VR Mode

VR Mode

Getting Started

VR Device

For experiencing VR Scene in VRmol, a VR device is required. VR devices such as HTC Vive, Oculus Rift, and Microsoft Mixed Reality are well-supported by VRmol. Specifically, for HTC Vive, you should install SteamVR from Steam library and setup the room environment in advance. The compatibility between these VR devices and web browsers listed in the following table has been successfully tested in VRmol.

Device	OS	Web Browser
Windows Mixed Reality*	Windows 10 (build 1903+)	Microsoft Edge(v81+) Google Chrome(v81+) Firefox Reality
HTC VIVE	Windows 10 (build 1903+)	Microsoft Edge(v81+) Google Chrome(v81+) Firefox Reality
Oculus Rift	Windows 10 (build 1903+)	Microsoft Edge(v81+) Google Chrome(v81+) Firefox Reality

*: Recommanded.

The operating elements in the VR device and their functions in VR mode are described as follows:

• Trigger. Select an object or enter a function by pressing TriggerButton.
• ThumbStickButton & ThumbPadButton for Structure translation and rotation. For HTC Vive, Up and Down area in ThumbStickButton is used to transit the structure. Left and Right area in ThumbStickButton is used to rotate the structure. The axis can be changed in VR menu. For Oculus Rift and Windows Mixed Reality, Up and Down area in ThumbPad is used to transit the structure. Left and Right area in ThumbPad is used to rotate the structure. The axis can be changed in VR menu.
• Grip Button. Show VR menu.

VR Controllers input map is shown below:

HTC Vive	Oculus Rift	Windows Mixed Reality
Setup docs	Setup docs	Setup docs, Hardware guidelines

Notably, the mouse in the desktop interface can also control structural operations in VR environment.

Entering VR Scene (V)

Access VRmol at https://VRmol.net through a WebVR enabled web browser, such as Microsoft Edge and Firefox Nightly. Once you finish typing the website and press Enter button, an VRmol user interface will appear as follows:

Click VR Mode button at the bottom of the VRmol user interface using the left mouse button, and the VR starting interface will appear as follows. Click the ENTER VR button by using the left mouse button to enter VR Scene.

Alternatively, you can also point the laser tip of the controller to ENTER VR button and press the trigger to Enter VR Scene.

Here is an example video of entering VR Mode.

VR Menu

Press Menu button on the controller, a VR menu will appear in front of you in VR Scene (as shown below).The VR menu contains four parts. The top part (labeled in red box) is a VR keyboard including a 26-character alphabet, 10 numbers and a deletion (<--) button; the other three parts consist of a main menu colored in blue, a submenu in green and an information board in pink.

Loading Structure (V)

Press Menu button on the controller to get VR menu. By pointing the laser tip of the controller to alphabet or number in the VR keyboard and pressing the trigger, and a 4-character PDB ID can be typed and the corresponding structure will be afterwards loaded into the VR Scene. Alternatively, the structure in PDB format can also be loaded into the VR environment by typing its PDB ID, inputing a remote URL (such as https://files.rcsb.org/view/1mbs.pdb) or uploading a local structural file in the VRmol Desktop user interface.

A screenshot of structure visualization with stereo view.

Press Menu button on the controller again, you will go back to the VR menu. By pointing the laser tip to options in other three parts of the menu and pressing the trigger, you can experience structrual visualization styles and analysis in VR Scene, as is concretely described in the following sections.

Here is a video for eploring the structure in VRmol VR mode.

Main Structure

Point the laser tip to "Main Structure" option in VR menu and press the trigger, and 12 different representation styles will appear in the submenu board, including Line, Backbone, Sphere, Stick, Ball & Rod, Tube, Ribbon-flat, Ribbon-ellipse, Ribbon-rectangle, Ribbon-strip, Ribbon-railway, Ribbon-SS. You can visualize the input structure in your favorable style by choosing the specific representation style.

Menu → Main Structure → Line

Menu → Main Structure → Backbone

Menu → Main Structure → Sphere

Menu → Main Structure → Stick

Menu → Main Structure → Ball & Rod

Menu → Main Structure → Tube

Menu → Main Structure → Ribbon-flat

Menu → Main Structure → Ribbon-ellipse

Menu → Main Structure → Ribbon-rectangle

Menu → Main Structure → Ribbon-strip

Menu → Main Structure → Ribbon-railway

Menu → Main Structure → Ribbon-SS

The gallery of these styles is shown below.

Line	Backbone	Sphere

Stick	Ball & Rod	Tube

Ribbon-flat	Ribbon-ellipse	Ribbon-rectangle

Ribbon-strip	Ribbon-railway	Ribbon-Secondary Structure

Ligand

Point the laser tip to "Ligand" in VR menu and press the trigger to choose the "ligand" option, and there will be 4 ligand representation styles in the submenu board: Line, Sphere, Stick, Ball & Rod.

Menu → Ligand → Line

Menu → Ligand → Sphere

Menu → Ligand → Stick

Menu → Ligand → Ball & Rod

The gallery of these styles is shown below.

Line	Sphere	Stick	Ball & Rod

Surface

The "Surface" option includes Van der Waals, Solvent excluded, Solvent accessible and Molecular surface. The transparence of the structure surface can be adjusted by pointing the laser tip to Opacity 1.0-0.5 in submenu and pressing the trigger. In addition, by pointing the laser tip to Wireframe in submenu and pressing the trigger, the structure surface can be viewed as meshed surface.

Menu → Surface → Van der Waals surface

Menu → Surface → solvent accessible surface

Menu → Surface → solvent excluded surface

Menu → Surface → molecular surface

The gallery of these styles is shown below.

