scholarly journals ShelXle: a Qt graphical user interface forSHELXL

2011 ◽  
Vol 44 (6) ◽  
pp. 1281-1284 ◽  
Author(s):  
Christian B. Hübschle ◽  
George M. Sheldrick ◽  
Birger Dittrich

ShelXleis a graphical user interface forSHELXL[Sheldrick, G. M. (2008).Acta Cryst.A64, 112–122], currently the most widely used program for small-molecule structure refinement. It combines an editor with syntax highlighting for theSHELXL-associated .ins (input) and .res (output) files with an interactive graphical display for visualization of a three-dimensional structure including the electron density (Fo) and difference density (Fo–Fc) maps. Special features ofShelXleinclude intuitive atom (re-)naming, a strongly coupled editor, structure visualization in various mono and stereo modes, and a novel way of displaying disorder extending over special positions.ShelXleis completely compatible with all features ofSHELXLand is written entirely in C++ using the Qt4 and FFTW libraries. It is available at no cost for Windows, Linux and Mac-OS X and as source code.

IUCrData ◽  
2019 ◽  
Vol 4 (8) ◽  
Author(s):  
Patrick Butler

The title tetranuclear stannoxane, [Sn4(C6H5)8(C6H4NO3)4O2]·1.5CHCl3·solvent, crystallized with two independent complex molecules, A and B, in the asymmetric unit together with 1.5 molecules of chloroform. There is also a region of disordered electron density, which was corrected for using the SQUEEZE routine [Spek (2015). Acta Cryst. C71, 9–18]. The oxo-tin core of each complex is in a planar `ladder' arrangement and each Sn atom is fivefold SnO3C2 coordinated, with one tin centre having an almost perfect square-pyramidal coordination geometry, while the other three Sn centres have distorted shapes. In the crystal, the complex molecules are arranged in layers, composed of A or B complexes, lying parallel to the bc plane. The complex molecules are linked by a number of C—H...O hydrogen bonds within the layers and between the layers, forming a supramolecular three-dimensional structure.


2000 ◽  
Vol 33 (1) ◽  
pp. 176-183 ◽  
Author(s):  
Guoguang Lu

In order to facilitate the three-dimensional structure comparison of proteins, software for making comparisons and searching for similarities to protein structures in databases has been developed. The program identifies the residues that share similar positions of both main-chain and side-chain atoms between two proteins. The unique functions of the software also include database processingviaInternet- and Web-based servers for different types of users. The developed method and its friendly user interface copes with many of the problems that frequently occur in protein structure comparisons, such as detecting structurally equivalent residues, misalignment caused by coincident match of Cαatoms, circular sequence permutations, tedious repetition of access, maintenance of the most recent database, and inconvenience of user interface. The program is also designed to cooperate with other tools in structural bioinformatics, such as the 3DB Browser software [Prilusky (1998).Protein Data Bank Q. Newslett.84, 3–4] and the SCOP database [Murzin, Brenner, Hubbard & Chothia (1995).J. Mol. Biol.247, 536–540], for convenient molecular modelling and protein structure analysis. A similarity ranking score of `structure diversity' is proposed in order to estimate the evolutionary distance between proteins based on the comparisons of their three-dimensional structures. The function of the program has been utilized as a part of an automated program for multiple protein structure alignment. In this paper, the algorithm of the program and results of systematic tests are presented and discussed.


Author(s):  
Dilovan S. Cati ◽  
Helen Stoeckli-Evans

The title compounds, C32H28N10O4· unknown solvent, (I), and C32H28N10O4, (II), are pyrazine-2,3,5,6-tetracarboxamide derivatives. In (I), the substituents are (pyridin-2-ylmethyl)carboxamide, while in (II), the substituents are (pyridin-4-ylmethyl)carboxamide. Both compounds crystallize in the monoclinic space groupP21/n, withZ′ = 1 for (I), andZ′ = 0.5 for (II). The whole molecule of (II) is generated by inversion symmetry, the pyrazine ring being situated about a center of inversion. In (I), the four pyridine rings are inclined to the pyrazine ring by 83.9 (2), 82.16 (18), 82.73 (19) and 17.65 (19)°. This last dihedral angle involves a pyridine ring that is linked to the adjacent carboxamide O atom by an intramolecular C—H...O hydrogen bond. In compound (II), the unique pyridine rings are inclined to the pyrazine ring by 33.3 (3) and 81.71 (10)°. There are two symmetrical intramolecular C—H...O hydrogen bonds present in (II). In the crystal of (I), molecules are linked by N—H...O and N—H...N hydrogen bonds, forming layers parallel to (10-1). The layers are linked by C—H...O and C—H...N hydrogen bonds, forming a three-dimensional framework. In the crystal of (II), molecules are linked by N—H...N hydrogen bonds, forming chains propagating along the [010] direction. The chains are linked by a weaker N—H...N hydrogen bond, forming layers parallel to the (101) plane, which are in turn linked by C—H...O hydrogen bonds, forming a three-dimensional structure. In the crystal of compound (I), a region of disordered electron density was treated with the SQUEEZE routine inPLATON[Spek (2015).Acta Cryst. C71, 9–18]. Their contribution was not taken into account during refinement. In compound (II), one of the pyridine rings is positionally disordered, and the refined occupancy ratio for the disordered Car—Car—Npyatoms is 0.58 (3):0.42 (3).


