News
Visualize Molecular Surfaces with Protein Workshop
02/28
The visibility and surface color of selected chains can be adjusted using Protein Workshop.
The molecular graphics program Protein Workshop1 can be used to generate molecular surfaces to aid in the display of quaternary structure, protein-protein interactions, and binding sites. This robust feature is able to handle very large assemblies, such as virus capsids.
Surfaces are created for all macromolecule chains in a PDB entry using an algorithm from D. Xu and Y. Zhang.2
A detailed description for using this feature includes: how to create molecular surfaces; color by surface, chain, and entity; make a specific surface transparent; and tips.
Protein Workshop can be launched from on every Structure Summary page. A link is located underneath the image of the biomacromolecule.
The program can also be used to generate high resolution images for publication.
Shown: PDB ID 1e79 The structure of the central stalk in bovine F(1)-ATPase at 2.4 A resolution. C. Gibbons, M.G. Montgomery, A.G.W. Leslie, J.E. Walker (2000) Nat.Struct.Biol. 7: 1055
- 1. J.L. Moreland, A.Gramada, O.V. Buzko, Q. Zhang and P.E. Bourne (2005) The Molecular Biology Toolkit (MBT): A modular platform for developing molecular visualization applications BMC Bioinformatics 6:21.
- 2. D. Xu and Y. Zhang. (2009) Generating Triangulated Macromolecular Surfaces by Euclidean Distance Transform. PLoS ONE 4: e8140.
