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
How do I launch Protein Workshop?
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)
How do I manipulate the Structure?
|Rotate||Left Click and Drag|
Middle Click and Drag
Shift + Left Click and Drag
Right Click and Drag
Ctrl + Left Click and Drag
|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
Change the Background Color
Click the "Change Background Color" button on the Shortcuts tab
Save a High-Resolution Image
Follow the tutorial (click here) for saving high-resolution images.
Viewing other Structures
You can load another structure directly using the file menu using one of three options:
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).
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).
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 do I change the Style and Colors of the Structure?
- Select your tool (visibility, style, colors, etc.)
- Choose either "Atom and Bonds" or "Ribbons"depending on what you want to change.
- Select an additional option, depending on the tool.
- Choose an item (structure, residue, chain, or atom) from the tree viewer or by clicking on the item in the 3D viewer window.
More advanced color options are available from the Shortcuts tab.
How do I use the Surfaces feature?
Coloring a surface
Surfaces can be colored by four properties:
Entity: unique macromolecule chains with identical sequence are colored the same
Toggling transparency and changing the color of a selected surface
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
- Choose Visiblity
- Choose Surfaces
- Choose a Chain
To change the color of a specific surface
- Select the Color tool
- Choose Surfaces
- Choose a Chain
Coloring by chain and entity
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.
Surfaces for large biological assemblies
The surface generation code is able to handle very large assemblies, such as virus capids.
Tips for manipulating surfaces
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.
How to Reference
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)