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  • Springer  (11)
  • International Union of Crystallography (IUCr)  (8)
  • 1
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXVI. Developments of the Sayre-equation tangent formula (1988)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 44 (1988), S. 353-357 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The Sayre-equation tangent formula (SETF) develops sets of phases tending to satisfy Sayre's equations for both large and small normalized structure factors. There are two components in the SETF, corresponding to contributions from phase triplets and quartets respectively. The development of objective algorithms for properly weighting these components and for gradually building up the quartet contribution has enabled the SETF, within the procedure SAYTAN, to be incorporated into MULTAN87, the latest version of the package. Examples of tests of MULTAN87 and its use in solving unknown structures are given.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767388000017
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  • 2
    Electronic Resource
    Electronic Resource
    Direct-Space Methods in Phase Extension and Phase Refinement. IV. The Double-Histogram Method. (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 252-256 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: In the conventional histogram-matching technique for phase extension and refinement for proteins a simple one-to-one transformation is made in the protein region to modify calculated density so that it will have some target histogram in addition to solvent flattening. This work describes an investigation where the density modification takes into account not only the current calculated density at a grid point but also some characteristic of the environment of the grid point within some distance R. This characteristic can be one of the local maximum density, the local minimum density or the local variance of density. The grid points are divided into ten groups, each containing the same number of grid points, for ten different ranges of value of the local characteristic. The ten groups are modified to give different histograms, each corresponding to that obtained under the same circumstances from a structure similar to the one under investigation. This process is referred to as the double-histogram matching method. Other processes which have been investigated are the weighting of structure factors when calculating maps with estimated phases and also the use of a factor to dampen the change of density and so control the refinement process. Two protein structures were used in numerical trials, RNApl [Bezborodova, Ermekbaeva, Shlyapnikov, Polyakov & Bezborodov (1988). Biokhimiya, 53, 965–973] and 2-Zn insulin [Baker, Blundell, Cutfield, Cutfield, Dodson, Dodson, Hodgkin, Hubbard, lsaacs, Reynolds, Sakabe, Sakabe & Vijayan (1988). Philos. Trans. R. Soc. London Ser. B, 319, 456--469]. Comparison of the proposed procedures with the normal histogram-matching technique without structure-factor weighting or damping gives mean phase errors reduced by up to 10° with map correlation coefficients improved by as much as 0.14. Compared to the normal histogram used with weighting of structure factors and damping, the improvement due to the use of the double-histogram method is usually of order 4° in mean phase error and an increase of 0.06–0.08 in the map correlation coefficient. It is concluded that the most reliable results are found with the local-maximum condition and with R in the range 0.5–0.6 Å.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995008456
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  • 3
    Electronic Resource
    Electronic Resource
    Direct-space methods in phase extension and phase determination. III. Phase refinement using Sayre"s equation (1995)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 51 (1995), S. 1036-1040 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: An algorithm is described for refining a set of phases to agree with the Sayre equation. All operations are carried out using Fourier transforms with modest computer-store requirements even for very large systems. The procedure is tested with two moderate-sized proteins, one containing heavy atoms, and is found to give good refinement with data at more than atomic resolution (1.17 Å) and useful, if less good, refinement when the data resolution is lower (1.5 Å). It is concluded that at atomic resolution, or slightly below, the Sayre equation still has something to offer both for phase refinement and phase extension, especially if used cautiously with weighted multiple isomorphous replacement phases acting as a constraint on the phase changes. Even when the Sayre equation on its own refines phases badly, or not at all, it may still make an important contribution in conjunction with other real-space refinement procedures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444995006469
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  • 4
