scholarly journals Electron density map as an aid in the sequencing of peptides.

1973 ◽  
Vol 70 (6) ◽  
pp. 1793-1794 ◽  
Author(s):  
M. J. Adams ◽  
G. C. Ford ◽  
P. J. Lentz ◽  
A. Liljas ◽  
M. G. Rossmann
Keyword(s):  
Electron Density ◽  
Density Map ◽  
Electron Density Map

A Comparison of Two Algorithms for Electron-Density Map Improvement by Introduction of Atomicity: Skeletonization, and Map Sorting Followed by Refinement

1998 ◽  
Vol 54 (1) ◽  
pp. 81-85 ◽  
Author(s):  
F. M. D. Vellieux
Keyword(s):  
Electron Density ◽  
Initial Density ◽  
Acta Cryst ◽  
Density Maps ◽  
Resolution Electron ◽  
Crystallographic Symmetry ◽  
Density Map ◽  
Ornithine Transcarbamoylase ◽  
Electron Density Map ◽  
Pseudo Atom

A comparison has been made of two methods for electron-density map improvement by the introduction of atomicity, namely the iterative skeletonization procedure of the CCP4 program DM [Cowtan & Main (1993). Acta Cryst. D49, 148–157] and the pseudo-atom introduction followed by the refinement protocol in the program suite DEMON/ANGEL [Vellieux, Hunt, Roy & Read (1995). J. Appl. Cryst. 28, 347–351]. Tests carried out using the 3.0 Å resolution electron density resulting from iterative 12-fold non-crystallographic symmetry averaging and solvent flattening for the Pseudomonas aeruginosa ornithine transcarbamoylase [Villeret, Tricot, Stalon & Dideberg (1995). Proc. Natl Acad. Sci. USA, 92, 10762–10766] indicate that pseudo-atom introduction followed by refinement performs much better than iterative skeletonization: with the former method, a phase improvement of 15.3° is obtained with respect to the initial density modification phases. With iterative skeletonization a phase degradation of 0.4° is obtained. Consequently, the electron-density maps obtained using pseudo-atom phases or pseudo-atom phases combined with density-modification phases are much easier to interpret. These tests also show that for ornithine transcarbamoylase, where 12-fold non-crystallographic symmetry is present in the P1 crystals, G-function coupling leads to the simultaneous decrease of the conventional R factor and of the free R factor, a phenomenon which is not observed when non-crystallographic symmetry is absent from the crystal. The method is far less effective in such a case, and the results obtained suggest that the map sorting followed by refinement stage should be by-passed to obtain interpretable electron-density distributions.

Electron-density maps

2002 ◽  
Author(s):  
David Blow
Keyword(s):  
Fourier Transform ◽  
Electron Density ◽  
Three Dimensional ◽  
Two Dimensions ◽  
Unit Cell ◽  
Density Maps ◽  
Wave Cycle ◽  
Density Map ◽  
The Fourier Transform ◽  
Electron Density Map

When everything has been done to make the phases as good as possible, the time has come to examine the image of the structure in the form of an electron-density map. The electron-density map is the Fourier transform of the structure factors (with their phases). If the resolution and phases are good enough, the electron-density map may be interpreted in terms of atomic positions. In practice, it may be necessary to alternate between study of the electron-density map and the procedures mentioned in Chapter 10, which may allow improvements to be made to it. Electron-density maps contain a great deal of information, which is not easy to grasp. Considerable technical effort has gone into methods of presenting the electron density to the observer in the clearest possible way. The Fourier transform is calculated as a set of electron-density values at every point of a three-dimensional grid labelled with fractional coordinates x, y, z. These coordinates each go from 0 to 1 in order to cover the whole unit cell. To present the electron density as a smoothly varying function, values have to be calculated at intervals that are much smaller than the nominal resolution of the map. Say, for example, there is a protein unit cell 50 Å on a side, at a routine resolution of 2Å. This means that some of the waves included in the calculation of the electron density go through a complete wave cycle in 2 Å. As a rule of thumb, to represent this properly, the spacing of the points on the grid for calculation must be less than one-third of the resolution. In our example, this spacing might be 0.6 Å. To cover the whole of the 50 Å unit cell, about 80 values of x are needed; and the same number of values of y and z. The electron density therefore needs to be calculated on an array of 80×80×80 points, which is over half a million values. Although our world is three-dimensional, our retinas are two-dimensional, and we are good at looking at pictures and diagrams in two dimensions.

Electron density map of chicken heart cytosol aspartate transaminase at 3.5 Å resolution

Nature ◽  
1980 ◽  
Vol 284 (5752) ◽  
pp. 189-190 ◽  
Author(s):  
V. V. Borisov ◽  
S. N. Borisova ◽  
N. I. Sosfenov ◽  
B. K. Vainshtein
Keyword(s):  
Electron Density ◽  
Aspartate Transaminase ◽  
Chicken Heart ◽  
Density Map ◽  
Electron Density Map

Solution of organic crystal structures from powder diffraction by combining simulated annealing and direct methods

2003 ◽  
Vol 36 (2) ◽  
pp. 230-238 ◽  
Author(s):  
Angela Altomare ◽  
Rocco Caliandro ◽  
Carmelo Giacovazzo ◽  
Anna Grazia Giuseppina Moliterni ◽  
Rosanna Rizzi
Keyword(s):  
Monte Carlo ◽  
Simulated Annealing ◽  
Electron Density ◽  
Powder Diffraction ◽  
Direct Methods ◽  
Molecular Geometry ◽  
Molecular Structures ◽  
Chemical Information ◽  
Density Map ◽  
Electron Density Map

Theab initiocrystal structure solution from powder diffraction data can be attemptedviadirect methods. If heavy atoms are present, they are usually correctly located; then some crystal chemical information can be exploited to complete the partial structure model. Organic structures are more resistant to direct methods; as an alternative, their molecular geometry is used as prior information for Monte Carlo methods. In this paper, a new procedure is described which combines the information contained in the electron density map provided by direct methods with a Monte Carlo method which uses simulated annealing as a minimization algorithm. A figure of merit has been designed based on the agreement between the experimental and calculated profiles, and on the positions of the peaks in the electron density map. The procedure is completely automatic and has been included inEXPO; its performance has been validated and tested for a set of known molecular structures.

scholarly journals Intrachain antiferromagnetic exchange in a 1D branched-chain built of two different copper(ii) centres interlinked by end-on azido and phenoxo bridges: electron density map, electrochemical and magnetic properties

RSC Advances ◽  
2015 ◽  
Vol 5 (74) ◽  
pp. 59926-59934 ◽  
Author(s):  
Farzaneh Fadaee ◽  
Mehdi Amirnasr ◽  
Krunoslav Prša ◽  
Philip Pattison ◽  
Noore Elahi Shaik ◽  
...  
Keyword(s):  
Magnetic Properties ◽  
Coordination Polymer ◽  
Electron Density ◽  
Antiferromagnetic Exchange ◽  
Density Map ◽  
Electrochemical And Magnetic Properties ◽  
Branched Chain ◽  
Electron Density Map

A 1D, end-on azido- and phenoxo-bridged, coordination polymer, [Cu2(μ-NAPPR)(μ1,1-N3)2]n (1), (NAPPR2− = 1,3-bis(naphthylideneimino)propane dianion), was synthesized and characterized.

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