Acta Crystallographica Section D

Biological Crystallography

Volume 65, Part 9 (September 2009)

research papers

Acta Cryst. (2009). D65, 921-931 [ doi:10.1107/S0907444909021933 ]

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

J. Praznikar, P. V. Afonine, G. Guncar, P. D. Adams and D. Turk

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.

Keywords: kick maps; OMIT maps; density-map calculation; model bias; maximum likelihood.