Crystal structure refinement with SHELXL
01 Jan 2015-Acta Crystallographica Section C-crystal Structure Communications (International Union of Crystallography)-Vol. 71, Iss: 1, pp 3-8
TL;DR: New features added to the refinement program SHELXL since 2008 are described and explained.
Abstract: The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.
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TL;DR: This work automates routine small-molecule structure determination starting from single-crystal reflection data, the Laue group and a reasonable guess as to which elements might be present.
Abstract: The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution extended if necessary. All space groups in the specified Laue group are tested to find which are consistent with the P1 phases. After applying the resulting origin shifts and space-group symmetry, the solutions are subject to further dual-space recycling followed by a peak search and summation of the electron density around each peak. Elements are assigned to give the best fit to the integrated peak densities and if necessary additional elements are considered. An isotropic refinement is followed for non-centrosymmetric space groups by the calculation of a Flack parameter and, if appropriate, inversion of the structure. The structure is assembled to maximize its connectivity and centred optimally in the unit cell. SHELXT has already solved many thousand structures with a high success rate, and is optimized for multiprocessor computers. It is, however, unsuitable for severely disordered and twinned structures because it is based on the assumption that the structure consists of atoms.
17,039 citations
Cites background or methods from "Crystal structure refinement with S..."
...This structure was published by Barkley et al. (2011) in the noncentrosymmetric space group P62c, but there are two warning signs: checkCIF (Spek, 2009) detects an inversion centre (a B alert) and the Flack parameter is dubious: the current SHELXL (Sheldrick, 2015) gives a value of 0.46 (11)....
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...This is similar to the CGLS refinement in SHELXL (Sheldrick, 2008, 2015) and is performed in parallel....
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TL;DR: The creation, maintenance, information content and availability of the Cambridge Structural Database (CSD), the world’s repository of small molecule crystal structures, are described.
Abstract: The Cambridge Structural Database (CSD) contains a complete record of all published organic and metal–organic small-molecule crystal structures. The database has been in operation for over 50 years and continues to be the primary means of sharing structural chemistry data and knowledge across disciplines. As well as structures that are made public to support scientific articles, it includes many structures published directly as CSD Communications. All structures are processed both computationally and by expert structural chemistry editors prior to entering the database. A key component of this processing is the reliable association of the chemical identity of the structure studied with the experimental data. This important step helps ensure that data is widely discoverable and readily reusable. Content is further enriched through selective inclusion of additional experimental data. Entries are available to anyone through free CSD community web services. Linking services developed and maintained by the CCDC, combined with the use of standard identifiers, facilitate discovery from other resources. Data can also be accessed through CCDC and third party software applications and through an application programming interface.
6,313 citations
Cites methods from "Crystal structure refinement with S..."
...The embedding of reflection data into the CIF by structure refinement programs such as SHELXL (Sheldrick, 2015) greatly simplifies this process....
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TL;DR: The SQUEEZE method is documents as an alternative means of addressing the solvent disorder issue and conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL, and many twinned structures containing disordered solvents are now also treatable by SQUEEze.
Abstract: The completion of a crystal structure determination is often hampered by the presence of embedded solvent molecules or ions that are seriously disordered. Their contribution to the calculated structure factors in the least-squares refinement of a crystal structure has to be included in some way. Traditionally, an atomistic solvent disorder model is attempted. Such an approach is generally to be preferred, but it does not always lead to a satisfactory result and may even be impossible in cases where channels in the structure are filled with continuous electron density. This paper documents the SQUEEZE method as an alternative means of addressing the solvent disorder issue. It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015). Acta Cryst. C71. In the press] and other refinement programs that accept externally provided fixed contributions to the calculated structure factors. The PLATON SQUEEZE tool calculates the solvent contribution to the structure factors by back-Fourier transformation of the electron density found in the solvent-accessible region of a phase-optimized difference electron-density map. The actual least-squares structure refinement is delegated to, for example, SHELXL. The current versions of PLATON SQUEEZE and SHELXL now address several of the unnecessary complications with the earlier implementation of the SQUEEZE procedure that were a necessity because least-squares refinement with the now superseded SHELXL97 program did not allow for the input of fixed externally provided contributions to the structure-factor calculation. It is no longer necessary to subtract the solvent contribution temporarily from the observed intensities to be able to use SHELXL for the least-squares refinement, since that program now accepts the solvent contribution from an external file (.fab file) if the ABIN instruction is used. In addition, many twinned structures containing disordered solvents are now also treatable by SQUEEZE. The details of a SQUEEZE calculation are now automatically included in the CIF archive file, along with the unmerged reflection data. The current implementation of the SQUEEZE procedure is described, and discussed and illustrated with three examples. Two of them are based on the reflection data of published structures and one on synthetic reflection data generated for a published structure.