    Electronic Resource
    Electronic Resource
    Direct-Space Methods in Phase Extension and Phase Refinement. VI. PERP (Phase Entension and Refinement Program) (1996)
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 1119-1124 
    Details
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Several techniques for extending and refining phases for macromolecular structures have been incorporated into a program package PERP. In addition to previously employed techniques such as solvent flattening and histogram matching, PERP includes a new way of applying the Sayre equation [Refaat, Tate & Woolfson (1995). Acta Cryst. D51, 1036–1040], low-density elimination [Shiono & Woolfson (1992). Acta Cryst. A48, 451–456] and two double-histogram methods [Refaat, Tate & Woolfson (1996). Acta Cryst. D52, 252–256]. PERP is an easy-to-use package controlled by keywords and provided with default parameters that usually give near-optimum results. Examples are given of refinement, and also extension and refinement, for six known protein structures with a variety of characteristics. In each case PERP gives a very satisfactory outcome as measured by improvements in the mean-phase-error and conventional map-correlation coefficient. The main conclusion is that the several methods used in sequence give more effective extension and refinement than using any single method alone.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0907444996008463
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  • 5
    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
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  • 6
    Electronic Resource
    Electronic Resource
    On the application of phase relationships to complex structures. XXIV. The Sayre tangent formula (1985)
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 41 (1985), S. 286-290 
    Details
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The application of the condition that a true set of phases for a substantial subset of normalized structure factors should satisfy Sayre's equation leads to a phase-refining equation called the Sayre tangent formula. Phases refined by this formula tend to satisfy Sayre's equation for a subset of E's containing some of large magnitude and some of small (ideally zero) magnitude. Trials indicate that the new formula, incorporated into a computer program SAYTAN, is more effective than MULTAN80, especially for symmorphic structures.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1107/S0108767385000617
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  • 7
    Electronic Resource
    Electronic Resource
    Three substituted 3-amino-2-benzoylaminopropenoic acid derivatives (1994)
    Oxford [u.a.] : International Union of Crystallography (IUCr)
    Acta crystallographica 50 (1994), S. 239-245 
    Details
    ISSN: 1600-5759
    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/S0108270193006997
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  • 8
    Electronic Resource
    Electronic Resource
    Concentration, Distribution, and Comparison of Selected Trace Elements in Bed Sediment and Fish Tissue in the South Platte River Basin, USA, 1992–1993 (1997)
    Springer
    Archives of environmental contamination and toxicology 32 (1997), S. 246-259 
    Details
    ISSN: 1432-0703
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Notes: Abstract. During August–November 1992 and August 1993, bed sediment and fish liver were sampled in the South Platte River Basin and analyzed for 45 elements in bed sediment and 19 elements in fish liver. The results for aluminum, arsenic, cadmium, chromium, copper, iron, lead, manganese, selenium, silver, uranium, and zinc are presented here. All 12 trace elements were detected in bed sediment, but not all were detected in fish liver or in all species of fish. A background concentration of trace elements in bed sediment was calculated using the cumulative frequency curves of trace element concentrations at all sites. Arsenic, cadmium, copper, lead, manganese, silver, uranium, and zinc concentrations were greater than background concentrations at sites in mining areas or at sites that have natural sources of these elements. Trace element concentrations in fish liver generally did not follow the same patterns as concentrations in bed sediment, although concentrations of aluminum and cadmium were higher in fish liver collected at mountain sites that had been disturbed by mining. Concentrations of aluminum, arsenic, cadmium, chromium, copper, iron, lead, silver, and zinc increased in bed sediments in urban areas. Iron, silver, and zinc concentrations in fish liver also increased in urban areas. Concentrations of cadmium, copper, silver, and zinc in fish liver increased in the agricultural areas of the basin. Downstream changes in trace element concentrations may be the result of geological changes in addition to changes in land use along the river.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002449900182
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  • 9
