ALIXE: a phase-combination tool for fragment-based molecular replacement

Acta Crystallographica. Section D, Structural Biology
Claudia MillánIsabel Usón

Abstract

Fragment-based molecular replacement exploits the use of very accurate yet incomplete search models. In the case of the ARCIMBOLDO programs, consistent phase sets produced from the placement and refinement of fragments with Phaser can be combined in order to increase their signal before proceeding to the step of density modification and autotracing with SHELXE. The program ALIXE compares multiple phase sets, evaluating mean phase differences to determine their common origin, and subsequently produces sets of combined phases that group consistent solutions. In this work, its use on different scenarios of very partial molecular-replacement solutions and its performance after the development of a much-optimized set of algorithms are described. The program is available both standalone and integrated within the ARCIMBOLDO programs. ALIXE has been analysed to identify its rate-limiting steps while exploring the best parameterization to improve its performance and make this software efficient enough to work on modest hardware. The algorithm has been parallelized and redesigned to meet the typical landscape of solutions. Analysis of pairwise correlation between the phase sets has also been explored to test whether this would provide ad...Continue Reading

References

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Mar 14, 2018·Acta Crystallographica. Section D, Structural Biology·Iracema CaballeroIsabel Usón
Mar 14, 2018·Acta Crystallographica. Section D, Structural Biology·Isabel Usón, George M Sheldrick
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Apr 14, 2018·Acta Crystallographica. Section D, Structural Biology·Claudia MillánIsabel Usón
May 3, 2018·Acta Crystallographica. Section D, Structural Biology·Richard J Gildea, Graeme Winter
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Ana MedinaMassimo D Sammito

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Citations

Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Rafael Junqueira BorgesIsabel Usón
Mar 7, 2020·Acta Crystallographica. Section D, Structural Biology·Ana MedinaMassimo D Sammito
Aug 4, 2020·Acta Crystallographica. Section D, Structural Biology·Logan S RichardsJose A Rodriguez
Oct 7, 2020·Acta Crystallographica. Section D, Structural Biology·Filomeno Sánchez RodríguezDaniel J Rigden

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Software Mentioned

_ SHREDDER
ALIXE
CHESCAT
ALEPH
CCP4
PyPI
Debian
LITE
CCP
BORGES

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