Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins

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Citation: Russ B. Altman and Christopher Hughes and Mark Gerstein. (1995) Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins. In KSL-95-26, March,1995.

Publication techreport ( Edit )
type Technical Report
bibtype techreport
Bibtex basics
author Russ B. Altman and Christopher Hughes and Mark Gerstein
title Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins
number KSL-95-26
institution Knowledge Systems, AI Laboratory
address Stanford, CA, USA
year 1995
month March
Bibtex more
note Medical Computer Science
Access Paper
abstract Most molecular graphics programs ignore any uncertainty in the atomic coordinates being displayed. Structures are displayed in terms of perfect points, spheres, and lines with no uncertainty. However, all experimental methods for defining structures, and many methods for predicting and comparing structures, associate uncertainties with each atomic coordinate. We have developed graphical representations that highlight these uncertainties. These representations are encapsulated in a new interactive display program,PROTEAND. PROTEAND represents structural uncertainty in three ways: (1) The traditional way. The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids. At each atom position,the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes. Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual a-helices. We illustrate the utility of these display modalities by the applying PROTEAND to the globin family of proteins, and show that certain types of structural variation are best illustrated with different methods of display.

KSL Technical Report ID: KSL-95-26
Facts about Methods for Displaying Macromolecular Structural Uncertainty: Application to the GlobinsRDF feed
Abstract Most molecular graphics programs ignore an … Most molecular graphics programs ignore any uncertainty in the atomic coordinates being displayed. Structures are displayed in terms of perfect points, spheres, and lines with no uncertainty. However, all experimental methods for defining structures, and many methods for predicting and comparing structures, associate uncertainties with each atomic coordinate. We have developed graphical representations that highlight these uncertainties. These representations are encapsulated in a new interactive display program,PROTEAND. PROTEAND represents structural uncertainty in three ways: (1) The traditional way. The program shows a collection of structures as superposed and overlapped stick-figure models. (2) Ellipsoids. At each atom position,the program shows an ellipsoid derived from a three-dimensional Gaussian model of uncertainty. This probabilistic model provides additional information about the relationship between atoms that can be displayed as a correlation matrix. (3) Rigid-body volumes. Using clouds of dots, the program can show the range of rigid-body motion of selected substructures, such as individual a-helices. We illustrate the utility of these display modalities by the applying PROTEAND to the globin family of proteins, and show that certain types of structural variation are best illustrated with different methods of display. strated with different methods of display.
Address Stanford, CA, USA  +
Author Russ B. Altman and Christopher Hughes and Mark Gerstein  +
Bibtype techreport  +
Has author Russ B. Altman and Christopher Hughes and Mark Gerstein  +
Has identifier KSL-95-26  +
Has publishing details March,1995  +
Has title Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins  +
Has where published KSL-95-26  +
Has year 1995  +
Institution Knowledge Systems, AI Laboratory  +
Ksl tr id KSL-95-26  +
Month March  +
Note Medical Computer Science
Number KSL-95-26  +
Process note NO  +
Title Methods for Displaying Macromolecular Structural Uncertainty: Application to the Globins  +
Year 1995  +
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