scholarly journals Exploiting structure similarity in refinement: automated NCS and target-structure restraints in BUSTER

2012 ◽  
Vol 68 (4) ◽  
pp. 368-380 ◽  
Author(s):  
Oliver S. Smart ◽  
Thomas O. Womack ◽  
Claus Flensburg ◽  
Peter Keller ◽  
Włodek Paciorek ◽  
...  
Keyword(s):  
Functional Form ◽  
Cyclic Peptide ◽  
Structure Refinement ◽  
Structural Similarity ◽  
Peptide Ligand ◽  
Macromolecular Structure ◽  
Target Structure ◽  
X Ray ◽  
Structure Similarity ◽  
The Difference

Maximum-likelihood X-ray macromolecular structure refinement in BUSTER has been extended with restraints facilitating the exploitation of structural similarity. The similarity can be between two or more chains within the structure being refined, thus favouring NCS, or to a distinct `target' structure that remains fixed during refinement. The local structural similarity restraints (LSSR) approach considers all distances less than 5.5 Å between pairs of atoms in the chain to be restrained. For each, the difference from the distance between the corresponding atoms in the related chain is found. LSSR applies a restraint penalty on each difference. A functional form that reaches a plateau for large differences is used to avoid the restraints distorting parts of the structure that are not similar. Because LSSR are local, there is no need to separate out domains. Some restraint pruning is still necessary, but this has been automated. LSSR have been available to academic users of BUSTER since 2009 with the easy-to-use -autoncs and -target target.pdb options. The use of LSSR is illustrated in the re-refinement of PDB entries 5rnt, where -target enables the correct ligand-binding structure to be found, and 1osg, where -autoncs contributes to the location of an additional copy of the cyclic peptide ligand.

Structure refinement of the layered composite crystal Sc2B1.1C3.2 in a five-dimensional formalism

2001 ◽  
Vol 57 (4) ◽  
pp. 449-457 ◽  
Author(s):  
Mitsuko Onoda ◽  
Ying Shi ◽  
A. Leithe-Jasper ◽  
Takaho Tanaka
Keyword(s):  
Structural Parameters ◽  
Structure Refinement ◽  
Three Dimensional ◽  
Layered Composite ◽  
Layered Compound ◽  
X Ray Diffraction ◽  
X Ray ◽  
Composite Crystal ◽  
The Difference ◽  
Insight Into

The crystal structure of a layered compound Sc2B1.1C3.2, scandium boride carbide (M r = 140.43), has been re-refined as a commensurate composite crystal using 1795 single-crystal X-ray diffraction intensities with I > 2\sigma(I) collected by Shi, Leithe-Jasper, Bourgeois, Bando & Tanaka [(1999), J. Solid State Chem. 148, 442–449]. The crystal is composed of two layered subsystem structures, i.e. Sc—C—Sc sandwiches and graphite-like layers of the composition B1/3C2/3. The structure refinement was performed in a five-dimensional formalism based on the trigonal superspace group P\bar{3}m1(p00)(0p0)0m0. The unit cell and other crystal data are a = b = 3.387 (1), c = 6.703 (2) Å, V = 66.59 (1) Å3, \boldsigma_{1} = (9/7 0 0), \boldsigma_{2} = (0 9/7 0), Z = 1, D x = 3.501 Mg m−1. Two different three-dimensional sections through the superspace were analyzed, corresponding to two different superstructure models, one with P\bar{3}m1 and the other with P\bar{3}m1. A random distribution of B and C was assumed in the graphite-like layer and 41 structural parameters were introduced. R F /wR F } were 0.0533/0.0482 and 0.0524/0.0476, respectively, for the first and second models. Although the difference between these R F or wR F values was too fine to exclude one of the models definitely, the advantages of using a superspace group were obvious. It not only brought about better convergence of refinement cycles by virtue of fewer parameters, but also gave an insight into the problem of symmetry of the superstructure.

