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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. 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. Chains and entities are colored by color schemes, which are carefully chosen combinations of colors or shades of color.
There are Πέτρος Λούκας Χαλκιάς* - Τα Θεσσαλικά Νο 1 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 Ken Vandermark / Paal Nilssen-Love - Lightning Over Water. 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 Πέτρος Λούκας Χαλκιάς* - Τα Θεσσαλικά Νο 1 C.
Brewer, The Pennsylvania State University. 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. Moreland, A. Gramada, O. Buzko, Qing Zhang and P. BMC Bioinformatics, Warning You are using a web browser that we do not support. Our website will not work properly. Please update to a newer version or download a new web browser, such as Chrome or Firefox.
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 General Trees - Tarzan on the item in the 3D viewer window.
More advanced color options are available from the Shortcuts tab. 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 : Πέτρος Λούκας Χαλκιάς* - Τα Θεσσαλικά Νο 1 are color coded according to hydrophobicity.
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