2,712 citations
Cites background or methods from "Crystal structure refinement with S..."
...…parameter values, the geometric parameter values themselves and the confidence factors R[F 2 > 2 (F 2)], wR(F 2) and S. Programs such as SHELXL (Sheldrick, 2008, 2015), CRYSTALS (Betteridge et al., 2003), JANA (Petřı́ček et al., 2014) and OLEX2 (Dolomanov et al., 2009) offer elaborate…...
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...It conveniently interfaces with the 2014 version of the least-squares refinement program SHELXL [Sheldrick (2015)....
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...The SQUEEZE procedure can be carried out using as input either name.cif and name.fcf data files or name.ins and name.hkl data files, where name is the chosen name for the data set [these are the usual files, respectively generated by, or used as input to, the SHELXL program (Sheldrick, 2015)]....
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...This paper describes the current SQUEEZE implementation that is based on new functionality included in the 2014 version of SHELXL (Sheldrick, 2015)....
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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 "Crystal structure refinement with S..."
...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: This hypothesis is attractive in that it provides a reasonable explanation of the further observation that the sodium efflux drops by some 20 pmole/cm2 sec when external potassium is removed, but it raises one serious difficulty which needs to be resolved.
Abstract: The experiments described in the preceding paper (Hodgkin & Keynes, 1955) show that metabolic inhibitors like dinitrophenol and cyanide produce large changes in the relative magnitude of the fluxes of potassium moving inwards and outwards across the membranes of giant axons from Sepia officinalis. For normal fibres recovering from stimulation the influx is 15-30 pmole/cm2 sec, while the efflux is 20-40 pmole/cm2 sec. On poisoning with dinitrophenol, which virtually abolishes the sodium efflux, the potassium influx is reduced to 2-3 pmole/cm2 sec, while the efflux remains the same or is slightly increased. These facts may be explained by supposing that in normal fibres there is, in addition to the passive potassium movements seen by themselves in poisoned fibres, an activeuptake ofpotassium, coupled to the extrusion ofsodium, and amounting to about 20 pmole/cm2 sec. This hypothesis is attractive in that it provides a reasonable explanation ofthe further observation that the sodium efflux drops by some 20 pmole/cm2 sec when external potassium is removed, but it raises one serious difficulty which needs to be resolved. According to the equation derived by Ussing (1949b) for independent passive transport of ions, the influx (Mi) and the efflux (M0) of a monovalent cation such as potassium should be related in the following way:
1,005 citations
"Crystal structure refinement with S..." refers background in this paper
...For over 50 years, the accepted model (Hodgkin & Keynes, 1955) for the potassium channel present in many living systems was that it involved the transport of both potassium ions and water molecules, based on the argument that adjacent binding sites could not be occupied by K+ cations because they…...
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TL;DR: A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions, which increases the possibilities for growth of the COD database and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.
