3D View (Jmol)

The 3D View page visualizes the PDB structures using Jmol (an open-source Java viewer for chemical structures in 3D, http://www.jmol.org/) and provides options to render structures in different styles and colors. Hover over the red circles in the screenshot below to explore different options.

Hover over the red circles in the screenshot below to explore different options. Hemoglobin entry 4hhb is used in this example.



Four Distinct Display Modes

Select from four modes of predefined style and color settings for Jmol. The default mode colors residues by 'Secondary Structure'. The 'Subunit' mode renders all protein subunits in different colors, and the 'Symmetry' mode emphasizes the point group symmetry or helical symmetry of a protein complex. The custom view can be used to access additional options for style, color, surface rendering, and more.

secondary structure
Secondary Structure

Renders structure in Cartoon style and colors by Secondary Structure

subunit structure
Subunit

Renders structure in Cartoon style and colors protein subunits in different colors. This mode is useful for visualizing quaternary structure.

symmetry mode
Symmetry

Renders structure in CPK style and colors subunits to emphasize symmetry of a protein complex (read more about color schemes). The structure is enclosed by a polyhedron and symmetry axes are drawn to elucidate the symmetry of a complex. For asymmetric structure, a rectangular box and the three axes of inertia are drawn.

custom view
Custom View

Provides full access to all styles and color schemes, options for surface and hydrogen bond display, change of background color, and toggling on/off autorotation.

 

Interactions

Basic Commands
Open Jmol Menu Right Click
Ctrl + Left Click
Left Click on Logo
Rotate Around X,Y Left Click and Drag
Move along X,Y
(= translate)
Shift + Left Double-Click and Drag
Middle Double-Click and Drag
Ctrl + Right Click and Drag
* Works both when clicking on the molecule or away from it.
Reset and Center Shift + Left Double-Click
Middle Double-Click
* Only works if double-click is done away from the molecule.
Rotate Around Z Shift + Left Click and Drag Horizontally
Middle Click and Drag Horizontally
Shift + Right Click and Drag Horizontally (possibly fails on OS X)
Zoom In / Out Shift + Left Click and Drag Vertically
Middle Click and Drag Vertically
Use Mouse Wheel