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abstract

Fitting spheres to electron density

Published: 13 June 2011 Publication History

Abstract

X-ray crystallography produces molecular models (spheres for every atom of the molecule) from electron density maps (distribution of electrons over 3d space). These maps seldom have enough resolution to identify hydrogens, which are added later using simple geometric rules. For example, the structure refinement toolbox PHENIX places hydrogen at a distance of 0.82 AA from the bonded oxygen nucleus, while the structure validation toolbox Molprobity places this hydrogen at a distance of 1 AA from the bonded oxygen. To harmonize these numbers we wanted to use bond lengths that were consistent with the electron density maps based on quantum calculations and hence at a higher resolution than experimentally determined maps. In this video we describe geometric tools based on curvature and contour trees for identifying spherical patches on the iso-surfaces of electron density. These tools allow us to determine lengths of hydrogen covalent bonds from high resolution electron density maps.

References

[1]
P. D. Adams et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Cryst. D, 66(2):213--221, Feb 2010.
[2]
P. V. Afonine, M. Mustyakimov, R. W. Grosse-Kunstleve, N. W. Moriarty, P. Langan, and P. D. Adams. Joint X-ray and neutron refinement with phenix.refine. Acta Crystallographica Section D, 66(11):1153--1163, Nov 2010.
[3]
H. Carr, J. Snoeyink, and U. Axen. Computing contour trees in all dimensions. Comp. Geom.: Theory Appl., 24:75--94, 2003.
[4]
V. B. Chen et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Cryst. D, 66(1):12--21, Jan 2010.
[5]
I. W. Davis and V. B. Chen. King. http://kinemage.biochem.duke.edu/software/king.php.
[6]
W. E. Lorensen and H. E. Cline. Marching cubes: A high resolution 3d surface construction algorithm. Comp Graphics, 21(4):163--169, 1987. (SIGGRAPH).
[7]
V. Natarajan, Y. Wang, P.-T. Bremer, V. Pascucci, and B. Hamann. Segmenting molecular surfaces. CAGD, 23(6):495--509, 2006.
[8]
G. M. Sheldrick. A short history of SHELX. Acta Crystallographica Section A, 64(1):112--122, Jan 2008.

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cover image ACM Conferences
SoCG '11: Proceedings of the twenty-seventh annual symposium on Computational geometry
June 2011
532 pages
ISBN:9781450306829
DOI:10.1145/1998196

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 13 June 2011

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Author Tags

  1. contour tree
  2. curvature
  3. sphere fitting
  4. structural biology
  5. surface segmentation

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SoCG '11
SoCG '11: Symposium on Computational Geometry
June 13 - 15, 2011
Paris, France

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Overall Acceptance Rate 625 of 1,685 submissions, 37%

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