International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.6, p. 153

Section 3.6.6.1.2. Phasing via molecular averaging

P. M. D. Fitzgerald,a* J. D. Westbrook,b P. E. Bourne,c B. McMahon,d K. D. Watenpaughe and H. M. Bermanf

aMerck Research Laboratories, Rahway, New Jersey, USA,bProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA,cResearch Collaboratory for Structural Bioinformatics, San Diego Supercomputer Center, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0537, USA,dInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England,eretired; formerly Structural, Analytical and Medicinal Chemistry, Pharmacia Corporation, Kalamazoo, Michigan, USA, and fProtein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, New Jersey, USA
Correspondence e-mail:  paula_fitzgerald@merck.com

3.6.6.1.2. Phasing via molecular averaging

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The data items in this category are as follows:

PHASING_AVERAGING [Scheme scheme39]

The bullet ([\bullet]) indicates a category key. The arrow ([\rightarrow]) is a reference to a parent data item.

When more than one copy of a molecule is present in the asymmetric unit, phases can be improved by averaging an electron-density map over the multiple images of the molecule. In some special cases with very high noncrystallographic symmetry, de novo phases have been derived by iterative application of molecular averaging, but more often averaging is used to improve phases determined by another method.

There are many protocols used for phasing with averaging and they are very varied. It was not thought to be appropriate to specify data items for any one approach in the current version of the mmCIF dictionary. The data items that are provided allow a text-based description of the protocol to be given; a formalism for recording a fully parsable description of molecular averaging needs to be developed for future revisions of the dictionary.

Data items in the PHASING_AVERAGING category allow free-text descriptions to be given of the method used for structure determination or phase improvement using averaging over multiple observations of the molecule in the asymmetric unit and of any specific details of the application of the method to the current structure determination (Example 3.6.6.2[link]). Note that the reference to the method is to be used to describe the method itself, and not as a reference to a software package; references to software packages would be made using data items in the SOFTWARE category.

Example 3.6.6.2. Phase improvement with molecular averaging for a hypothetical structure described with data items in the PHASING_AVERAGING category.

[Scheme scheme41]








































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