A short history of SHELX
01 Jan 2008-Acta Crystallographica Section A (International Union of Crystallography)-Vol. 64, Iss: 1, pp 112-122
TL;DR: 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.
Abstract: An account is given of the development of the SHELX system of computer programs from SHELX-76 to the present day. In addition to identifying useful innovations that have come into general use through their implementation in SHELX, a critical analysis is presented of the less-successful features, missed opportunities and desirable improvements for future releases of the software. An attempt is made to understand how a program originally designed for photographic intensity data, punched cards and computers over 10000 times slower than an average modern personal computer has managed to survive for so long. SHELXL is the most widely used program for small-molecule refinement and SHELXS and SHELXD are often employed for structure solution despite the availability of objectively superior programs. SHELXL also finds a niche for the refinement of macromolecules against high-resolution or twinned data; SHELXPRO acts as an interface for macromolecular applications. SHELXC, SHELXD and SHELXE are proving useful for the experimental phasing of macromolecules, especially because they are fast and robust and so are often employed in pipelines for high-throughput phasing. This paper could serve as a general literature citation when one or more of the open-source SHELX programs (and the Bruker AXS version SHELXTL) are employed in the course of a crystal-structure determination.
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TL;DR: In this paper, a large scale synthesis, crystal structure, and optical characterization of the 2D (CH3(CH2)3NH3)n−1PbnI3n+1 (n = 1, 2, 3, 4, ∞) perovskites is presented.
Abstract: The hybrid two-dimensional (2D) halide perovskites have recently drawn significant interest because they can serve as excellent photoabsorbers in perovskite solar cells. Here we present the large scale synthesis, crystal structure, and optical characterization of the 2D (CH3(CH2)3NH3)2(CH3NH3)n−1PbnI3n+1 (n = 1, 2, 3, 4, ∞) perovskites, a family of layered compounds with tunable semiconductor characteristics. These materials consist of well-defined inorganic perovskite layers intercalated with bulky butylammonium cations that act as spacers between these fragments, adopting the crystal structure of the Ruddlesden–Popper type. We find that the perovskite thickness (n) can be synthetically controlled by adjusting the ratio between the spacer cation and the small organic cation, thus allowing the isolation of compounds in pure form and large scale. The orthorhombic crystal structures of (CH3(CH2)3NH3)2(CH3NH3)Pb2I7 (n = 2, Cc2m; a = 8.9470(4), b = 39.347(2) A, c = 8.8589(6)), (CH3(CH2)3NH3)2(CH3NH3)2Pb3I10 (...
1,451 citations
01 Feb 2014
TL;DR: The crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, paving the way for the rational design of new, versatile genome-editing technologies.
Abstract: The CRISPR-associated endonuclease Cas9 can be targeted to specific genomic loci by single guide RNAs (sgRNAs). Here, we report the crystal structure of Streptococcus pyogenes Cas9 in complex with sgRNA and its target DNA at 2.5 Å resolution. The structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgRNA:DNA heteroduplex in a positively charged groove at their interface. Whereas the recognition lobe is essential for binding sgRNA and DNA, the nuclease lobe contains the HNH and RuvC nuclease domains, which are properly positioned for cleavage of the complementary and noncomplementary strands of the target DNA, respectively. The nuclease lobe also contains a carboxyl-terminal domain responsible for the interaction with the protospacer adjacent motif (PAM). This high-resolution structure and accompanying functional analyses have revealed the molecular mechanism of RNA-guided DNA targeting by Cas9, thus paving the way for the rational design of new, versatile genome-editing technologies.
1,311 citations
TL;DR: An expert system for macromolecular crystallography data reduction is presented, which builds on existing software to automate the complete data reduction process from images to merged structure factor amplitudes.
Abstract: An expert system for macromolecular crystallography data reduction is presented, which builds on existing software to automate the complete data reduction process from images to merged structure factor amplitudes. This can automatically identify multi-wedge, multi-pass and multiwavelength data sets and includes explicit procedures to test for crystallographic special cases. With the push towards high-thoughput crystallography at synchrotron beamlines and automation of structure solution, the ability to reduce data with no user input fills an important gap in the pipeline.
1,222 citations
Additional excerpts
...Despite the low anomalous form factor of sulfur at 0.9 Å (0.2 e ) phasing and density modification was successful with SHELXC, D and E (Sheldrick, 2008) thanks to the excellent data quality and high resolution....
