A viewer that visualizes 3D protein and nucleic acid structures in a high-quality ribbon style.
Protein Workshop offers the same default styles and colors as Simple Viewer, but has options to
change styles, colors, and visibility, and add labels to atoms and residues. Protein Workshop also supports molecular surfaces to aid in the display of quaternary structure,
protein-protein interactions, and binding sites. Surfaces are created for all macromolecule chains in a PDB entry using the algorithm from D. Xu, Y. Zhang (2009) Generating Triangulated Macromolecular
Surfaces by Euclidean Distance Transform. PLoS ONE 4(12): e8140
A link to Protein Workshop 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)
carbon - green
hydrogen - white
oxygen - red
nitrogen - blue
sulfur - yellow
phosphorus - orange
Click the "Change Background Color" button on the Shortcuts tab
Follow the tutorial (click here) for saving high-resolution images.
You can load another structure directly using the file menu using one of three options:
Use the File -> Open PDB ID option to load a new structure by the 4-letter PDB ID (example 1STP).
Use the File -> Open File option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats:
Use the File -> Open ULR option to load a structure in the PDB (*.pdb) and PDBML/XML (*.xml) file format (Description of file formats:
More advanced color options are available from the Shortcuts tab.
Surfaces can be colored by four properties:
The visibility and color surfaces for selected chains can be adjusted using the Visibility and Colors
tools from the toolbar after surfaces have been generated for all chains in a PDB entry.
To change the transparency of a specific surface
To change the color of a specific surface
Chains and entities are colored by color schemes, which are carefully chosen combinations of colors or
shades of color.
There are three types of color schemes available: sequential, diverging, and qualitatitive. The default
color palette (5 colors) will be adjusted by the number of chains or number of entities to render the
surface. In case there is only a single chain or entity, try the Single color option instead. All colors of the
sequential color scheme are colorblind safe, however, not all colors schemes from the diverging and qualitative
colors are colorblind safe. A description for each color scheme is available as a mouse-over. These
color schemes have been adopted from ColorBrewer developed by C.
Brewer, The Pennsylvania State University.
The surface generation code is able to handle very large assemblies, such as virus capids.
When displaying a large assembly such as a virus capsid, turn visibility of the ribbons off. This will
significantly decrease memory requirements and will increase the responsiveness of the application. Parts of ribbons occasionally protrude through the molecular surface. Again, turning off ribbons will
solve this problem.
Protein Workshop 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)
The RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics:
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.