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: On the basis of the powder second-harmonic generation (SHG) measurement, BiSr(3)(YO)(3)(BO(3))(4) belongs to the phase-matchable class with a SHG response of about 3 × KDP.
Abstract: The synthesis, crystal structure, crystal growth, and characterization of a new noncentrosymmetric rare-earth borate BiSr3(YO)3(BO3)4 are reported. BiSr3(YO)3(BO3)4 belongs to gaudefroyite type of ...
26 citations
TL;DR: Two series of eight polycarboxylate lanthanide coordination complexes, namely, [Ln(cpia)2]·4H2O {Ln = Eu (4), Gd (5), Tb (6), Er (7), and Lu (8), have been synthesized by self-assembly and characterized by IR, thermogravimetric analysis, and X-ray crystallography.
Abstract: Two series of eight polycarboxylate lanthanide coordination complexes, namely, [Ln(cpia)(H2O)2]·4H2O {Ln = Ce (1), Nd (2), and Sm (3)} and [Ln(cpia)(H2O)n]2·2H2O {Ln = Eu (4), Gd (5), Tb (6), Er (7), and Lu (8), n = 5 in 4–7; n = 4 in 8} {H3cpia = N-[4-(carboxymethoxy)phenyl]iminodiacetic acid}, have been synthesized by self-assembly and characterized by IR, thermogravimetric analysis, and X-ray crystallography. Complexes 1–3 are isomorphic featuring two-dimensional double layer structures, while the isomorphic complexes 4–8 exhibit [2 + 2] rectangle metallomacrocycle structures. Further, photoluminescence (PL) spectra of complexes 2, 4, and 6 show the strong characteristic luminescence of Eu(III), Tb(III), and Nd(III) ions, respectively, suggesting that cpia3– is able to efficiently sensitize the luminescence of lanthanide ions.
26 citations
TL;DR: In this article, three pyridyl functionalized bis(pyrazol-1-yl)methanes were synthesized by the reactions of (2-hydroxyphenyl)bis(Pyrazol 1-yl)-methane with chloromethylpyridine.
Abstract: Three pyridyl functionalized bis(pyrazol-1-yl)methanes, namely 2-[(4-pyridyl)methoxyphenyl] bis(pyrazol-1-yl)methane (L1), 2-[(4-pyridyl)methoxyphenyl]bis(3,5-dimethylpyrazol-1-yl)methane (L2) and 2-[(3-pyridyl)methoxyphenyl]bis(pyrazol-1-yl)methane (L3) have been synthesized by the reactions of (2-hydroxyphenyl)bis(pyrazol-1-yl)methanes with chloromethylpyridine. Treatment of these three ligands with R2SnCl2 (R = Et, n-Bu or Ph) yields a series of symmetric 2:1 adducts of (L)2SnR2Cl2 (L = L1, L2 or L3), which have been confirmed by elemental analysis and NMR spectroscopy. The crystal structures of (L2)2Sn(n-Bu)2Cl2·0.5C6H14 and (L3)2SnEt2Cl2 determined by X-ray crystallography show that the functionalized bis(pyrazol-1-yl)methane acts as a monodentate ligand through the pyridyl nitrogen atom, and the pyrazolyl nitrogen atoms do not coordinate to the tin atom. The cytotoxic activity of these complexes for Hela cells in vitro was tested. Copyright © 2010 John Wiley & Sons, Ltd.
26 citations
TL;DR: In this article, the lattice parameters were determined by least-squares refinement of 18 reflections from powder X-ray diffraction data obtained from the annealed PdGa sample.
Abstract: PdGa, cubic, P213 (no. 198), a = 4.89695(6) Å, V = 117.4 Å, Z = 4, Rgt(F) = 0.024, wRref(F) = 0.035, T = 295 K. Source of material Large single crystals of PdGa were obtained by Czochralski growth from the melt as described in [1]. The melt consisted of Pd (99.9 %, ChemPur) and Ga (99.99 %, ChemPur) in an atomic ratio of 45:55. The metals were pre-reacted in glassy carbon crucibles under inert argon atmosphere in a high-frequency induction furnace. Single crystals used in this study were obtained from the bottom of the as grown Czochralski crystal and were annealed at 800 °C for 24 h in dynamic vacuum at 10 mbar prior to the X-ray diffraction experiments. For the lattice parameter determination a small part of the bottom of the large crystal was crushed and annealed as described above. WDXS measurements were performed on a CAMECA SX100 (W filament, 25 kV) with Pd50Ga50 (by chemical analysis via ICP-OES) as standard. Experimental details Single crystal data were collected using a Rigaku R-axis SPIDER diffractometer with monochromated Ag K+ radiation. Determination and refinement of the crystal structure were performed with the SHELX-97 software [2]. Spence [3] defined the two absolute structures of the FeSi type as form A (Fe in 4a with x = 0.1358, Si in 4a with x = 0.844) and form B (Fe in 4a with x = 0.8642, Si in 4a with x = 0.156). Models of both absolute structures were refined for PdGa without twin model and resulted in considerable differences in Rgt,A = 0.028 and Rgt,B = 0.040, respectively. Further refinement of form A as inversion twin resulted in a Flack parameter of 0.05(1), confirming the proper parameter set. Refining site occupancy for both atoms resulted in fully occupied sites within one e.s.d. This excludes mutual site occupation in the crystal as is expected due to the covalent interactions in the compound [4]. To verify the absolute structure refinement, the mean-square Friedel intensity difference was determined according to Flack and Shmueli [5]. The resulting value of 10 ( = 261 is sufficiently high to confirm the selected set of parameters and setting of the crystal structure. The lattice parameters were determined by least-squares refinement of 18 reflections from powder X-ray diffraction data obtained from the annealed PdGa sample (Huber Image Plate Guinier camera G670, Cu K+1 radiation, ! = 1.540562 Å, LaB6 as internal standard, a = 4.15692 Å, WinCSD [6]). WDXS measurements resulted in a composition of Pd51.3(4)Ga48.7(4).
26 citations
Cites methods from "A short history of SHELX"
...: 196.20 cm−1 Diffractometer, scan mode: Rigaku R-axis SPIDER, % 2,max: 99.64° N(hkl)measured, N(hkl)unique: 2834, 765 Criterion for Iobs, N(hkl)gt: Iobs > 2 )(Iobs), 714 N(param)refined: 9 Programs: SHELXL-97 [2], WinCSD [5] Table 1....
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...Determination and refinement of the crystal structure were performed with the SHELX-97 software [2]....
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...64° N(hkl)measured, N(hkl)unique: 2834, 765 Criterion for Iobs, N(hkl)gt: Iobs > 2 )(Iobs), 714 N(param)refined: 9 Programs: SHELXL-97 [2], WinCSD [5] Table 1....
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TL;DR: In this article, a series of TiO 2 -supported copper(I) dyes, [Cu(L anchor ) (L ancillary )] + with L anchor ǫ= 2,2′:4′,4″:2″,2‴-quaterpyridine (1), 4,4′-bis(6-methyl-[2,2-bipyridin]-4-yl)-1,1′-Biphenyl (2 ), or 4,6′-dimethyl]-2, 2′-b
26 citations
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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