Simple Viewer

A viewer that visualizes 3D protein and nucleic acid structures in a high-quality ribbon style.

 

How do I launch Simple Viewer?

A link to Simple Viewer is available on any Structure Summary page in the Biological Assembly and Asymmetric Unit widget.

Read the guide about launching Java Web Start applications (http://www.pdb.org/pdb/static.do?p=Viewers/webstart_troubleshooting.jsp)

 

How do I rotate or move the Structures?

Basic Commands
Rotate Left Click and Drag
Zoom Middle Click and Drag
Shift + Left Click and Drag
Translation Right Click and Drag
Ctrl + Left Click and Drag

 

How do I change the Style and Colors of the Structure?

Simple Viewer renders structures in the following fixed styles and color schemes. If you want to change styles and colors, or use more advanced options, use Protein Workshop or Ligand Explorer.

Feature Rendering Style Color
Protein Chain Ribbon Rainbow spectrum from N-terminus (blue) to C-terminus (red)
Nucleic Acid Chain Ribbon Rainbow spectrum from 5' end (blue) to 3' end (red)
Ligands and Modified Residues Ball-and-Stick Atoms are colored by element:

carbon - green
hydrogen - white
oxygen - red
nitrogen - blue
sulfur - yellow
phosphorus - orange

A full list of element colors can be found at: http://jmol.sourceforge.net/jscolors

 

How do I save a High-Resolution Image?

Follow the tutorial (click here) for saving high-resolution images.

 

How can I view other Structures?

You can load another structure directly using the file menu using one of three options:

  1. Load a structure using the PDB ID

    Use the File -> Open PDB ID option to load a new structure by the 4-letter PDB ID (example 1STP).

  2. Load a structure from a file

    Use the File -> Open File option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats: http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp).

  3. Load a structure from a URL

    Use the File -> Open ULR option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats: http://www.pdb.org/pdb/static.do?p=file_formats/index.jsp).

 

How to Reference

Simple Viewer can be referenced with:

J.L. Moreland, A.Gramada, O.V. Buzko, Qing Zhang and P.E. Bourne "The Molecular Biology Toolkit (MBT): A Modular Platform for Developing Molecular Visualization Applications". BMC Bioinformatics, 6:21 (2005)