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inria-00100701, version 1

Direct phasing by binary integer programming

Vladimir Y. Lunin a, Alexandre Urzhumtsev b, Alexander Bockmayr () c1

N° A01-R-307 || lunin01a (2001)

Résumé : The phase problem is one of the major problems in crystallography. In the absence of phase information, a variety of electron density distributions is consistent with the observed magnitudes. This ambiguity may be reduced significantly if the distribution values are restricted to 0 or 1 values, i.e. when the object of search is an envelope rather than a continuous electron density distribution. The density values are linked to the observed magnitudes and unknown phases by a system of non­linear equations. We present a method to replace these equations by a system of linear inequalities. As a consequence, powerful tools of integer linear programming may be applied to solve the phase problem. This novel approach was tested on calculated and experimental data for a known protein structure. At the moment, the size of the grid for the envelope calculation is the major limitation of the approach. Nevertheless, even for a very small grid, some structure information can be extracted and used as a starting point for further phase improvement or as a way to solve the molecular replacement problem.

  • a –  MOSCOW, RUSSIA
  • b –  UHP NANCY
  • c –  UNIVERSITE HENRI POINCARE
  • 1 :  MODBIO (INRIA Lorraine - LORIA)
  • INRIA – CNRS : UMR7503 – Université Henri Poincaré - Nancy I – Université Nancy II – Institut National Polytechnique de Lorraine (INPL)
  • Domaine : Informatique/Autre
  • Mots-clés : integer programming – crystallography – phasing || programmation entière – cristallographie – phasage
  • Référence interne : A01-R-307 || lunin01a
  • Commentaire : Rapport interne.
 
  • inria-00100701, version 1
  • oai:hal.inria.fr:inria-00100701
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  • Soumis le : Mardi 26 Septembre 2006, 14:49:48
  • Dernière modification le : Jeudi 28 Septembre 2006, 15:22:47