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2 edition of Heavy atom crystal structures interpretation of the Patterson function by computer. found in the catalog.

Heavy atom crystal structures interpretation of the Patterson function by computer.

Hans van der Meer

Heavy atom crystal structures interpretation of the Patterson function by computer.

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Published by s.n. in [s.l .
Written in English

    Subjects:
  • Crystallography -- Data processing.,
  • Crystallography, Mathematical.

  • The Physical Object
    Pagination73 p. :
    Number of Pages73
    ID Numbers
    Open LibraryOL15160479M

    The book shows how an understanding of crystal structures, both inorganic and organic may be built up from simple ideas of atomic and molecular packing. Beginning with (two dimensional) examples of patterns and tilings, the concepts of lattices, symmetry point and space groups are developed.   A twinned crystal is an aggregate in which different domains are joined together according to a specific symmetry operation: the twin law. The diffraction patterns derived from different domains are rotated, reflected or inverted with respect to each other, depending on the nature of the relationship between the different domains, and weighted according to the quantity of a particular . The process begins with datafiles .sca,.hkl, etc) containing amplitudes (or intensities) of structure factors, a sequence file, the wavelength of the X-rays used in data collection, and the anomalously-scattering atom or atoms in the crystal. The AutoSol Wizard identifies heavy-atom sites, calculates phases, carries out density modification.


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Heavy atom crystal structures interpretation of the Patterson function by computer. by Hans van der Meer Download PDF EPUB FB2

Automated computer interpretation of the Patterson function using superposition techniques provides an effective way of locating heavy atoms in small moiety structures, and — normally from isomorphous or anomalous difference data — also in by: 4. Patterson methods are often the first choice for the solution of structures containing a few heavy atoms.

The initial information provided by the identification of the correct atomic position of the heavy atom and some of the other atoms allows one to begin to calculate structure factors. Comparing parent and heavy atom data sets.

30 The upper and lower images are two precession photographs, showing the l=0 level of reciprocal space. The upper is the original protein crystal. The lower is after soaking in heavy atom solution.

Note changes in intensity. the heavy atoms from those vectors and afterwards finding the remaining atoms. Though convenient, the heavy atom method is not absolutely necessary to solve a complex small-molecule structure.

Since a Patterson map contains multiple images of the structure, superposition of multiple copies of the map shifted by an interatomic. On the basis of a generalized symmetry minimum function several computer-oriented methods for interpreting Patterson functions and for locating the position of heavy-atom fragments in crystals.

Automated computer interpretation of the Patterson function using superposition techniques provides an effective way of locating heavy atoms in small moiety structures, and — normally from. The Patterson Function The Patterson function can be computed from the experimental data No phase information is needed The Patterson function is a 3 dimensional ‘map’ with maxima corresponding to inter atomic vectors Huh.

If you have an atom at x 1 and x 2, The Patterson function will have peaks at 0,0,0 (x 1-x 1 ; x 2 -x 2) x 1-x 2 x 2-x 1.

The Patterson Function •The Patterson function can be computed from the experimental data –No phase information is needed •The Patterson function is a 3 Heavy atom crystal structures interpretation of the Patterson function by computer. book ‘map’ with maxima corresponding to inter atomic vectors –Huh.

–If you have an atom at x 1 and x 2, The Patterson function will have peaks at •0,0,0 (x 1-x 1 ; x 2 -x. In each method, trial partial structures for heavy or anomalously scattering atoms are often obtained by the inspection of difference-Patterson functions or by semiautomated analysis.

These initial structures are refined against the observed data and are used to generate initial phases. and a collection of papers is found in a book by Rossmann [9]. The more recent direct-space computer programs dedicated to ab initio solution of crystal structures from powder diffraction data are all commercial, with GUIs (Graphical User Interfaces) for MS Windows, and with the consequence that access to the source code is lost.

Crystallography Made Crystal Clear is designed to meet the need for an X-ray analysis that is between brief textbook sections and complete treatments. The book provides non-crystallographers with an intellectually satisfying explanation of the principles of how protein models are gleaned from X-ray analysis.

