Library

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    Electronic Resource
    Electronic Resource
    A flexible and efficient procedure for the solution and phase refinement of protein structures (2000)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 56 (2000), S. 1137-1147 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An ab initio method is described for solving protein structures for which atomic resolution (better than 1.2 Å) data are available. The problem is divided into two stages. Firstly, a substructure composed of a small percentage (∼5%) of the scattering matter of the unit cell is positioned. This is used to generate a starting set of phases that are slightly better than random. Secondly, the full structure is developed from this phase set. The substructure can be a constellation of atoms that scatter anomalously, such as metal or S atoms. Alternatively, a structural fragment such as an idealized α-helix or a motif from some distantly related protein can be orientated and sometimes positioned by an extensive molecular-replacement search, checking the correlation coefficient between observed and calculated structure factors for the highest normalized structure-factor amplitudes |E|. The top solutions are further ranked on the correlation coefficient for all E values. The phases generated from such fragments are improved using Patterson superposition maps and Sayre-equation refinement carried out with fast Fourier transforms. Phase refinement is completed using a novel density-modification process referred to as dynamic density modification (DDM). The method is illustrated by the solution of a number of known proteins. It has proved fast and very effective, able in these tests to solve proteins of up to 5000 atoms. The resulting electron-density maps show the major part of the structures at atomic resolution and can readily be interpreted by automated procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S090744490000932X
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 2
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXXVI: some experiments with a small protein without heavy atoms (1999)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 168-172 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The direct-methods program MULTAN88 has been applied to a known protein, ribonuclease (RNAP1), containing 808 non-H atoms, including five S atoms, plus 83 ordered solvent water molecules. Phase sets with mean phase errors between 69 and 75° were selected by modified figures of merit for trials with the full data at 1.17 Å resolution and also with restricted data at 1.25 and 1.5 Å resolution. These figures of merit had previously only been applied to protein structures containing heavy atoms, and this is the first demonstration of their usefulness with no heavy atom present. An initial set of 1091 phases from a 1.17 Å trial was developed by an objective procedure to give the full structure with a residual of 0.21, which agrees well with the published structure.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444998006374
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 3
    Electronic Resource
    Electronic Resource
    Physics of simple liquids edited by H. N. V. Temperley, J. S. Rowlinson and G. S. Rushbrooke (1969)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 25 (1969), S. 642-642 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739469001471
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 4
    Electronic Resource
    Electronic Resource
    Anomalous scattering edited by S. Ramaseshan and S. C. Abrahams (1976)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 32 (1976), S. 1037-1038 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739476002179
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 5
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XVI. A random approach to structure determination (1978)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 34 (1978), S. 883-892 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: With triple-phase relationships treated as linear equations it is possible to refine a set of phases from given initial values. Phases so obtained are better than those found by refining to self-consistency with the tangent formula. An investigation of the radius of convergence of the least-squares refinement process showed that a substantially correct solution may often be found even starting with random phases. Systems containing up to 300 phases have been investigated and the results and their implications are discussed. It is concluded that the random approach can, at the very least, be used to obtain 70--100 phases as a good starting point for phase development. There is also the possibility of obtaining a sufficient number of phases directly to define a reasonably complex structure, especially with a computer augmented by an array processor. A problem which can arise with linear equations, as with the tangent formula, is that the phases obtained do not adequately define the enantiomorph and give an E map with a pseudo centre of symmetry. Two methods of overcoming this problem are described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739478001837
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 6
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XV. Magic determinants (1978)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 34 (1978), S. 870-883 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A magic determinant is a Karle-Hauptman determinant in which the phases of reflexions forming the elements are expressed in magic-integer representation. By means of appropriate algorithms, which are described, magic determinants may be found, up to order 30, which have a high content of large E's. The value of the magic determinant depends on the values of the independent variables (usually two) in terms of which the magic-integer-represented phases are defined. Maxima are sought in a map of magic-determinant values and these give trial values for the constituent phases. These phases may be refined by maximizing one or more of the largest eigenvalues of the matrix of elements. Applications to five different structures are described and the usefulness and limitations of the magic-determinant concept are discussed. It is concluded that Karle-Hauptman determinants, chosen in the way described, provide a very discriminating figure of merit. However, the structure factors they contain usually provide a rather poor base for subsequent phase development and this limits the usefulness of the magic-determinant approach.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739478001825
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 7
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XIX. Magic-integer representation of a large set of phases: the MAGEX procedure (1981)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 37 (1981), S. 566-572 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Long one-dimensional magic-integer sequences are used to express the phases of 10-20 primary reflexions. The magic-integer representation of phases is extended to other secondary reflexions through strong triple- phase relationships involving one secondary and two primary reflexions. In the MAGEX procedure multiple magic-integer representations of the secondaries are sought and the error involved in their subsequent use in a conventional ψ map is much reduced. In view of the large number of primary reflexions the indices of the terms included in the ψ map are large and maps may be computed at up to 220 points. Further reflexions, in batches of ten or so, may be added to the initial set by the further use of magic integers and small-scale maps. When the base of estimated phases is sufficiently large then the phase information is extended by the controlled use of the tangent formula. Examples of the successful application of MAGEX are described.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739481001290
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 8
    Electronic Resource
    Electronic Resource
    A linear equation for products of normalized structure factors. I. Fourier formalism (1981)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 37 (1981), S. 548-552 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new relationship between products of two structure factors with coefficients calculated as the Fourier transform of a modified Patterson function is presented. The relation is alternatively expressed in terms of triple phase invariants and also a new weighted form of Sayre's equation [Sayre (1952). Acta Cryst. 5, 60-65] emerges as a special case. The advantages of the new equations with respect to Sayre's equation are discussed and, with simple one-dimensional models, examples of direct calculation of the cosines of triple-phase invariants are included.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739481001265
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 9
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXI. An extension to the MAGEX procedure (1982)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 38 (1982), S. 683-685 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the previously described MAGEX procedure [Hull, Viterbo, Woolfson & Zhang Shao-Hui (1981). Acta Cryst. A37, 566-572] trial phases found from a ψ map were refined by a parameter-shift process which maximized a function depending on the overall satisfaction of the triple-phase relationships. Advantages have been found in using a different function which has a somewhat stronger physical basis. Two algorithms are described which may be used either for centrosymmetric structures or for individual reflexions which can take only restricted phase values.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0567739482001387
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
  • 10
    Electronic Resource
    Electronic Resource
    Application of the Ps-function method to macromolecular structure determination (1989)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 45 (1989), S. 794-797 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Ps function derived from anomalous-dispersion data [Okaya, Saito, & Pepinsky (1955). Phys. Rev. 98, 1857-1858] has been tested with observed data for an Hg derivative of a small protein, avian pancreatic polypeptide [Glover, Moss, Tickle, Pitts, Haneef, Wood & Blundell (1985). Adv. Biophys. 20, 1-12]. The Ps map was superimposed on the four Hg sites via a sum function and negative densities were eliminated from the resultant map. This map, with appropriate density inserted at Hg sites, closely resembles a map calculated with true phases; the two maps have a correlation coefficient of 0-67. For 2109 reflexions the unweighted mean phase error is 39.9° but with |FoFc| weighting this reduces to 29.5°.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767389007646
    Library Location Call Number Volume/Issue/Year Availability
    BibTip Others were also interested in ...
    Paper (German National Licenses)
    Fulltext
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...