Representing thermal vibrations and uncertainty in molecular surfaces

Chang Ha Lee; Amitabh Varshney

doi:10.1117/12.458813

12 March 2002 Representing thermal vibrations and uncertainty in molecular surfaces

Chang Ha Lee, Amitabh Varshney

Proceedings Volume 4665, Visualization and Data Analysis 2002; (2002) https://doi.org/10.1117/12.458813
Event: Electronic Imaging, 2002, San Jose, California, United States

Abstract

The smooth molecular surface is defined as the surface which an external probe sphere touches as it is rolled over the spherical atoms of a molecule. The previous methods to compute smooth molecular surface assumed that each atom in a molecule has a fixed position without thermal motion or uncertainty. In real world, the position of an atom in a molecule is fuzzy because of its uncertainty in protein structure determination and thermal energy of the atom. In this paper, we propose a method to compute smooth molecular surface for fuzzy atoms. The Gaussian distribution is used for modeling the fuzziness of each atom, and an extended-radius p-probability sphere is computed for each atom with a certain confidence level. An extended-radius p-probability sphere is defined for atom i as the smallest sphere containing the atom i with a probability p. The fuzzy molecular surface is defined as a collection of molecular surfaces constructed from extended-radius p-probability spheres for each probability p. We have implemented a program for visualizing three-dimensional molecular structures including the fuzzy molecular surface using multi-layered transparent surfaces, where the surface of each layer has a different confidence level and the transparency associated with the confidence level.

Citation Download Citation

Chang Ha Lee and Amitabh Varshney "Representing thermal vibrations and uncertainty in molecular surfaces", Proc. SPIE 4665, Visualization and Data Analysis 2002, (12 March 2002); https://doi.org/10.1117/12.458813

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