POP-OUT | CLOSE

Protein Workshop

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?


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
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

 

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:

  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 do I change the Style and Colors of the Structure?

  1. Select your tool (visibility, style, colors, etc.)
  2. Choose either "Atom and Bonds" or "Ribbons"depending on what you want to change.
  3. Select an additional option, depending on the tool.
  4. 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?


To turn on surfaces, move the surface transparency slider all the way to the right to display an opaque surface. Move the slider to the left to increase the transparency. Surfaces can be turned off by moving the slider to the off position.

 

Coloring a surface


Surfaces can be colored by four properties:


Chain: each macromolecule chain is rendered in a different color or shade of color

Entity: unique macromolecule chains with identical sequence are colored the same



Single Color: all chains are colored by the same color

Hydrophobicity: residues are color coded according to hydrophobicity

 


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

  1. Choose Visiblity
  2. Choose Surfaces
  3. Choose a Chain

To change the color of a specific surface

  1. Select the Color tool
  2. Choose Surfaces
  3. 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)