2016 ◽  
Author(s):  
Richard Bruskiewich ◽  
Kenneth Huellas-Bruskiewicz ◽  
Farzin Ahmed ◽  
Rajaram Kaliyaperumal ◽  
Mark Thompson ◽  
...  

AbstractKnowledge.Bio is a web platform that enhances access and interpretation of knowledge networks extracted from biomedical research literature. The interaction is mediated through a collaborative graphical user interface for building and evaluating maps of concepts and their relationships, alongside associated evidence. In the first release of this platform, conceptual relations are drawn from the Semantic Medline Database and the Implicitome, two compleme ntary resources derived from text mining of PubMed abstracts.Availability— Knowledge.Bio is hosted at http://knowledge.bio/ and the open source code is available at http://bitbucket.org/sulab/kb1/.Contact— [email protected]; [email protected]


1995 ◽  
Vol 50 (9) ◽  
pp. 1377-1381 ◽  
Author(s):  
Olaf Reckeweg ◽  
H.-Jürgen Meyer

AbstractThe new compounds A4[Nb6Cl12(N3)6](H2O)2 (A = Rb, Cs) were synthesized from In4[Nb6Cl12Cl6] by substituting six terminal Cl ligands and the In+ ions in methanolic solution. An X-ray structure refinement was performed on single-crystal data of Rb4[Nb6Cl12(N3)6](H2O)2 (1) (space group P1̄, Z = 1, a = 912.5(1) pm, b = 937.2(1) pm, c = 1062.0(1) pm, α = 96.88(2)°, β = 101.89(1)°, γ = 101.44(2)°) and Cs4[Nb6Cl12(N3)6](H2O)2 (2) (space group PI, Z = 1, a = 920.9(5) pm, b = 947.9(7) pm, c = 1091.8(7) pm, α = 96.89(6)°, β = 103.35(5)°, γ = 101.60(5)°. Each of the centrosymmetric [Nb6Cl12(N3)6]4- ions of the isotypic compounds contains six terminal azide groups at the corners of the octahedral niobium cluster (d̄Nb-N = 226(1) pm (1), 225(1) pm (2), bond angles Nb-N-N 120-127°). The [Nb6Cl12(N3)6]4- ions are linked via Rb-N and Rb-Cl interactions of the Rb+ ions to form a three-dimensional structure. Crystals of the compounds react explosively on heating or mechanical pressure.


Author(s):  
Barbara Modec

Single crystals of a triclinic polymorphic form ofmer-μ-oxalato-bis[chloridotripyridinecobalt(II)] pyridine disolvate, [Co2(C2O4)Cl2(C5H5N)6]·2C5H5N, have been prepared by solvothermal methods. The structure and geometric parameters strongly resemble those of the previously reported monoclinic polymorph [Bolte (2006).Acta Cryst.E62, m597–m598]. In both polymorphic forms, the dinuclear complex molecules are located on a crystallographic centre of inversion, with the CoIIcations in a distorted octahedral environment consisting of a chloride ligand, three pyridine ligands and a chelating bis-bidentate oxalate ligand. This last serves as a bridging ligand between two CoIIcations. The polymorphs differ in the mutual orientation of their pyridine ligands in the dinuclear molecules and in their intermolecular connectivity. In the triclinic polymorph, C—H...O, C—H...Cl, C—H...π and π–π interactions link the dinuclear molecules into a three-dimensional structure. Pyridine solvent molecules are attached to this structureviaweak interactions.


1995 ◽  
Vol 1995 (1) ◽  
pp. 61-66 ◽  
Author(s):  
Mark Reed ◽  
Henrik Rye

ABSTRACT A comprehensive model of the dynamic, three-dimensional physical fates of contaminants in the marine environment has been developed. For oil spills, dissolution of aromatics from surface slicks and entrained oil droplets are the source of potential effects for biota in the water column. Oil on the surface and along shorelines provides the basis for evaluation of impacts on birds, marine mammals, and recreational activities. A graphical user interface couples the model to a variety of environmental databases and tools to facilitate specific applications and viewing of simulation results.


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