enabled by default.

macOS

VR support in macOS is currently limited.

Mobile

VR mode also works well on most mobile devices. The WebVR API on Android is easy to access. In contrast, WebVR access on iOS is currently challenging. iOS mobile Safari does not allow webpages to hide the browser address bar, as required for VR visualization using mobile (e.g., Google Cardboard) headsets. Additionally, iOS does not allow the mobile Safari browser to access the device's orientation sensors by default, making it impossible for ProteinVR to respond to head movements. Apple requires all third-party browsers on iOS (e.g., Chrome, Firefox) to use the same WebKit framework and JavaScript engine that Safari does, so it is not possible to overcome these challenges by switching to another browser.

To eliminate the address bar on iOS, users should install ProteinVR as a progressive web app (PWA). PWA installation places a ProteinVR icon on the device's home screen and allows ProteinVR to run in full-screen mode. Simply visit the ProteinVR website via mobile Safari and use the browser's "Share> Add to Home Screen" menu item. Additionally, users must enable access to the device-orientation sensors (even if running ProteinVR as a PWA) via Settings > Safari > Motion & Orientation Access. We are hopeful that Apple will simplify this process in the future as it expands its VR support.

Device-Orientation Mode

Device-orientation mode is ideal when viewing ProteinVR scenes on mobile devices with orientation sensors. If ProteinVR detects such sensors, it automatically updates its viewport to match the orientation of the device itself. Users can thus view their molecular structures from different angles by physically reorienting their devices. ProteinVR also uses teleportation navigation in device-orientation mode. A similar navigation sphere (placed in the direction the mobile device is pointing) indicates the current teleport destination. To teleport to the location of the sphere, the user simply taps on the mobile-device screen.

In our experience, Google Chrome on Android provides the easiest device-orientation experience. On iOS, users must explicitly enable access to the device-orientation sensors via Settings > Safari > Motion & Orientation Access.

Desktop Mode

If neither a VR headset nor an orientation sensor is available, ProteinVR runs in desktop mode. Desktop mode uses a standard keyboard-and-mouse navigation system similar to that commonly used in video games. The arrow keys (or WASD keys) move forward, backward, and sideways. Clicking and dragging with the mouse changes the viewing angle. If the user clicks on the full-screen button in the main window (Figure 1D), ProteinVR instead changes the viewing angle whenever the mouse moves, without requiring an accompanying click. Teleportation navigation is also available for those who wish to use it. To teleport to the navigation sphere, the user need only press the space bar. As desktop mode uses only well-established web technologies, it runs on virtually any modern browser.

Leader Mode

Finally, ProteinVR can run in "leader mode." This mode transforms the program into a powerful presentation tool. In many scenarios, multiple users may wish to visualize the same ProteinVR scene together. A technology called WebRTC enables direct communication between leader and follower instances. When running in "leader" mode, ProteinVR broadcasts the user's location in the 3D scene, as well as information about how the molecule of interest is currently represented. Broadcasting is available from VR headsets, Android phones, laptops, and desktops. Safari and iOS are not currently supported. In contrast, when running in "follower" mode, ProteinVR receives this information from the designated leader and automatically updates the scene to match whatever the leader is currently seeing. Only 2D (desktop-mode-style) viewing is available in follower mode because VR viewing-angle updates independent of head movements often cause VR sickness.

Running ProteinVR on Your Own Computer

Most users will wish to simply access the already compiled, publicly available ProteinVR web app at http://durrantlab.com/pvr/. If you wish to instead run ProteinVR on your own UNIX-like computer (LINUX, macOS, etc.), follow these instructions:

  1. Download the latest proteinvr_web_app.zip file from the Releases page
  2. Uncompress the file: unzip proteinvr_web_app.zip
  3. Change to the new proteinvr/ directory: cd proteinvr
  4. Start a local server. Python2 provides one out of the box: python -m SimpleHTTPServer 8000
  5. Access the server from your web-browser: http://localhost:8000/ or perhaps http://0.0.0.0:8000/

Running ProteinVR on other operating systems (e.g., Windows) should be similar.

Compiling ProteinVR

The vast majority of users will not need to compile ProteinVR on their own. Simply use the already compiled files in the proteinvr_web_app.zip file, available through the Releases page. If you need to make modifications to the source code, these instructions should help with re-compiling on UNIX-like systems:

  1. Clone or download the git repository: git clone http://git.durrantlab.com/jdurrant/protein-vr.git
  2. Change into the new protein-vr directory: cd protein-vr
  3. Install the required npm packages: npm install
  4. Fix any vulnerabilities: npm audit fix
  5. Make sure ImageMagick and Python are installed system wide, and that convert and python work from the command line
  6. To deploy a dev server: npm run start
  7. To compile the contents of src/ to dist/: npm run build

Dedication

ProteinVR is dedicated to the memory of Dr. Karen Curto.

About

ProteinVR is a web-based application that allows users to view protein/ligand structures in virtual reality (VR) from their mobile, desktop, or VR-headset-based web browsers. Molecular structures are displayed within 3D environments that give useful biological context and allow users to situate themselves in 3D space.

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