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TL;DR: Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low‐electron density and presumed conformational disorder.
Abstract: Determination of side-chain conformations is an important step in protein structure prediction and protein design. Many such methods have been presented, although only a small number are in widespread use. SCWRL is one such method, and the SCWRL3 program (2003) has remained popular because of its speed, accuracy, and ease-of-use for the purpose of homology modeling. However, higher accuracy at comparable speed is desirable. This has been achieved in a new program SCWRL4 through: (1) a new backbone-dependent rotamer library based on kernel density estimates; (2) averaging over samples of conformations about the positions in the rotamer library; (3) a fast anisotropic hydrogen bonding function; (4) a short-range, soft van der Waals atom–atom interaction potential; (5) fast collision detection using k-discrete oriented polytopes; (6) a tree decomposition algorithm to solve the combinatorial problem; and (7) optimization of all parameters by determining the interaction graph within the crystal environment using symmetry operators of the crystallographic space group. Accuracies as a function of electron density of the side chains demonstrate that side chains with higher electron density are easier to predict than those with low-electron density and presumed conformational disorder. For a testing set of 379 proteins, 86% of χ1 angles and 75% of χ1+2 angles are predicted correctly within 40° of the X-ray positions. Among side chains with higher electron density (25–100th percentile), these numbers rise to 89 and 80%. The new program maintains its simple command-line interface, designed for homology modeling, and is now available as a dynamic-linked library for incorporation into other software programs. Proteins 2009. © 2009 Wiley-Liss, Inc.
1,217 citations
TL;DR: TOPAS and its academic variant TOPAS-Academic are nonlinear least-squares optimization programs written in the C++ programming language and their functionality and architecture are described.
Abstract: TOPAS and its academic variant TOPAS-Academic are nonlinear least-squares optimization programs written in the C++ programming language. This paper describes their functionality and architecture. The latter is of benefit to developers seeking to reduce development time. TOPAS allows linear and nonlinear constraints through the use of computer algebra, with parameter dependencies, required for parameter derivatives, automatically determined. In addition, the objective function can include restraints and penalties, which again are defined using computer algebra. Of importance is a conjugate gradient solution routine with bounding constraints which guide refinements to convergence. Much of the functionality of TOPAS is achieved through the use of generic functionality; for example, flexible peak-shape generation allows neutron time-of-flight (TOF) peak shapes to be described using generic functions. The kernel of TOPAS can be run from the command line for batch mode operation or from a closely integrated graphical user interface. The functionality of TOPAS includes peak fitting, Pawley and Le Bail refinement, Rietveld refinement, single-crystal refinement, pair distribution function refinement, magnetic structures, constant wavelength neutron refinement, TOF refinement, stacking-fault analysis, Laue refinement, indexing, charge flipping, and structure solution through simulated annealing.
1,210 citations
Cites methods from "A short history of SHELX"
...To formulate SHELX (Sheldrick, 2008, 2015) type restraints the following INP script, keywords in italic, could be used: pen_weight = 1; penalties_weighting_K1 = (Get(r_wp)/Get(r_exp))^2; do_errors_include_restraints save_best_chi2 restraint = Sqrt(w) (yt-y); where Sqrt(w) is simply the square root of the restraint weight used by SHELX....
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...To formulate SHELX (Sheldrick, 2008, 2015) type restraints the following INP script, keywords in italic, could be used: pen_weight = 1; penalties_weighting_K1 = (Get(r_wp)/Get(r_exp))^2; do_errors_include_restraints save_best_chi2 restraint = Sqrt(w) (yt-y); where Sqrt(w) is simply the square root…...
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References
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TL;DR: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics.
Abstract: CCP4mg is a project that aims to provide a general-purpose tool for structural biologists, providing tools for X-ray structure solution, structure comparison and analysis, and publication-quality graphics. The map-fitting tools are available as a stand-alone package, distributed as `Coot'.
27,505 citations
"A short history of SHELX" refers methods in this paper
...Coot (Emsley & Cowtan, 2004) can create this map directly from the SHELXL .fcf file (created using the LIST 6 instruction) and can also read and write the SHELXL .res and .ins files....
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...A64, 112–122 George M. Sheldrick A short history of SHELX 117 deposition), name.fcf [a CIF format file containing observed and calculated structure factors, suitable for direct input into a graphics program such as Coot (Emsley & Cowtan, 2004)] and name.pdb (PDB output)....
