Java PDB viewer designed to display and analyze structural information.

WebMol Viewer Website

Software Requirements

  • Internet Explorer 6.0 on Windows XP
  • Safari on Mac OS 10.3.3
  • Mozilla 1.6 on Linux (Redhat 8.0)
  • Java 1.4+


Hardware Requirements

  • CPU: 400 MHz
  • RAM: 128 MB

Sequence Viewer

The sequence viewer displays the amino acid sequence of a particular structure. The left side is the label of the chain. Clicking on this label displays the chain color options.

This allows the user to change visibility or color of the chain in the sequence viewer and the structure viewer.

Individual residues my be highlighted by clicking and dragging in the sequence window. To change the selection color click on the selection color box in the control panel window. The residue count highlights how many residues have been highlighted.


Control Panel

The control panel contains several options for displaying chains based on calculated values and residue properties.

For example: To highlight a chain based on Residue B Factor, select a chain under the Chain IDs label. Then select a choice under the Calculated Values option. The corresponding chain color will change in the sequence viewer and the structure viewer according to these values:

Reset will reload the structure to its original state.


Structure Viewer

Basic Commands
Rotate Around Left Click and Drag
Move along X,Y
(= translate)
Ctrl + Left Click and Drag
Zoom In / Out Alt + Left Click and Drag
Select Click on a vertex to select the residue. This will select the corresponding residue in the sequence viewer.