Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

Liebschner, Dorothee; Afonine, Pavel V.; Urzhumtsev, Alexandre G.; Adams, Paul D.

doi:10.1016/bs.mie.2020.01.007

Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix

Book · Wed Feb 12 23:00:00 EST 2020 · Methods in Enzymology

DOI:https://doi.org/10.1016/bs.mie.2020.01.007· OSTI ID:1983880

Liebschner, Dorothee ^[1]; Afonine, Pavel V. ^[1]; Urzhumtsev, Alexandre G. ^[2]; Adams, Paul D. ^[3]

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch (France); Université de Lorraine, Nancy (France)
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); University of California, Berkeley, CA (United States)

A fundamental prerequisite for implementing new procedures of atomic model refinement against neutron diffraction data is the efficient handling of hydrogen atoms. The riding hydrogen model, which constrains hydrogen atom parameters to those of the non-hydrogen atoms, is a plausible parameterization for refinements. This work describes the implementation of the riding hydrogen model in the Computational Crystallography Toolbox and in Phenix. Riding hydrogen atoms can be found in several different configurations that are characterized by specific geometries. For each configuration, the hydrogen atom parameterization and the expressions for the gradients of refinement target function with respect to non-hydrogen parameters are described.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER); US National Institutes of Health (NIH)

DOE Contract Number:: AC02-05CH11231

OSTI ID:: 1983880

Journal Information:: Methods in Enzymology, Journal Name: Methods in Enzymology Vol. 634; ISSN 0076-6879

Publisher:: Elsevier

Country of Publication:: United States

Language:: English

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References (34)

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