scholarly journals Interactive visualization tools for the structural biologist

2013 ◽  
Vol 46 (5) ◽  
pp. 1518-1520 ◽  
Author(s):  
Benjamin T. Porebski ◽  
Bosco K. Ho ◽  
Ashley M. Buckle
Keyword(s):  
Structural Biology ◽  
Data Bank ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Software Packages ◽  
Organizational Problem ◽  
Visualization Tools ◽  
Macintosh Operating System

In structural biology, management of a large number of Protein Data Bank (PDB) files and raw X-ray diffraction images often presents a major organizational problem. Existing software packages that manipulate these file types were not designed for these kinds of file-management tasks. This is typically encountered when browsing through a folder of hundreds of X-ray images, with the aim of rapidly inspecting the diffraction quality of a data set. To solve this problem, a useful functionality of the Macintosh operating system (OSX) has been exploited that allows custom visualization plugins to be attached to certain file types. Software plugins have been developed for diffraction images and PDB files, which in many scenarios can save considerable time and effort. The direct visualization of diffraction images and PDB structures in the file browser can be used to identify key files of interest simply by scrolling through a list of files.

scholarly journals Practical Aspects of the SAMPL Challenge: Providing an Extensive Experimental Data Set for the Modeling Community

2009 ◽  
Vol 14 (10) ◽  
pp. 1245-1250 ◽  
Author(s):  
Janet Newman ◽  
Vincent J. Fazio ◽  
Tom T. Caradoc-Davies ◽  
Kim Branson ◽  
Thomas S. Peat
Keyword(s):  
Evaluation Study ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Software Application ◽  
X Ray Crystallography ◽  
Software Packages ◽  
Structure Solution ◽  
Fragment Library ◽  
Extensive Experimental Data

To provide an experimental basis for a comprehensive molecular modeling evaluation study, 500 fragments from the Maybridge fragment library were soaked into crystals of bovine pancreatic trypsin and the structures determined by X-ray crystallography. The soaking experiments were performed in both single and pooled aliquots to determine if combination of fragments is an appropriate strategy. A further set of data was obtained from co-crystallizing the pooled fragments with the protein. X-ray diffraction data were collected on approximately 1000 crystals at the Australian Synchrotron, and these data were subsequently processed, and the preliminary analysis was performed with a custom software application (Jigsaw), which combines available software packages for structure solution and analysis.

scholarly journals MeshAndCollect: an automated multi-crystal data-collection workflow for synchrotron macromolecular crystallography beamlines

2015 ◽  
Vol 71 (11) ◽  
pp. 2328-2343 ◽  
Author(s):  
Ulrich Zander ◽  
Gleb Bourenkov ◽  
Alexander N. Popov ◽  
Daniele de Sanctis ◽  
Olof Svensson ◽  
...  
Keyword(s):  
Hierarchical Cluster ◽  
Data Sets ◽  
Macromolecular Crystallography ◽  
X Ray Diffraction ◽  
Data Set ◽  
X Ray ◽  
Partial Data ◽  
Final Data ◽  
Dispersion Technique

Here, an automated procedure is described to identify the positions of many cryocooled crystals mounted on the same sample holder, to rapidly predict and rank their relative diffraction strengths and to collect partial X-ray diffraction data sets from as many of the crystals as desired. Subsequent hierarchical cluster analysis then allows the best combination of partial data sets, optimizing the quality of the final data set obtained. The results of applying the method developed to various systems and scenarios including the compilation of a complete data set from tiny crystals of the membrane protein bacteriorhodopsin and the collection of data sets for successful structure determination using the single-wavelength anomalous dispersion technique are also presented.

Improved crystallographic data for graphite

2003 ◽  
Vol 18 (2) ◽  
pp. 150-154 ◽  
Author(s):  
J. Y. Howe ◽  
C. J. Rawn ◽  
L. E. Jones ◽  
H. Ow
Keyword(s):  
Powder Diffraction ◽  
Figure Of Merit ◽  
Interlayer Spacing ◽  
X Ray Diffraction ◽  
Hexagonal Cell ◽  
Data Set ◽  
X Ray ◽  
Cell Dimensions ◽  
Unit Cell Dimensions

Powder diffraction pattern of SP-1 graphite has been obtained using synchrotron X-ray diffraction. Unit cell dimensions were calculated using a least-squares analysis that refined to a |Δ2θ°| of no more than 0.007. A hexagonal cell was determined with a space group of P63/mmc (194), a=2.4617(2) and c=6.7106 (4) Å. The Smith/Synder figure of merit is 167 based upon 11 peaks, which indicates that the quality of this data set is superior to the existing PDF card for graphite, 41-1487. It is also emphasized that the interlayer spacing of graphite should be 3.355(1) Å. Using GAS and EXPGUI codes, a new set of calculated powder diffraction data based upon the interlayer spacing of 3.555 Å is generated. A comparison with the current calculated card, 75-1621, has also been made.

