Dataset Information

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

ABSTRACT: 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 (sigma(A)) weighted. Analysis shows that they are comparable and correspond better to the final model than sigma(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.

SUBMITTER: Praznikar J

PROVIDER: S-EPMC2733881 | biostudies-literature | 2009 Sep

REPOSITORIES: biostudies-literature

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

Pražnikar Jure J Afonine Pavel V PV Guncar Gregor G Adams Paul D PD Turk Dusan D

Acta crystallographica. Section D, Biological crystallography 20090806 Pt 9

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 (sigma(A)) ...[more]

PMID: 19690370

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Dataset Information

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

Publications

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

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