Inclusion of weak high-resolution X-ray data for improvement of a group II intron structure

2010 ◽  
Vol 66 (9) ◽  
pp. 988-1000 ◽  
Author(s):  
Jimin Wang
Keyword(s):  
Structure Refinement ◽  
Group Ii Intron ◽  
Macromolecular Structure ◽  
X Ray ◽  
Solvent Models ◽  
Acceptable Quality ◽  
Experimental Phasing ◽  
Intron Structure ◽  
Group Ii

It is common to report the resolution of a macromolecular structure with the highest resolution shell having an averaged I/σ(I) ≥ 2. Data beyond the resolution thus defined are weak and often poorly measured. The exclusion of these weak data may improve the apparent statistics and also leads to claims of lower resolutions that give some leniency in the acceptable quality of refined models. However, the inclusion of these data can provide additional strong constraints on atomic models during structure refinement and thus help to correct errors in the original models, as has recently been demonstrated for a protein structure. Here, an improved group II intron structure is reported arising from the inclusion of these data, which helped to define more accurate solvent models for density modification during experimental phasing steps. With the improved resolution and accuracy of the experimental phases, extensive revisions were made to the original models such that the correct tertiary interactions of the group II intron that are essential for understanding the chemistry of this ribozyme could be described.

Quaternion Model of Fast Video Quality Assessment Based on Structural Similarity Normalization

2013 ◽  
Vol 380-384 ◽  
pp. 3982-3985
Author(s):  
Gang Li ◽  
Ainiwaer Aizimaiti ◽  
Yan Liu
Keyword(s):  
Video Processing ◽  
Quality Evaluation ◽  
Video Quality ◽  
Structural Similarity ◽  
Similarity Comparison ◽  
Data Set ◽  
Contour Feature ◽  
Structure Similarity ◽  
The Difference ◽  
Video Quality Evaluation

Video quality evaluation methods have been widely studied because of an increasing need in variety of video processing applications, such as compression, analysis, communication, enhancement and restoration. The quaternion models are also widely used to measure image or video quality. In this paper, we proposed a new quaternion model which mainly describes the contour feature, surface feature and temporal information of the video. We use structure similarity comparison to normalize four quaternion parts respectively, because each part of the quaternion use different metric. Structure similarity comparison is also used to measure the difference between reference videos and distortion videos. The results of experiments show that the new method has good correlation with perceived video quality when tested on the video quality experts group (VQEG) Phase I FR-TV test data set.

Difference Fourier Analysis of Glucose Embedded and Frozen Hydrated Purple Membrane

1982 ◽  
Vol 40 ◽  
pp. 74-75
Author(s):  
Jules S. Jaffe ◽  
Robert M. Glaeser
Keyword(s):  
Purple Membrane ◽  
Data Set ◽  
High Resolution Data ◽  
X Ray ◽  
X Ray Crystallography ◽  
Fourier Techniques ◽  
Versus Protein ◽  
The Difference ◽  
Difference Fourier ◽  
Ideal Method

Although difference Fourier techniques are standard in X-ray crystallography it has only been very recently that electron crystallographers have been able to take advantage of this method. We have combined a high resolution data set for frozen glucose embedded Purple Membrane (PM) with a data set collected from PM prepared in the frozen hydrated state in order to visualize any differences in structure due to the different methods of preparation. The increased contrast between protein-ice versus protein-glucose may prove to be an advantage of the frozen hydrated technique for visualizing those parts of bacteriorhodopsin that are embedded in glucose. In addition, surface groups of the protein may be disordered in glucose and ordered in the frozen state. The sensitivity of the difference Fourier technique to small changes in structure provides an ideal method for testing this hypothesis.

Antiphase Boundaries in Ordered Ni3FE Crystals

1969 ◽  
Vol 27 ◽  
pp. 62-63
Author(s):  
Y. H. Liu
Keyword(s):  
Domain Size ◽  
Antiphase Domain ◽  
X Ray Diffraction ◽  
X Ray ◽  
Hardening Mechanism ◽  
Superlattice Structure ◽  
Disordered Phase ◽  
Domain Boundaries ◽  
Atomic Scattering ◽  
The Difference

Ordered Ni3Fe crystals possess a LI2 type superlattice similar to the Cu3Au structure. The difference in slip behavior of the superlattice as compared with that of a disordered phase has been well established. Cottrell first postulated that the increase in resistance for slip in the superlattice structure is attributed to the presence of antiphase domain boundaries. Following Cottrell's domain hardening mechanism, numerous workers have proposed other refined models also involving the presence of domain boundaries. Using the anomalous X-ray diffraction technique, Davies and Stoloff have shown that the hardness of the Ni3Fe superlattice varies with the domain size. So far, no direct observation of antiphase domain boundaries in Ni3Fe has been reported. Because the atomic scattering factors of the elements in NijFe are so close, the superlattice reflections are not easily detected. Furthermore, the domain configurations in NioFe are thought to be independent of the crystallographic orientations.