scholarly journals X-ray diffraction analysis of kaolin M1 and M2 via the Williamson–Hall and Warren–Averbach methods

2021 ◽  
pp. 174751982098472
Author(s):  
Lalmi Khier ◽  
Lakel Abdelghani ◽  
Belahssen Okba ◽  
Djamel Maouche ◽  
Lakel Said
Keyword(s):  
Grain Size ◽  
High Temperature ◽  
Low Temperature ◽  
Diffraction Analysis ◽  
Mechanical Resistance ◽  
X Ray Diffraction ◽  
Integral Breadth ◽  
X Ray ◽  
Mullite Phase

Kaolin M1 and M2 studied by X-ray diffraction focus on the mullite phase, which is the main phase present in both products. The Williamson–Hall and Warren–Averbach methods for determining the crystallite size and microstrains of integral breadth β are calculated by the FullProf program. The integral breadth ( β) is a mixture resulting from the microstrains and size effect, so this should be taken into account during the calculation. The Williamson–Hall chart determines whether the sample is affected by grain size or microstrain. It appears very clearly that the principal phase of the various sintered kaolins, mullite, is free from internal microstrains. It is the case of the mixtures fritted at low temperature (1200 °C) during 1 h and also the case of the mixtures of the type chamotte cooks with 1350 °C during very long times (several weeks). This result is very significant as it gives an element of explanation to a very significant quality of mullite: its mechanical resistance during uses at high temperature remains.

scholarly journals XRD Data Visualization, Processing and Analysis with d1Dplot and d2Dplot Software Packages

Proceedings ◽  
2020 ◽  
Vol 62 (1) ◽  
pp. 9
Author(s):  
Oriol Vallcorba ◽  
Jordi Rius
Keyword(s):  
Data Analysis ◽  
Data Visualization ◽  
X Ray Diffraction ◽  
Specific Data ◽  
X Ray ◽  
Software Packages ◽  
Compound Database ◽  
Synchrotron Light ◽  
User Friendly ◽  
Transformation Processes

The d1Dplot and d2Dplot computer programs have been developed as user-friendly tools for the inspection and processing of 1D and 2D X-ray diffraction (XRD) data, respectively. d1Dplot provides general tools for data processing and includes the ability to generate comprehensive 2D plots of multiple patterns to easily follow transformation processes. d2Dplot is a full package for 2D XRD data. Besides general processing tools, it includes specific data analysis routines for the application of the through-the-substrate methodology [Rius et al. IUCrJ 2015, 2, 452–463]. Both programs allow the creation of a user compound database for the identification of crystalline phases. The software can be downloaded from the ALBA Synchrotron Light Source website and can be used free of charge for non-commercial and academic purposes.

Study of the quality of GaAs thin film on Si substrate by X-ray diffraction method

1990 ◽  
Vol 7 (7) ◽  
pp. 308-311
Author(s):  
Li Chaorong ◽  
Mai Zhenhong ◽  
Cui Shufan ◽  
Zhou Junming ◽  
Yutian Wang
Keyword(s):  
Thin Film ◽  
Diffraction Method ◽  
X Ray Diffraction ◽  
Si Substrate ◽  
X Ray

scholarly journals High temperature structural study of decagonal Al-Cu-Rh quasicrystal.

2014 ◽  
Vol 70 (a1) ◽  
pp. C94-C94
Author(s):  
Pawel Kuczera ◽  
Walter Steurer
Keyword(s):  
Structural Changes ◽  
Configurational Entropy ◽  
Lattice Vibrations ◽  
X Ray Diffraction ◽  
Stabilization Mechanism ◽  
X Ray ◽  
Comparative Structure ◽  
The Stability

The structure of d(ecagonal)-Al-Cu-Rh has been studied as a function of temperature by in-situ single-crystal X-ray diffraction in order to contribute to the discussion on energy or entropy stabilization of quasicrystals (QC) [1]. The experiments were performed at 293 K, 1223 K, 1153 K, 1083 K, and 1013 K. A common subset of 1460 unique reflections was used for the comparative structure refinements at each temperature. The results obtained for the HT structure refinements of d-Al-Cu-Rh QC seem to contradict a pure phasonic-entropy-based stabilization mechanism [2] for this QC. The trends observed for the ln func(I(T1 )/I(T2 )) vs.|k⊥ |^2 plots indicate that the best on-average quasiperiodic order exists between 1083 K and 1153 K, however, what that actually means is unclear. It could indicate towards a small phasonic contribution to entropy, but such contribution is not seen in the structure refinements. A rough estimation of the hypothetic phason instability temperature shows that it would be kinetically inaccessible and thus the phase transition to a 12 Å low T structure (at ~800 K) is most likely not phason-driven. Except for the obvious increase in the amplitude of the thermal motion, no other significant structural changes, in particular no sources of additional phason-related configurational entropy, were found. All structures are refined to very similar R-values, which proves that the quality of the refinement at each temperature is the same. This suggests, that concerning the stability factors, some QCs could be similar to other HT complex intermetallic phases. The experimental results clearly show that at least the ~4 Å structure of d-Al-Cu-Rh is a HT phase therefore entropy plays an important role in its stabilisation mechanism lowering the free energy. However, the main source of this entropy is probably not related to phason flips, but rather to lattice vibrations, occupational disorder unrelated to phason flips like split positions along the periodic axis.