    Electronic Resource
    Electronic Resource
    Organochlorine Compounds in Bed Sediment and Fish Tissue in the South Platte River Basin, USA, 1992–1993 (1996)
    Springer
    Archives of environmental contamination and toxicology 30 (1996), S. 62-78 
    Details
    ISSN: 1432-0703
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Notes: Abstract. Bed-sediment and fish-tissue samples were collected in the South Platte River Basin to determine the occurrence and distribution of organochlorine compounds in the basin. During August-November 1992 and August 1993, bed sediment (23 sites) and fish tissue (subset of 19 sites) were sampled and analyzed for 32 organochlorine compounds in bed sediment and 27 compounds in fish tissue. More types of organochlorine compounds were detected in fish tissue than in bed sediment. Total DDT, p,p′-DDE, o,p′-DDE, p,p′-DDD, total PCB, Dacthal®, dieldrin, cis-chlordane, cis-nonachlor, trans-nonachlor, and p,p′-DDT were detected in fish tissue at 〉25% of the sites; p,p′-DDE, total DDT, cis-chlordane, and trans-chlordane were detected in bed sediment at 〉25% of the sites. Organochlorine concentrations in bed sediment and fish tissue were related to land-use settings. Few organochlorine compounds were detected at minimally impacted sites located in rangeland, forest, and built-up land-use settings. Chlordane-related compounds and p,p′-methoxychlor in bed sediment and fish tissue, endrin in fish tissue, and endosulfan I in bed sediment were associated with urban and mixed (urban and agricultural) sites. Dacthal® in bed sediment and fish tissue was associated with agricultural sites. The compounds HCB, γ-HCH, PCA, and toxaphene were detected only at mixed land-use sites. Although DDT and DDT-metabolites, dieldrin, and total PCB were detected in urban, mixed, and agricultural land-use settings, highest mean concentrations were detected at mixed land-use sites. Mixed land-use sites had the greatest number of organochlorine compounds detected in fish tissue, whereas urban and mixed sites had the greatest number of organochlorine compounds detected in bed sediment. Measuring concentrations of organochlorine compounds in bed sediment and fish tissue at the same site offers a more complete picture of the persistence of organochlorine compounds in the environment and their relation to land-use settings.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s002449900009
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  • 10
    Electronic Resource
    Electronic Resource
    Organochlorine compounds in bed sediment and fish tissue in the South Platte River Basin, USA, 1992–1993 (1996)
    Springer
    Archives of environmental contamination and toxicology 30 (1996), S. 62-78 
    Details
    ISSN: 1432-0703
    Source: Springer Online Journal Archives 1860-2000
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Medicine
    Notes: Abstract Bed-sediment and fish-tissue samples were collected in the South Platte River Basin to determine the occurrence and distribution of organochlorine compounds in the basin. During August–November 1992 and August 1993, bed sediment (23 sites) and fish tissue (subset of 19 sites) were sampled and analyzed for 32 organochlorine compounds in bed sediment and 27 compounds in fish tissue. More types of organochlorine compounds were detected in fish tissue than in bed sediment. Total DDT, p,p′-DDE, o,p′-DDE, p,p′-DDD, total PCB, Dacthal®, dieldrin, cis-chlordane, cis-nonachlor, trans-nonachlor, and p,p′-DDT were detected in fish tissue at 〉25% of the sites; p,p′-DDE, total DDT, cis-chlordane, and trans-chlordane were detected in bed sediment at 〉25% of the sites. Organochlorine concentrations in bed sediment and fish tissue were related to land-use settings. Few organochlorine compounds were detected at minimally impacted sites located in rangeland, forest, and built-up land-use settings. Chlordane-related compounds and p,p′-methoxychlor in bed sediment and fish tissue, endrin in fish tissue, and endosulfan I in bed sediment were associated with urban and mixed (urban and agricultural) sites. Dacthal® in bed sediment and fish tissue was associated with agricultural sites. The compounds HCB, γ-HCH, PCA, and toxaphene were detected only at mixed land-use sites. Although DDT and DDT-metabolites, dieldrin, and total PCB were detected in urban, mixed, and agricultural land-use settings, highest mean concentrations were detected at mixed land-use sites. Mixed land-use sites had the greatest number of organochlorine compounds detected in fish tissue, whereas urban and mixed sites had the greatest number of organochlorine compounds detected in bed sediment. Measuring concentrations of organochlorine compounds in bed sediment and fish tissue at the same site offers a more complete picture of the persistence of organochlorine compounds in the environment and their relation to land-use settings.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00211330
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