X-ray Structure Refinement and Vibrational Spectroscopy of Ca8Gd2 (PO4)6 O2

2013 ◽  
Vol 12 (10) ◽  
pp. 719-726
Author(s):  
R. Ayadi ◽  
Mohamed Boujelbene ◽  
T. Mhiri
Keyword(s):  
Solid State ◽  
General Formula ◽  
Vibrational Spectroscopy ◽  
Powder Diffraction ◽  
Infrared Spectra ◽  
Solid State Reaction ◽  
Structure Refinement ◽  
Unit Cell ◽  
Cell Group ◽  
X Ray

The present paper is interested in the study of compounds from the apatite family with the general formula Ca10 (PO4)6A2. It particularly brings to light the exploitation of the distinctive stereochemistries of two Ca positions in apatite. In fact, Gd-Bearing oxyapatiteCa8 Gd2 (PO4)6O2 has been synthesized by solid state reaction and characterized by X-ray powder diffraction. The site occupancies of substituents is0.3333 in Gd and 0.3333 for Ca in the Ca(1) position and 0. 5 for Gd in the Ca (2) position.  Besides, the observed frequencies in the Raman and infrared spectra were explained and discussed on the basis of unit-cell group analyses.

scholarly journals Deep learning for visualization and novelty detection in large X-ray diffraction datasets

2021 ◽  
Vol 7 (1) ◽  
Author(s):  
Lars Banko ◽  
Phillip M. Maffettone ◽  
Dennis Naujoks ◽  
Daniel Olds ◽  
Alfred Ludwig
Keyword(s):  
Thin Film ◽  
Crystal Structure ◽  
Artificial Intelligence ◽  
Deep Learning ◽  
Novelty Detection ◽  
Structural Similarity ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Patterns ◽  
Post Hoc

AbstractWe apply variational autoencoders (VAE) to X-ray diffraction (XRD) data analysis on both simulated and experimental thin-film data. We show that crystal structure representations learned by a VAE reveal latent information, such as the structural similarity of textured diffraction patterns. While other artificial intelligence (AI) agents are effective at classifying XRD data into known phases, a similarly conditioned VAE is uniquely effective at knowing what it doesn’t know: it can rapidly identify data outside the distribution it was trained on, such as novel phases and mixtures. These capabilities demonstrate that a VAE is a valuable AI agent for aiding materials discovery and understanding XRD measurements both ‘on-the-fly’ and during post hoc analysis.

scholarly journals Ability of radiofrequency echographic multispectrometry to identify osteoporosis status in elderly women with type 2 diabetes

2021 ◽  
Author(s):  
Carla Caffarelli ◽  
Maria Dea Tomai Pitinca ◽  
Antonella Al Refaie ◽  
Elena Ceccarelli ◽  
Stefano Gonnelli
Keyword(s):  
Type 2 Diabetes ◽  
Lumbar Spine ◽  
Elderly Women ◽  
Fragility Fractures ◽  
Dual Energy ◽  
Healthy Controls ◽  
Diagnosis Of Osteoporosis ◽  
X Ray ◽  
The Difference

Abstract Background Patients with type 2 diabetes (T2DM) have an increased or normal BMD; however fragility fractures represent one of the most important complications of T2DM. Aims This study aimed to evaluate whether the use of the Radiofrequency Echographic multi spectrometry (REMS) technique may improve the identification of osteoporosis in T2DM patients. Methods In a cohort of 90 consecutive postmenopausal elderly (70.5 ± 7.6 years) women with T2DM and in 90 healthy controls we measured BMD at the lumbar spine (LS-BMD), at femoral neck (FN-BMD) and total hip (TH-BMD) using a dual-energy X-ray absorptiometry device; moreover, REMS scans were also carried out at the same axial sites. Results DXA measurements were all higher in T2DM than in non-T2DM women; instead, all REMS measurements were lower in T2DM than in non T2DM women. Moreover, the percentage of T2DM women classified as “osteoporotic”, on the basis of BMD by REMS was markedly higher with respect to those classified by DXA (47.0% vs 28.0%, respectively). On the contrary, the percentage of T2DM women classified as osteopenic or normal by DXA was higher with respect to that by REMS (48.8% and 23.2% vs 38.6% and 14.5%, respectively). T2DM women with fragility fractures presented lower values of both BMD-LS by DXA and BMD-LS by REMS with respect to those without fractures; however, the difference was significant only for BMD-LS by REMS (p < 0.05). Conclusions Our data suggest that REMS technology may represent a useful approach to enhance the diagnosis of osteoporosis in patients with T2DM.