The understanding of these concepts will foster wise use of the models, including the 4/5(1). Extensive discussion of crystals and lattices, symmetry, crystal systems and geometry, x-ray diffraction, determination of atomic positions, and more.

Well-chosen selection of problems, with answers. Ideal for crystallography course or as supplement to physical chemistry courses. illustrations. edition. and sulfur atoms by computer interpretation of the super-sharpened Patterson vector superposition mini-mum function [8], followed by automatic iterative expansion to the full structure [9], without the need for interactive graphics etc.

Cytochrome c6 fulfilled all. Interpretation of crystal structure determinations Huub Kooijman each atom behaves as a point scatterer of X-radiation. 1 Any periodic function can be described as the sum of a series of sine and cosine terms, differing in the order n.

The coefficients cn of the terms are. Scheme of a Patterson function derived from a crystal containing three atoms in the unit cell. To obtain this function graphically from a known crystal structure (left figure) all possible interatomic vectors are plotted (center figure).

These vectors are then moved parallel to themselves to the origin of the Patterson unit cell (right figure). The first textbook for teaching this method to users with little mathematical background logically presents the theory and fundamentals in an easily comprehensible, self-contained way.

The result is a must-have for advanced undergraduate students, as well as masters and graduate students and Price: $ • To solve a heavy atom structure using the Patterson interpretation program PATTY. The only required input data are the crystal data and reflection data. After location of the heavy atoms (which could include S or P atoms in a light atom structure) the structure.

The application of the Patterson technique to locate strongly scattering atoms is often called the heavy atom method (which comes from the fact that heavy atoms scatter x-rays better and the Patterson technique is most often applied to analyze x-ray diffraction data).

This allows constructing of a partial structure model ("heavy7' atoms only), which for the most part define phase angles of all. The molecular-replacement method also encompasses the use of noncrystallographic redundancy within a crystal or between crystal forms to phase and refine crystal structures.

Applications of Patterson and molecular-replacement techniques to structure determination including Patterson interpretation methods, rotation functions, translation. The Patterson superposition procedure in SHELXS was originally designed for the location of heavier atoms in small moiety structures, but it turns out that it can also be used to locate heavy atom sites for macromolecular F data (see Chapter 15).

The crystal structure of trechmannite, AgS2, h been determined with the use of three-dimensional intensity data. The crystal is rhombohedral, having the unit-cell dimensions arh = Ä, a r h = ° 17', at,«= A, Obex = Ä, space group Cfj--J There are 6 (rh.) or 18 (hex.) formula units in the cell.

The structure w solved b y interpretation of a three-dimensional. Patterson superpositionThe Patterson function implicitly contains all the information about the structure. A map calculated with Fourier coefficients E o F o E frag has the phases derived from the fragment and is a sharpened Patterson superposition map.

Obtaining an electron-density map from X-ray diffraction data can be difficult and time-consuming even after the data have been collected, largely because MIR and MAD structure determinations currently require many subjective evaluations of the qualities of trial heavy-atom partial structures before a correct heavy-atom solution is obtained.

A set of criteria for evaluating the quality of. Determine the superposition structure or at least the heavy atom positions(s) in. Determine the complementary structure or the real structure.

Compute and discuss the Patterson function of the complementary structure, if this corresponds to the systematically weak reflection.

Apply 'Direct methods' (see above). MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to. Crystal structure analysis/determination Analysis/determination of the crystal.

distance vectors. Patterson function. Points to the distribution and position of „heavy atoms“ in the unit cell →heavy atom method. Realisation of a crystal structur determination. Determin.

of the. Since the cell of the Patterson function is the same size as the cell of the crystal, the Patterson function is much more densely packed than the corresponding electron density map. This higher density of peaks causes many peaks in the Patterson map to be overlapped.

The greater intrinsic breadth of Patterson peaks accentuates this overlap. However, most MAD structures have many anomalous scattering atoms and the Patterson function is too complicated for manual interpretation.

