Visualize Molecular Surfaces with 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.