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
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 36 (1980), S. 3100-3102 
    ISSN: 1600-5740
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 2
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 21 (1988), S. 490-495 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: A phased translation function, which takes advantage of prior phase information to determine the position of an oriented molecular replacement model, is examined. The function is the coefficient of correlation between the electron density computed with the prior phases and the electron density of the translated model, evaluated in reciprocal space as a Fourier transform. The correlation coefficient used in this work is closely related to an overlap function devised by Colman, Fehlhammer & Bartels [in Crystallographic Computing Techniques (1976), edited by F. R. Ahmed, K. Huml & B. Sedlacek, pp. 248–258. Copenhagen: Munksgaard]. Tests with two protein structures, one of which was solved with the help of the phased translation function, show that little phase information is required to resolve the translation problem, and that the function is relatively insensitive to misorientation of the model.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 3
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A new software suite, called Crystallography & NMR System (CNS), has been developed for macromolecular structure determination by X-ray crystallography or solution nuclear magnetic resonance (NMR) spectroscopy. In contrast to existing structure-determination programs the architecture of CNS is highly flexible, allowing for extension to other structure-determination methods, such as electron microscopy and solid-state NMR spectroscopy. CNS has a hierarchical structure: a high-level hypertext markup language (HTML) user interface, task-oriented user input files, module files, a symbolic structure-determination language (CNS language), and low-level source code. Each layer is accessible to the user. The novice user may just use the HTML interface, while the more advanced user may use any of the other layers. The source code will be distributed, thus source-code modification is possible. The CNS language is sufficiently powerful and flexible that many new algorithms can be easily implemented in the CNS language without changes to the source code. The CNS language allows the user to perform operations on data structures, such as structure factors, electron-density maps, and atomic properties. The power of the CNS language has been demonstrated by the implementation of a comprehensive set of crystallographic procedures for phasing, density modification and refinement. User-friendly task-oriented input files are available for nearly all aspects of macromolecular structure determination by X-ray crystallography and solution NMR.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 4
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 42 (1986), S. 140-149 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Unrefined or partially refined models of macromolecules are generally incomplete and typically have large coordinate errors. It is shown that phase probability equations appropriate for a perfect partial structure lead to inaccurate estimates of phase probabilities in such cases. Therefore, it is necessary to use equations that have been derived allowing for errors in the partial structure. A method is given to estimate the parameter σA in these phase probability expressions from the observed and calculated structure factor amplitudes. From the variation of σA with resolution, one can estimate the mean coordinate error for the model. Electron density maps calculated using partial structure phases are biased towards the partial structure. When there are coordinate errors, a new expression for the non-centric Fourier coefficients [(2m|FN| - D|FcP|) exp(iαcP)] is required to suppress this model bias. Judged by correlation coefficients comparing electron density maps with the correct and the partial structure maps, the Fourier coefficients derived here are superior to others currently in use.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 5
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 52 (1996), S. 659-668 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: When crystal structures of proteins or small molecules are used to address questions of scientific relevance, the accuracy and precision of the atomic coordinates are crucial. Accordingly, the atomic model is generally improved by refining it to improve agreement with the observed diffraction data. The refinement of crystal structures is conventionally based on least-squares methods but such procedures are handicapped since conditions necessary for the use of the least-squares target are not satisfied. It is proposed here that refinement should be based on maximum likelihood and two maximum-likelihood targets have been implemented in the program XPLOR. Preliminary tests with protein structures give dramatic results. Compared to least-squares refinement, maximum-likelihood refinement can achieve more than twice the improvement in average phase error. The resulting electron-density maps are correspondingly clearer and suffer less from model bias.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 6
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 7
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Applied crystallography online 20 (1987), S. 517-521 
    ISSN: 1600-5767
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Geosciences , Physics
    Notes: The development of a new translation-function program is reported. It is one that uses a linear correlation coefficient to determine the correct position of an oriented molecule in the crystal cell. The method has been implemented in a computer program called BRUTE. The program can also refine the orientation of the model and accept a set of atoms with fixed positions. Comparison of the correlation coefficient with other translation functions indicates that it is comparable to or slightly better than the rest. The most important feature of the program is its ability to adjust the orientation of the model. This allows for errors in the orientation obtained from the rotation function to be corrected.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 8
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 57 (2001), S. 1373-1382 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: The molecular-replacement method works well with good models and simple unit cells, but often fails with more difficult problems. Experience with likelihood in other areas of crystallography suggests that it would improve performance significantly. For molecular replacement, the form of the required likelihood function depends on whether there is ambiguity in the relative phases of the contributions from symmetry-related molecules (e.g. rotation versus translation searches). Likelihood functions used in structure refinement are appropriate only for translation (or six-dimensional) searches, where the correct translation will place all of the atoms in the model approximately correctly. A new likelihood function that allows for unknown relative phases is suitable for rotation searches. It is shown that correlations between sequence identity and coordinate error can be used to calibrate parameters for model quality in the likelihood functions. Multiple models of a molecule can be combined in a statistically valid way by setting up the joint probability distribution of the true and model structure factors as a multivariate complex normal distribution, from which the conditional distribution of the true structure factor given the models can be derived. Tests in a new molecular-replacement program, Beast, show that the likelihood-based targets are more sensitive and more accurate than previous targets. The new multiple-model likelihood function has a dramatic impact on success.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 9
    Electronic Resource
    Electronic Resource
    Copenhagen : International Union of Crystallography (IUCr)
    Acta crystallographica 55 (1999), S. 1759-1764 
    ISSN: 1399-0047
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: Outliers are observations which are very unlikely to be correct, as judged by independent observations or other prior information. Such unexpected observations are treated, effectively, as being more informative about possible models, so they can seriously impede the course of structure determination and refinement. The best way to detect and eliminate outliers is to collect highly redundant data, but it is not always possible to make multiple measurements of every reflection. For non-redundant data, the prior expectation given either by a Wilson distribution of intensities or model-based structure-factor probability distributions can be used to detect outliers. This captures mostly the excessively strong reflections, which dominate the features of electron-density maps or, even more so, Patterson maps. The outlier rejection tests have been implemented in a program, Outliar.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
  • 10
    Electronic Resource
    Electronic Resource
    [S.l.] : International Union of Crystallography (IUCr)
    Acta crystallographica 48 (1992), S. 104-113 
    ISSN: 1600-5724
    Source: Crystallography Journals Online : IUCR Backfile Archive 1948-2001
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Notes: A systematic search approach to the automatic refinement of protein structures could reduce the need for manual intervention. In this approach, possible conformations for a segment of the polypeptide chain are generated systematically and the trial segments are scored for their agreement with the observed diffraction data. The sampling of conformational space is sufficiently exhaustive that reasonable conformations should be included. A number of score functions have been tested, including local electron-density correlations and global structure-factor agreements. The score functions vary in their predictive power as well as in their bias toward the conformation found in the current refined model, but the best score functions have reasonable predictive power. Related functions can be used to indicate which regions of the model fit poorly, reducing the need for manual inspection of models in electron density.
    Type of Medium: Electronic Resource
    Signatur Availability
    BibTip Others were also interested in ...
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...