Two general approaches have emerged for using MAD data to solve the anomalous scattering substructure. The first approach is based on automated interpretation of the Patterson function in combination with.

The image of such a structure at the heavy atom will differ considerably from its other images. Several techniques exist for determining a model of a structure under study from a Patterson function; the most powerful are the superposition techniques, which have permitted the analysis of the function to be formalized and to be performed by computer.

Outline of Crystallography for Biologists is intended for researchers and students in the biological sciences who require an insight into the methods of X-ray crystallography without needing to learn all the relevant theory.

The main text is purely descriptive and is readable by those with minimal mathematical knowledge. Some mathematical detail is given throughout in boxes, but these can be. An application of Patterson methods in crystal structure determination.

For a compound containing a heavy atom (i.e. one with a significantly higher atomic scattering factor than the others present) the diffraction phases calculated from the position of the heavy atom are used to compute a first approximate electron density map.

SARA11 Program for the refinement of various parameters of III-V and II-VI semiconductors (ZnS and elemental (diamond) semiconductors. To refine parameters in the harmonic, anharmonic and charge transfer approximations.

Refines individual thermal, scale, extinction parameters and the charge transfer from one atom to the other in ZnS type structures. Interpretation of Patterson maps lies at the foundation of most macromolecular structure elucidation processes, both in determining the position of heavy atoms and/or anomalous scatterers for the isomorphous replacement and anomalous-scattering methods, and in determining the orientation and position of a homologous protein model for the molecular replacement method.

The analysis of the crystal structure was carried out by interpretation of the Patterson function and by three-dimensional Fourier syntheses. An isotropic refinement gave a final R index of 0" for measured reflexions. Fe and P show the usual octahedral and tetrahedral coordination respectively.

Several methods for the automatic determination of heavy-atom structures have been developed and extensively tested. The methods are based on a combination of vector superposition in space group P 1 with a symmetry minimum function.

The peaks of the symmetry minimum function are used as trial origin shifts in the translational search for the cell origin. To solve a heavy atom structure using the Patterson interpretation program PATTY.

The only required input data are the crystal data and reflection data. After location of the heavy atoms (which could include S or P atoms in a light atom structure) the structure. A trial structure was arrived at by the "heavy atom" method after the coordinates of the two independent bromine atoms had been revealed by three-dimensional Patterson synthesis.

The structure was refined by the full-matrix least-squares method to an agreement factor ofwhich indicates a satisfactory solution of the structure. The crystal. Crystal Structure Analysis: A Primer Glusker J.P., Trueblood K.N.

Crystal Structure Analysis, Third Edition, explains how and why the detailed three-dimensional architecture of molecules can be determined by an analysis of the diffraction patterns obtained when X-rays or neutrons are scattered by the atoms in single crystals. Keywords: Fourier analysis, Fourier coefficients, structure factors, Patterson function, heavy atom, isomorphous replacement, direct methods, Abbe theory Oxford Scholarship Online requires a subscription or purchase to access the full text of books within the service.

Patterson functions have traditionally been used to solve the positions of the heavy atoms, but beyond about 20 or 30 sites automated Patterson interpretation becomes increasingly difficult (the number of peaks increases as the square of the number of atoms).

Structure factors of centrosymmetric crystals Friedel's law Laue groups Structure factors of sodium chloride Extinctions due to glide planes Extinctions due to screw axes Chapter 6 Determination of atomic positions Solutions of structure factor equations The Patterson function Heavy-atom methods.Two classes of functions for the location of heavy atoms and for solution of crystal structures Two classes of functions for the location of heavy atoms and for solution of crystal structures RAMAN, S.; LIPSCOMB, WILLIAM N.

Two classes of functions are presented for the location of anomalous scatterers in one crystal or the replaceable atoms in a pair of isomorphous crystals.Patterson function.

By the nature of the method, the Patterson function contains an image of the structure. However, this image, for a structure containing N atoms, is superimposed with N-1 other images making interpretation of even a simple structure nontrivial.

The difficulty in obtaining a solution from a Patterson map often inhibits the.