NonVR Mode
Operation on the structure is controlled by mouse.
| Operation | Mouse Usage |
|---|---|
| Rotate | Press & hold LEFT mouse button, then move. |
| Translate | Press & hold RIGHT mouse button, then move. |
| Zoom | Scroll UP to zoom in; scroll DOWN to zoom out. |
Users can access VRmol at https://vrmol.net through any WebGL supported browsers. Then type a PDB code (like 1MBS) in the textbox and then press enter button. A structure will appear in the user interface. In addition, VRmol also surpports loading structure by inputing a remote URL (such as https://files.rcsb.org/view/1mbs.pdb) or uploading a local structural file.
By clicking "Main Structure" option in the interface, you can view 12 different representation styles for "Main Structure", including Line, Backbone, Sphere, Stick, Ball & Rod, Tube, Ribbon-flat, Ribbon-ellipse, Ribbon-rectangle, Ribbon-strip, Ribbon-railway, Ribbon-SS.
Main Structure → Line
Main Structure → Backbone
Main Structure → Sphere
Main Structure → Stick
Main Structure → Ball & Rod
Main Structure → Tube
Main Structure → Ribbon-flat
Main Structure → Ribbon-ellipse
Main Structure → Ribbon-rectangle
Main Structure → Ribbon-ellipse
Main Structure → Ribbon-strip
Main Structure → Ribbon-railway
Main Structure → Ribbon-Secondary Structure
The gallery of the styles is shown below.
| Line | Backbone | Sphere |
|---|---|---|
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| Stick | Ball & Rod | Tube |
|---|---|---|
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| Ribbon-flat | Ribbon-ellipse | Ribbon-rectangle |
|---|---|---|
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| Ribbon-strip | Ribbon-railway | Ribbon-Secondary Structure |
|---|---|---|
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By clicking "Ligand", you can select ligand representation styles.
You can view the ligand in four representation styles by clicking these affiliated options, including Line, Sphere, Stick, Ball & Rod .
Ligand → Line
Ligand → Sphere
Ligand → Stick
Ligand → Ball & Rod
| Line | Sphere | Stick | Ball & Rod |
|---|---|---|---|
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The "Surface" option includes Van der Waals, Solvent excluded, Solvent accessible and Molecular surface. The transparency of structure surface can be adjusted by clicking 1.0-0.5 in the affiliated options. In addition, by selecting Wireframe, the structure surface can be viewed as meshed surface.
Surface → Van der Waals surface
Surface → Solvent accessible surface
Surface → Solvent excluded surface
Surface → Molecular surface
Surface → 1.0 (Transparency)
Surface → 0.8 (Transparency)
Surface → Wireframe
The gallery of the surface representation styles is shown below.
| Van der Waals surface | Solvent excluded surface | Solvent accessible surface |
|---|---|---|
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| Molecular surface | Van der Waals surface with Wireframe | Van der Waals surface with transparency(0.8) |
|---|---|---|
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By choosing options in "Color", the structure can be variedly colored according to 10 different schemes, such as Element, **Residue **,Secondary structure,Representation, Chain, B-factor, Spectrum, Chain Spectrum, Hydrophobicity, Sequence Conservation.
Color → By Element
Color → By Residue
Color → By Second Structure
Color → By Representation
Color → By B-Factor
Color → By Spectrum
Color → By Chain Spectrum
Color → By Hydrophobicity
Color → By Conservation
The gallery of the color schema is shown below.
| Color by Element | Color by Residue | Color by Second Structure |
|---|---|---|
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| Color by Representation | Color by B-Factor | Color by Spectrum |
|---|---|---|
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| Color by Chain Spectrum | Color by Hydrophobicity | Color by Conservation |
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You can highlight specific fragments by presenting them with varied representation styles. Firstly, click "Fragment", and two affiliated options, Region and Editing, will appear.
Click the Region option, and the Fragment panel will appear as follows. The steps for representation of the selected fragments are labeled in the panel.
Here is an example video for fragment regions.
Structure Editing provides a method to replace one amino acid with another one. Click "Fragment", and then click its affiliated option Editing.
Here will appear an editing panel as follows. In this panel, you can select a specific chain by selecting its chain ID, and then select the residue that you want to replace. Next select the target residue and its representation style in the resulting structure. Finally, click Replace button in the panel, and you will see the original residue is replaced by the target residue highlighted by your selected representation style. Notably, the edited structure can be exported as a new PDB file by click "Export" option in the VRmol user interface.
Here is an example videos for structure editing in VRmol.
"Mutation" option provides a handy way to view genomic variation sites in the target structure by connecting to TCGA, CCLE, ExAc and dbSNP databases. By clicking "Mutation", TCGA, CCLE, ExAC and dbSNP will apear. And you can view genomic mutation sites (highlighted by twinkling balls) on the loaded structure by selecting these databases.
Mutation → TCGA
Mutation → CCLE
Mutation → ExAc
Mutation → dbSNP
Here is an example video for visualizing genomic variation. Try it
"Drugs" option in VRmol provides a handy way for the structure-related drugs visualization and drug molecules docking analysis. In "Drugs" option, choose Load Drug, and the structure-related drug (from DrugBank databse) will be loaded into the user interface. And choose Drug Random Migration to perform drug docking. You can define the searching space in drug docking by clicking Show BoxHelper for getting more efficient and meaningful docking results. Once you click Show BoxHelper, there will appear a "Box Helper Limit" board in the upper right of the user interface, where searching space can be defined by inputing x, y and z coordinates.
Here is an example video for drug docking. Try it
If the input structure (PDB) has corresponding density map (like electron microscopy density map in EMDB), you can easily load this density map by clicking "Density Map" and then Load Density Map (as shown in the following figure). And the loaded density map can be visualized in several representation styles as listed in "Control panel for density map" in the following figure.
Density Map → Load Density Map
"Surface" (I), "Slice" (II) and "Solid" (III) representation styles of density map are shown below.
Notably, a local individual density map can also be directly uploaded by clicking "+Upload" button in the user interface.