Averaged kick maps: less noise, more signal…and probably less bias

Journal Article · Tue Sep 01 00:00:00 EDT 2009 · Acta Crystallographica. Section D: Biological Crystallography

DOI:https://doi.org/10.1107/S0907444909021933· OSTI ID:22347951

Pražnikar, Jure ^[1]; Afonine, Pavel V. ^[2]; Gunčar, Gregor ^[1]; Adams, Paul D. ^[2]; Turk, Dušan ^[1]

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1. Jožef Stefan Institute (Slovenia)
2. Lawrence Berkeley National Laboratory, Berkeley (United States)

Averaged kick maps are the sum of a series of individual kick maps, where each map is calculated from atomic coordinates modified by random shifts. These maps offer the possibility of an improved and less model-biased map interpretation. Use of reliable density maps is crucial for rapid and successful crystal structure determination. Here, the averaged kick (AK) map approach is investigated, its application is generalized and it is compared with other map-calculation methods. AK maps are the sum of a series of kick maps, where each kick map is calculated from atomic coordinates modified by random shifts. As such, they are a numerical analogue of maximum-likelihood maps. AK maps can be unweighted or maximum-likelihood (σ{sub A}) weighted. Analysis shows that they are comparable and correspond better to the final model than σ{sub A} and simulated-annealing maps. The AK maps were challenged by a difficult structure-validation case, in which they were able to clarify the problematic region in the density without the need for model rebuilding. The conclusion is that AK maps can be useful throughout the entire progress of crystal structure determination, offering the possibility of improved map interpretation.

• OSTI ID: 22347951
• Journal Information: Acta Crystallographica. Section D: Biological Crystallography, Vol. 65, Issue Pt 9; Other Information: PMCID: PMC2733881; PMID: 19690370; PUBLISHER-ID: dz5160; OAI: oai:pubmedcentral.nih.gov:2733881; Copyright (c) Pražnikar et al. 2009; This is an open-access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.; Country of input: International Atomic Energy Agency (IAEA); ISSN 0907-4449
• Country of Publication: Denmark
• Language: English

Related Subjects

75 CONDENSED MATTER PHYSICS
SUPERCONDUCTIVITY AND SUPERFLUIDITY
ANNEALING
ATOMS
CALCULATION METHODS
CRYSTAL STRUCTURE
CRYSTALS
DENSITY
NOISE
VALIDATION