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...Although many of the options in SHELXPRO have been made obsolete by better verification tools and Coot (Emsley & Cowtan, 2004), it is still recommended for interconverting PDB and SHELX format files and preparing the first SHELXL refinement job....
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TL;DR: In this article, a phase annealing method, related to the simulated-annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution.
Abstract: A number of extensions to the multisolution approach to the crystallographic phase problem are discussed in which the negative quartet relations play an important role. A phase annealing method, related to the simulated annealing approach in other optimization problems, is proposed and it is shown that it can result in an improvement of up to an order of magnitude in the chances of solving large structures at atomic resolution. The ideas presented here are incorporated in the program system SHELX-90; the philosophical and mathematical background to the direct-methods part (SHELXS) of this system is described.
14,787 citations
TL;DR: In this article, the behaviour of the Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds.
Abstract: The behaviour of Rogers's η parameter for enantiomorph-polarity estimation is examined theoretically and experimentally on simulated intensity data for seven well-assorted compounds. An alternative parameter x, based on incoherent scattering from twin components related by a centre of symmetry, is also considered. It is found that both parameters are very well adapted to implementation in a least-squares program and converge well. The η parameter can give false and over-precise indications of chirality-polarity for structures which are nearly centrosymmetric, whereas the x parameter does not have this fault and converges more rapidly than η.
9,932 citations
"A short history of SHELX" refers background in this paper
...This possesses the flexibility necessary for handling merohedral and non-merohedral twins and enables a racemic twinning parameter to be refined to establish the correct absolute configuration (Flack, 1983)....
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10 Mar 1970
8,159 citations
"A short history of SHELX" refers background in this paper
...These days such padding is less desirable and there are excellent programs such as enCIFer (Allen et al., 2004) for working with CIF files, so CIFTAB is now effectively redundant....
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TL;DR: Geometrical validation around the Cα is described, with a new Cβ measure and updated Ramachandran plot, and Favored and allowed ϕ,ψ regions are also defined for Pro, pre‐Pro, and Gly (important because Gly ϕ‐ψ angles are more permissive but less accurately determined).
Abstract: Geometrical validation around the Calpha is described, with a new Cbeta measure and updated Ramachandran plot. Deviation of the observed Cbeta atom from ideal position provides a single measure encapsulating the major structure-validation information contained in bond angle distortions. Cbeta deviation is sensitive to incompatibilities between sidechain and backbone caused by misfit conformations or inappropriate refinement restraints. A new phi,psi plot using density-dependent smoothing for 81,234 non-Gly, non-Pro, and non-prePro residues with B < 30 from 500 high-resolution proteins shows sharp boundaries at critical edges and clear delineation between large empty areas and regions that are allowed but disfavored. One such region is the gamma-turn conformation near +75 degrees,-60 degrees, counted as forbidden by common structure-validation programs; however, it occurs in well-ordered parts of good structures, it is overrepresented near functional sites, and strain is partly compensated by the gamma-turn H-bond. Favored and allowed phi,psi regions are also defined for Pro, pre-Pro, and Gly (important because Gly phi,psi angles are more permissive but less accurately determined). Details of these accurate empirical distributions are poorly predicted by previous theoretical calculations, including a region left of alpha-helix, which rates as favorable in energy yet rarely occurs. A proposed factor explaining this discrepancy is that crowding of the two-peptide NHs permits donating only a single H-bond. New calculations by Hu et al. [Proteins 2002 (this issue)] for Ala and Gly dipeptides, using mixed quantum mechanics and molecular mechanics, fit our nonrepetitive data in excellent detail. To run our geometrical evaluations on a user-uploaded file, see MOLPROBITY (http://kinemage.biochem.duke.edu) or RAMPAGE (http://www-cryst.bioc.cam.ac.uk/rampage).
3,963 citations
"A short history of SHELX" refers background or methods in this paper
...…were deliberately left out so that backbone and side-chain torsion angles could be used for verification purposes, e.g. using the molprobity (Lovell et al., 2003) server at http://molprobity.biochem.duke.edu/, but this verification shows, especially for refinements against twinned data at…...
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...Verification of the geometry with e.g. molprobity (Lovell et al., 2003) plus warning signs from a SHELXL refinement indicate where the model may need changing or alternative conformations included....
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