DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs

Autor: Pavel V. Afonine, Ralf W. Grosse-Kunstleve, Nigel W. Moriarty, Witold R. Rudnicki, Anna Makal, Paulina M. Dominiak, Szymon Migacz, Paul D. Adams, Michal Chodkiewicz, Jarosław A. Kalinowski

Publikováno v: Journal of applied crystallography, vol 51, iss Pt 1
Chodkiewicz, ML; Migacz, S; Rudnicki, W; Makal, A; Kalinowski, JA; Moriarty, NW; et al.(2018). DiSCaMB: a software library for aspherical atom model X-ray scattering factor calculations with CPUs and GPUs:. Journal of Applied Crystallography, 51(1), 193-199. doi: 10.1107/S1600576717015825. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/7qp958sb

It has been recently established that the accuracy of structural parameters from X-ray refinement of crystal structures can be improved by using a bank of aspherical pseudoatoms instead of the classical spherical model of atomic form factors. This co

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::5273fcaedbfb129027c3eaab49262754
https://doi.org/10.1107/s1600576717015825

Macromolecular X-ray structure determination using weak, single-wavelength anomalous data

Autor: Randy J. Read, Ralf W. Grosse-Kunstleve, James M. Holton, Paul D. Adams, Airlie J. McCoy, Nathaniel Echols, Thomas C. Terwilliger, Gábor Bunkóczi

Publikováno v: Nature methods
Bunkóczi, Gábor; McCoy, Airlie J; Echols, Nathaniel; Grosse-Kunstleve, Ralf W; Adams, Paul D; Holton, James M; et al.(2015). Macromolecular X-ray structure determination using weak, single-wavelength anomalous data.. Nature methods, 12(2), 127-130. UC Office of the President: Multicampus Research Programs and Initiatives (MRPI); a funding opportunity through UC Research Initiatives (UCRI). Retrieved from: http://www.escholarship.org/uc/item/8h47k843

We describe a likelihood-based method for determining the substructure of anomalously scattering atoms in macromolecular crystals that allows successful structure determination by single-wavelength anomalous diffraction (SAD) X-ray analysis with weak

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::bcb6626296cda992efa2897c003a910c
https://doi.org/10.1038/nmeth.3212

Bulk-solvent and overall scaling revisited: faster calculations, improved results

Autor: Ralf W. Grosse-Kunstleve, Pavel V. Afonine, Alexandre Urzhumtsev, Paul D. Adams

Publikováno v: Acta Crystallographica Section D: Biological Crystallography

A fast analytical method for calculating mask-based bulk-solvent scale factors and overall anisotropic correction factors is introduced.
A fast and robust method for determining the parameters for a flat (mask-based) bulk-solvent model and overa

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::626d5a22076ed9eed4de71839152dded
https://doi.org/10.1107/s0907444913000462

Improved crystallographic models through iterated local density-guided model deformation and reciprocal-space refinement

Autor: Thomas C. Terwilliger, Paul D. Adams, Li-Wei Hung, Ralf W. Grosse-Kunstleve, Pavel V. Afonine, Axel T. Brunger, Randy J. Read

Publikováno v: Acta Crystallographica Section D: Biological Crystallography

A density-based procedure is described for improving a homology model that is locally accurate but differs globally. The model is deformed to match the map and refined, yielding an improved starting point for density modification and further model-bu

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::8bb20e85e9293a6f2c932cb67ceb0ece
https://doi.org/10.1107/s0907444912015636

Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution

Autor: Pavel V. Afonine, Paul D. Adams, David S. Richardson, Jane S. Richardson, Nathaniel Echols, Jeffrey J. Headd, Ralf W. Grosse-Kunstleve, Vincent B. Chen, Nigel W. Moriarty

Publikováno v: Acta Crystallographica Section D: Biological Crystallography
Headd, JJ; Echols, N; Afonine, PV; Grosse-Kunstleve, RW; Chen, VB; Moriarty, NW; et al.(2012). Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallographica Section D: Biological Crystallography, 68(4), 381-390. doi: 10.1107/S0907444911047834. Lawrence Berkeley National Laboratory: Retrieved from: http://www.escholarship.org/uc/item/88p5c2p4
Acta crystallographica. Section D, Biological crystallography, vol 68, iss Pt 4

Recent developments in PHENIX are reported that allow the use of reference-model torsion restraints, secondary-structure hydrogen-bond restraints and Ramachandran restraints for improved macromolecular refinement in phenix.refine at low resolution.