scholarly journals Understanding conductivity in molecular switches: a real space approach in octaphyrins

2016 ◽  
Vol 18 (17) ◽  
pp. 11829-11838 ◽  
Author(s):  
T. Woller ◽  
N. Ramos-Berdullas ◽  
M. Mandado ◽  
M. Alonso ◽  
F. de Proft ◽  
...  
Keyword(s):  
Electron Density ◽  
Molecular Switches ◽  
Real Space ◽  
Expanded Porphyrins ◽  
Space Approach

In recent years, expanded porphyrins have emerged as a promising class of π-conjugated switches whose conductance is studied from the electron density.

Ab initio structure determination of cytochrome c6 by combined reciprocal space-real space approach

2003 ◽  
Vol 218 (1) ◽  
Author(s):  
K. Chowdhury ◽  
S. Ghosh ◽  
M. Mukherjee
Keyword(s):  
Cytochrome C ◽  
Ab Initio ◽  
Structure Determination ◽  
Direct Method ◽  
Real Space ◽  
Reciprocal Space ◽  
Cytochrome C6 ◽  
Ab Initio Structure ◽  
Space Approach

AbstractThe direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c

Positrons in metals: A real-space approach

1979 ◽  
Vol 20 (1) ◽  
pp. 21-32 ◽  
Author(s):  
Pierre F. Maldague
Keyword(s):  
Real Space ◽  
Space Approach

Validation of carbohydrate structures: not just nomenclature

2014 ◽  
Vol 70 (a1) ◽  
pp. C1481-C1481
Author(s):  
Jon Agirre ◽  
Kevin Cowtan
Keyword(s):  
Protein Data Bank ◽  
Correlation Coefficient ◽  
Electron Density ◽  
Systematic Study ◽  
Data Bank ◽  
Real Space ◽  
Space Correlation ◽  
Structure Factors ◽  
Ring Distortion ◽  
Experimental Electron Density

Despite the key implications carbohydrates have in a multitude of pathological processes, a large number of the sugar-containing structures deposited into the Protein Data Bank (PDB) show nomenclature errors [1] that persist even after the remediation of the PDB archive [2]. Here we present the results from a systematic study of the conformation and ring distortion of cyclic carbohydrate models for which structure factors have been deposited into the PDB. These models have also been scored using a real-space correlation coefficient calculated between model and experimental electron density. The results have enabled us to produce a database of well-refined carbohydrate structures for use in the framework of an automated sugar-detecting software, to be announced shortly.

EDMA: a computer program for topological analysis of discrete electron densities

2012 ◽  
Vol 45 (3) ◽  
pp. 575-580 ◽  
Author(s):  
Lukáš Palatinus ◽  
Siriyara Jagannatha Prathapa ◽  
Sander van Smaalen
Keyword(s):  
Computer Program ◽  
Electron Density ◽  
Critical Points ◽  
Topological Analysis ◽  
Three Dimensional ◽  
Real Space ◽  
Principal Curvatures ◽  
Electron Densities ◽  
Structure Solution ◽  
Aperiodic Crystals

EDMAis a computer program for topological analysis of discrete electron densities according to Bader's theory of atoms in molecules. It locates critical points of the electron density and calculates their principal curvatures. Furthermore, it partitions the electron density into atomic basins and integrates the volume and charge of these atomic basins.EDMAcan also assign the type of the chemical element to atomic basins based on their integrated charges. The latter feature can be used for interpretation ofab initioelectron densities obtained in the process of structure solution. A particular feature ofEDMAis that it can handle superspace electron densities of aperiodic crystals in arbitrary dimensions.EDMAfirst generates real-space sections at a selected set of phases of the modulation wave, and subsequently analyzes each section as an ordinary three-dimensional electron density. Applications ofEDMAto model electron densities have shown that the relative accuracy of the positions of the critical points, the electron densities at the critical points and the Laplacian is of the order of 10−4or better.

A real space approach to study the effect of off-diagonal disorder on superconductivity

2010 ◽  
Vol 470 (15-16) ◽  
pp. 640-647 ◽  
Author(s):  
Shreemoyee Ganguly ◽  
Indra Dasgupta ◽  
Abhijit Mookerjee
Keyword(s):  
Real Space ◽  
Diagonal Disorder ◽  
Space Approach

Software for handling macromolecular envelopes

1999 ◽  
Vol 55 (4) ◽  
pp. 941-944 ◽  
Author(s):  
G. Jacob Kleywegt ◽  
Thomas A. Jones
Keyword(s):  
Electron Density ◽  
Local Density ◽  
Computer Programs ◽  
Real Space ◽  
Atomic Model ◽  
Density Correlation ◽  
Phase Extension ◽  
Crystallographic Symmetry ◽  
Averaging Techniques ◽  
Electron Density Averaging

Macromolecular phase-refinement and phase-extension calculations using real-space electron-density averaging techniques require accurate envelopes (or masks) to define the boundaries of each domain or molecule whose density is to be averaged. An extensive set of tools, implemented in four computer programs (O, MAMA, COMA and MASKIT) are described which can be used to generate such envelopes (either from an atomic model or based on local density-correlation maps), to improve them, to remove overlap owing to crystallographic or non-crystallographic symmetry, to display them and to manipulate them in a variety of manners.

scholarly journals Statistical quality indicators for electron-density maps

2012 ◽  
Vol 68 (4) ◽  
pp. 454-467 ◽  
Author(s):  
Ian J. Tickle
Keyword(s):  
Electron Density ◽  
Statistical Significance ◽  
Significance Test ◽  
Real Space ◽  
Structure Model ◽  
Space Correlation ◽  
The Real ◽  
Difference Density ◽  
Density Maps ◽  
The Difference

The commonly used validation metrics for the local agreement of a structure model with the observed electron density, namely the real-space R (RSR) and the real-space correlation coefficient (RSCC), are reviewed. It is argued that the primary goal of all validation techniques is to verify the accuracy of the model, since precision is an inherent property of the crystal and the data. It is demonstrated that the principal weakness of both of the above metrics is their inability to distinguish the accuracy of the model from its precision. Furthermore, neither of these metrics in their usual implementation indicate the statistical significance of the result. The statistical properties of electron-density maps are reviewed and an improved alternative likelihood-based metric is suggested. This leads naturally to a χ2 significance test of the difference density using the real-space difference density Z score (RSZD). This is a metric purely of the local model accuracy, as required for effective model validation and structure optimization by practising crystallographers prior to submission of a structure model to the PDB. A new real-space observed density Z score (RSZO) is also proposed; this is a metric purely of the model precision, as a substitute for other precision metrics such as the B factor.

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