scholarly journals Morphological consistency of bilateral hip joints in adults based on the X-ray and CT data

2021 ◽  
Author(s):  
Ran Zhao ◽  
Hong Cai ◽  
Hua Tian ◽  
Ke Zhang
Keyword(s):  
Hip Joint ◽  
Morphological Difference ◽  
Medullary Cavity ◽  
Size Difference ◽  
Single Plane ◽  
X Ray ◽  
Stem Size ◽  
The Difference ◽  
Ct Data ◽  
Anatomical Parameters

Abstract Purpose The application of the anatomical parameters of the contralateral hip joint to guide the preoperative template of the affected side relies on the bilateral hip symmetry. We investigated the bilateral hip symmetry and range of anatomical variations by measurement and comparison of bilateral hip anatomical parameters. Methods This study included 224 patients (448 hips) who were diagnosed with osteoarthritis (OA) and avascular necrosis (AVN) of the femur head, and underwent bilateral primary total hip arthroplasty (THA) in our hospital from January 2012 to August 2020. Imaging data included 224 patients X-ray and 30 CT data at the end of the cohort. Anatomical parameters, including the acetabular abduction angle and trochanteric height, were measured using the Noble method. Postoperative measurements included stem size, difference of leg length and offset. Results Except for the isthmus width, there were no significant differences in the anatomical morphology of the hip joint. Among the demographic factors, there was a correlation between body weight and NSA. Among various anatomical parameters, a correlation was present between medullary cavity widths of T + 20, T, and T − 20. The difference in the use of stem size is not due to the morphological difference of bilateral medullary cavity, but due to the different of 1- or 2-stage surgery. Conclusion Bilateral symmetry was present among the patients with normal morphology of the hip medullary cavity, theoretically confirming the feasibility of structural reconstruction of the hip joint using the hip joint on the uninjured side. Additionally, the difference in the morphology of the hip medullary cavity is not present in a single plane but is synergistically affected by multiple adjacent planes.

Structure Investigations of Agonists of the Natural Neurotransmitter Acetylcholine, IV [1]. X-Ray Structure Analyses of Trimethylpentylammonium-chloride and (4-Acetoxybutyl) trimethylammonium-iodide

1986 ◽  
Vol 41 (5-6) ◽  
pp. 618-626
Author(s):  
Alfred Gieren ◽  
Michail Kokkinidis
Keyword(s):  
Structure Refinement ◽  
Pharmacological Action ◽  
Ammonium Nitrogen ◽  
Carbonyl Oxygen ◽  
Type B ◽  
Orthorhombic Space Group ◽  
Space Group ◽  
X Ray ◽  
Structure Investigations ◽  
Automatic Diffractometer

The crystal structures of the title compounds which display cholinergic activity at the ganglionic receptor have been determined by X-ray structure analysis. [(CH3)3N+C5H11]Cl- (1) crystallizes in the orthorhombic space group Pbnm with half a formula unit per asymmetric unit, a = 11.381(14). b = 12.871(17), c = 7.316(4) Å. The intensities of 1106 independent reflections were collected with an automatic diffractometer. The structure refinement converged at R = 0.133 for the 355 observed reflections. The cation of 1 is disordered. [(CH3)3N + (CH2)4-O-C(O)-CH3]I- (2) crystallizes in the orthorhombic space group P212121 with four formula units per unit cell, a = 16.783(8), b = 10.276(6), c = 7.427(10) Å. The intensities of 1469 independent reflections were collected. The structure refinement converged at R = 0.071 for 1383 observed reflections. In both compounds the trimethylammonio methyl groups are coordinated nearly tetrahedrally by four anions in the first coordination sphere. Anions which occupy a special face type (B) of the tetrahedron of the (CH3)3N+ -CH2-group may be treated as a “model binding site” of the receptor. In the crystal structure of 2 the anions occupying B-type faces form together with the ammonium nitrogen and the carbonyl oxygen so called “Activity triangles”. The almost equal geometries of these activity triangles are correlated with the mode of pharmacological action.

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