VistaPDB VistaPDB Manual -> Models -> Surface Models

Surface Models

Surface models represent the solvent accessible surface of a macromolecule. Grooves, pockets, and bulges are readily visible using surface models. Several types of models are supported:

Abstract: the abstract surface model is a simple model that can be used to readily identify surface patches that are potential binding or active sites.

Charge: Surface charges can be identified using this model. Positive charges are represented by blue, and negative charges by red.

Hydrophobicity: Hydrophobic patches can be visualized using this model. Patches are colored blue.

Surface Models are created dynamically, and make take some time to complete. Surface models are constructed using a modified form of the algorithm described by Connolly (Science, 221, 709-713). This algorithm uses a probe of a certain radius that 'rolls' over the molecule. Surface models can be created with or without (default) this probe. Use the preferences window to change the use of the probe as well as the probe radius. Surface reconstruction is perfomed using the marching cubes algorithm.