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.
Renders structure in Cartoon style and colors by Secondary Structure
Renders structure in Cartoon style and colors protein subunits in different colors. This mode is useful for visualizing quaternary structure.
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.
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.
|Open Jmol Menu||
Ctrl + Left Click
Left Click on Logo
|Rotate Around X,Y||Left Click and Drag|
Move along X,Y
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
* 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