The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected
@article{Bourhis2015TheAO, title={The anatomy of a comprehensive constrained, restrained refinement program for the modern computing environment – Olex2 dissected}, author={Luc J. Bourhis and Oleg V. Dolomanov and Richard J. Gildea and Judith A. K. Howard and Horst Puschmann}, journal={Acta Crystallographica. Section A, Foundations and Advances}, year={2015}, volume={71}, pages={59 - 75} }
An in-depth presentation is given of olex2.refine, the new refinement engine integrated in the Olex2 program.
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References
SHOWING 1-10 OF 53 REFERENCES
Structure refinement: some background theory and practical strategies
- Computer Science
- 2008
This paper aims to discuss well established algorithms in nonmathematical language, with the intention of enabling crystallographers to use their favourite programs effectively.
REFMAC5 for the refinement of macromolecular crystal structures
- ChemistryActa crystallographica. Section D, Biological crystallography
- 2011
The general principles behind the macromolecular crystal structure refinement program REFMAC5 are described.
PHENIX: a comprehensive Python-based system for macromolecular structure solution
- ChemistryActa crystallographica. Section D, Biological crystallography
- 2010
The PHENIX software for macromolecular structure determination is described and its uses and benefits are described.
Towards automated crystallographic structure refinement with phenix.refine
- ChemistryActa crystallographica. Section D, Biological crystallography
- 2012
This paper presents an overview of the major phenix.refine features, with extensive literature references for readers interested in more detailed discussions of the methods.
Efficient anisotropic refinement of macromolecular structures using FFT.
- ChemistryActa crystallographica. Section D, Biological crystallography
- 1999
All the tests show that anisotropic refinement not only reduces the R value and Rfree but also improves the fit to geometric targets, indicating that this parameterization is valuable for improving models derived from experimental data.
A short history of SHELX.
- ChemistryActa crystallographica. Section A, Foundations of crystallography
- 2008
This paper could serve as a general literature citation when one or more of the open-source SH ELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
CRYSTALS version 12: software for guided crystal structure analysis
- Materials Science, Chemistry
- 2003
The determination of small-molecule structures from single-crystal X-ray data is being carried out by researchers with little or no crys- tallographic training. At the same time, completely automatic…
The crystallographic information file (CIF) : a new standard archive file for crystallography
- Computer Science
- 1991
The specification of a new standard Crystallographic Information File (CIF) is described, based on the Self-Defining Text Archive and Retrieval (STAR) procedure, and the CIF Core Dictionary is presented in full.
On structure refinement using data from a twinned crystal
- Chemistry
- 1982
Refinements leading to accurate structural parameters are possible by using the measured data F2o of a twinned crystal with exactly superimposed reciprocal lattices and accumulating the sum for the n…
Atomic Dispacement Parameter Nomenclature. Report of a Subcommittee on Atomic Displacement Parameter Nomenclature
- Geology
- 1996
Modern X-ray and neutron diffraction techniques can give precise parameters that describe dynamic or static displacements of atoms in crystals. However, confusing and inconsistent terms and symbols…