Crystalline and Electrical Properties of Ferroelectric Silver Niobate-tantalate thin Films

2000 ◽  
Vol 655 ◽  
Author(s):  
Jung-Hyuk Koh ◽  
S.I. Khartsev ◽  
Alex Grishin ◽  
Vladimir Petrovsky
Keyword(s):  
Temperature Stability ◽  
Frequency Dispersion ◽  
Processing Temperature ◽  
High Temperature Stability ◽  
X Ray Diffraction ◽  
Ferroelectric State ◽  
X Ray ◽  
Ferroelectric Hysteresis ◽  
First Time

AbstractFor the first time AgTa0.38Nb0.62O3 (ATN) films have been grown on the La0.7Sr0.3CoO3 (LSCO)/LaAlO3 single crystal as well as onto Pt80Ir20 (PtIr) polycrystalline substrate. Comprehensive X-ray diffraction analyses reveal epitaxial quality of ATN and LSCO films on the LaAlO3(001) substrate, while ATN/PtIr films have been found to be (001) preferentially oriented. Dielectric spectroscopy performed for ATN films and bulk ceramics in a wide temperature range 77 to 420 K shows the structural monoclinic M1-to-monoclinic M2 phase transition occurs in films at the temperature 60 °C lower than in ceramics. The tracing of the ferroelectric hysteresis P-E loops indicates the ferroelectric state in ATN films at temperatures below 125 K and yields remnant polarization of 0.4 μC/cm2 @ 77 K. Weak frequency dispersion, high temperature stability of dielectric properties as well as low processing temperature of 550 °C make ATN films to be attractive for various applications.

Characterization of Natural and Synthesized FeTiO3 Crystals With RBS/PIXE/XRD

1997 ◽  
Vol 07 (03n04) ◽  
pp. 265-275
Author(s):  
R. Q. Zhang ◽  
S. Yamamoto ◽  
Z. N. Dai ◽  
K. Narumi ◽  
A. Miyashita ◽  
...  
Keyword(s):  
Single Crystals ◽  
Ion Beam ◽  
Pressure Control ◽  
Floating Zone ◽  
X Ray Diffraction ◽  
X Ray ◽  
Beam Analysis ◽  
Ppm Level

Natural FeTiO 3 (illuminate) and synthesized FeTiO 3, single crystals were characterized by Rutherford backscattering spectroscopy combined with channeling technique and particle-induced x-ray emission (RBS-C and PIXE). The results obtained by the ion beam analysis were supplemented by the x-ray diffraction analysis to identify the crystallographic phase. Oriented single crystals of synthesized FeTiO 3 were grown under the pressure control of CO 2 and H 2 mixture gas using a single-crystal floating zone technique. The crystal quality of synthesized FeTiO 3 single crystals could be improved by the thermal treatment but the exact pressure control is needed to avoid the precipitation of Fe 2 O 3 even during the annealing procedure. Natural FeTiO 3 contains several kinds of impurities such as Mn , Mg , Na and Si . The synthesized samples contain Al , Si and Na which are around 100 ppm level as impurities. The PBS-C results of the natural sample imply that Mn impurities occupy the Fe sublattice in FeTiO 3 or in mixed phase between ilmenite and hematite.

scholarly journals Purification, crystallization and preliminary X-ray diffraction analysis of the effector protein PevD1 fromVerticillium dahliae

2012 ◽  
Vol 68 (7) ◽  
pp. 802-805 ◽  
Author(s):  
Lei Han ◽  
Zheng Liu ◽  
Xinqi Liu ◽  
Dewen Qiu
Keyword(s):  
Pathogenic Fungus ◽  
Sodium Formate ◽  
Diffusion Method ◽  
Effector Protein ◽  
X Ray Diffraction ◽  
Hanging Drop ◽  
Dispersion Method ◽  
Data Set ◽  
X Ray ◽  
Anomalous Signal

The effector protein PevD1 from the pathogenic fungusVerticillium dahliaewas purified and crystallized using the hanging-drop vapour-diffusion method. Native crystals appeared in a solution consisting of 4.0 Msodium formate. A native data set was collected at 1.9 Å resolution at 100 K using an in-house X-ray source. Because of the absence of useful methinione in the protein sequence, derivative crystals that contained iodine were obtained by soaking in 1.25 Mpotassium iodide, and a data set that contained anomalous signal was collected using the same X-ray facility at a wavelength of 1.54 Å. The single-wavelength anomalous dispersion method was used to successfully solve the structure based on the anomalous signal generated from iodine.

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