Van der Waals surface	Van der Waals surface with Wireframesolvent accessible surface	Van der Waals surface with transparency(0.8)

Van der Waals surface with transparency(0.5)	solvent accessible surface	solvent excluded surface

Color Scheme

By choosing options in "Color" submenu in VR menu, the structure can be variedly colored according to 10 different schemes, such Element, **Residue **,Secondary structure,Representation, Chain, B-factor, Spectrum, Chain Spectrum, Hydrophobicity, Sequence Conservation.

Menu → Color → Element

Menu → Color → Residue

Menu → Color → Secondary Structure

Menu → Color → Representation

Menu → Color → Chain

Menu → Color → B-factor

Menu → Color → Spectrum

Menu → Color → Chain Spectrum

Menu → Color → Hydrophobicity

Menu → Color → Conservation

The gallery of these styles is shown below.

Color by Element	Color by Residue	Color by Secondary Structure

Color by Representation	Color by B-Factor	Color by Spectrum

Color by Chain Spectrum	Color by Hydrophobicity	Color by Conservation

Measurement (V)

In VR menu, choose "Measure" and there will be Distance and Angle appearing in the submenu.

Point the laser tip to Distance option and press the trigger, the VR Scene containing the structure will appear. Point the laser tip to a residue and press the trigger to select it; then point the laser tip to another residue and press the trigger to select the second one. The distance between these two residues will be automatically presented.

Point the laser tip to Angle option and press the trigger, and then select three residues in the VR Scene. The angle among them will be automatically presented.

Menu → Measure → Distance

Menu → Measure → Angle

Here is an example video for computing distance in VR.

Drag (V)

"Drag" option is designed for dragging specific elements in the structure. By selecting Drag Chain, Drag Ligand, Drag Residue or Drag Drug, you can drag the individual chain, ligand, residue or drug of the structure in VR Scene.

Here is an example video for dragging specific elements in VR.

Fragmentation (V)

You can highlight specific fragments by presenting them with varied representation styles in the VR Scene. Firstly, enter "Fragment" in VR menu, and 12 representation styles will appear in submenu. Then choose a target representation style, and the VR Scene containing the input structure will apear. Next pick two residues by using the laser tip and pressing the trigger, and you will see the highlighted fragments presented with the previously-chosen representation style in VR scene.

Menu → Fragment

A selected fragment is highlighted with Ball&Rod style.

Here is an example video for fragments visualization.

Structure Editing (V)

"Editing" provides a method to replace one amino acid with another one. Enter "Editing" in VR menu, and 20 types of amino acids will appear in the submenu. Choose the target type residue in the submenu by pointing the laser tip to it and pressing the trigger. Then pick the residue that you want to replace in the structure in VR Scene by pointing the laser tip to it and pressing the trigger, and you will see the picked residue is replaced by the target residue.

Menu → Editing

The edited structure can be exported as a new PDB file by using Export PDB in "Export" option in VR menu.

Here is an example video for structure editing in VR Scene.

Genomic Variations (V)

"Mutation" option in VR menu provides a handy way to view genomic variation sites in the target structure by connecting to TCGA, CCLE and ExAc databases. By choosing "Mutation" in VR menu, TCGA, CCLE and ExAC will apear in submenu board. And you can view genomic mutation sites (highlighted by twinkling balls) in the loaded structure by selecting these databases.

Menu → Mutation → TCGA

Menu → Mutation → CCLE

Menu → Mutation → ExAc

Here is an example video for genomic variations visualization. Try it

Drug Docking (V)

In "Drugs" option in VR menu, choose Load Drug, and the structure-related drug (from DrugBank databse) will be loaded into the VR Scene. Press Menu button in the controller, and go back to VR menu. And choose Drug Random Migration to interactively perform drug docking in VR Scene.

Menu → Drugs → Load Drugs → docking

An example video for interactive docking in VR mode. Try it

Speech Recognition

VRmol provides speech recognition option, enabling users to operate the structure by speaking commands (the commands in English are listed below). Chinese commands can be accessed here.

Category	Command
Visualization Mode	go to desktop mode
	go to virtual reality mode
	go to travel mode
Main structure style	change to dot style
	change to line style
	change to backbone style
	change to sphere style
	change to stick style
	change to ball and rod style
	change to tube style
	change to second structure style
	hide main structure
	show main structure
Ligand structure style	change Ligand to line style
	change Ligand to sphere style
	change Ligand to stick style
	change Ligand to ball and rod style
	hide ligand structure
	show ligand structure
Show Other	show water
	hide water
	show hydrogen bond
	hide hydrogen bond
	show mutation
	hide mutation
Surface	show the surface of main structure
	show transparency
	show mesh
	hide the surface of main structure
Color	color by element
	color by residue
	color by second structure
	color by chain
	color by b-factor
	color by spectrum
	color by hydrophobicity
	color by conservation
Interaction	open dragging function
	open labelling function
	rotation
	rotation by x
	rotation by y
	rotation by z
	clockwise rotation
	anticlockwise rotation
	move
	move along x
	move along y
	move along z
	move forward
	move backward

In VR menu, select "Speech" options. And then follow these steps:

1. Choose a language by pointing the laser tip to Chinese Voice or English Voice and pressing the trigger. The default language is English.
2. Point Voice in VR menu, and press down the trigger.
3. Hold on pressing the trigger untill you finish speaking the command. The voice will be recorded and automatically uploaded to the server for recognization.
4. VRmol will operate the structure according to the recognized command.

Menu → Speech → Voice