Abstract: Using an open-access distribution model, the Crystallography Open Database (COD, http://www .crystallography.net) collects all known ‘small molecule / small to medium sized unit cell’ crystal structures and makes them available freely on the Internet. As of today, the COD has aggregated � 150 000 structures, offering basic search capabilities and the possibility to download the whole database, or parts thereof using a variety of standard open communication protocols. A newly developed website provides capabilities for all registered users to deposit published and so far unpublished structures as personal communications or pre-publication depositions. Such a setup enables extension of the COD database by many users simultaneously. This increases the possibilities for growth of the COD database, and is the first step towards establishing a world wide Internet-based collaborative platform dedicated to the collection and curation of structural knowledge.
826 citations
"Crystal structure refinement with S..." refers methods in this paper
...A simple solution would be for journals to require a confirmation that the full data have been deposited with the CSD (Bruno & Groom, 2014) or COD (Gražulis et al., 2012), analogous to the way in which the PDB requires deposition of the structural and reflection data before issuing a PDB ID. 2.3....
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TL;DR: A description is given of a maximum-likelihood approach to absolute structure determinations of biologically active molecules and how this approach can be applied to solve the mystery of why polyene-like structures occur in nature.
Abstract: A new probabilistic approach is introduced for the determination of the absolute structure of a compound which is known to be enantiopure based on Bijvoet-pair intensity differences. The new method provides relative probabilities for different models of the chiral composition of the structure. The outcome of this type of analysis can also be cast in the form of a new value, along with associated standard uncertainty, that resembles the value of the well known Flack x parameter. The standard uncertainty we obtain is often about half of the standard uncertainty in the value of the Flack x parameter. The proposed formalism is suited in particular to absolute configuration determination from diffraction data of biologically active (pharmaceutical) compounds where the strongest resonant scattering signal often comes from oxygen. It is shown that a reliable absolute configuration assignment in such cases can be made on the basis of Cu Kα data, and in some cases even with carefully measured Mo Kα data.
675 citations
"Crystal structure refinement with S..." refers methods in this paper
...…a substantial overestimation of the standard uncertainty of the Flack parameter, and that postrefinement methods using either a Bayesian approach (Hooft et al., 2008) or quotients or differences of the Friedel opposites as observations (Parsons et al., 2013) give more reasonable estimates of the…...
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TL;DR: 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.
Abstract: The specification of a new standard Crystallographic Information File (CIF) is described. Its development is based on the Self-Defining Text Archive and Retrieval (STAR) procedure [Hall (1991). J. Chem. Inf. Comput. Sci. 31, 326-333]. The CIF is a general, flexible and easily extensible free-format archive file; it is human and machine readable and can be edited by a simple text editor. The CIF is designed for the electronic transmission of crystallographic data between individual laboratories, journals and databases: it has been adopted by the International Union of Crystallography as the recommended medium for this purpose. The file consists of data names and data items, together with a loop facility for repeated items. The data names, constructed hierarchically so as to form data categories, are self-descriptive within a 32-character limit. The sorted list of data names, together with their precise definitions, constitutes the CIF Dictionary (Core Version 1991). The CIF Core Dictionary is presented in full and covers the fundamental and most commonly used data items relevant to crystal structure analysis. The Dictionary is also available as an electronic file suitable for CIF computer applications. Future extensions to the Dictionary will include data items used in more specialized areas of crystallography.
425 citations
"Crystal structure refinement with S..." refers background in this paper
...…insisting that experimental crystallographic data should be deposited, several leading chemical journals still only require the deposition of a CIF (Hall et al., 1991) containing just the results of the crystal structure determination and not the X-ray or neutron reflection data used to determine…...
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TL;DR: The Protein Data Bank began as a grassroots effort in 1971 and has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries.
Abstract: The Protein Data Bank began as a grassroots effort in 1971. It has grown from a small archive containing a dozen structures to a major international resource for structural biology containing more than 40000 entries. The interplay of science, technology and attitudes about data sharing have all played a role in the growth of this resource.
407 citations
"Crystal structure refinement with S..." refers methods in this paper
...The PDB (Protein Data Bank; Berman, 2008) has required the deposition of reflection data since February 2008 and virtually all journals that report biological crystal structures, including high-profile journals such as Nature and Science, require a PDB ID for the structure....
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