Phasing diffuse scattering. Application of the SIR2002 algorithm to the non-crystallographic phase problem

A new phasing algorithm has been used to determine the phases of diffuse elastic X-ray scattering from a non-periodic array of gold balls of 50 nm diameter. Two-dimensional real-space images, showing the charge-density distribution of the balls, have been reconstructed at 50 nm resolution from transmission diffraction patterns recorded at 550 eV energy. The reconstructed image fits well with scanning electron microscope (SEM) image of the same sample. The algorithm, which uses only the density modification portion of the SIR2002 program, is compared with the results obtained via the Gerchberg-Saxton-Fienup HIO algorithm. In this way the relationship between density modification in crystallography and the HiO algorithm used in signal and image processing is elucidated.Comment: 7 pages, 12 figure

The Patterson deconvolution method for the<i>ab-initio</i>structure solution of large proteins

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Philosophy as political technē: The tradition of invention in Simondon’s political thought

Gilbert Simondon has recently attracted the interest of political philosophers and theorists, despite he is rather renowned as a philosopher of technics – as the author of Of the Mode of Existence of Technical Objects – who also elaborated a general theory of complex systems in Individuation in the Light of the Notions of Form and Information. A group of scholars has developed Gilles Deleuze’s early suggestion that Simondon’s social ontology might offer the basis for a re-theorisation of radical democracy. Others, following Herbert Marcuse, have instead focused on Simondon’s analysis of the relationship between technology and society. However, only a joint study of Simondon’s two major works can reveal their implicit political stakes. As I will argue, Simondon’s anti-Aristotelianism and his anti-Heideggerian understanding of the Greek origins of philosophy, allow us to conceive philosophical thought as a ‘tradition of invention’, that is, a pedagogical technē endowed with the political task of maintaining the openness of the social system and allowing normative invention to emerge from within

Protein phasing at non-atomic resolution by combining Patterson and VLD techniques

Phasing proteins at non-atomic resolution is still a challenge for any ab initio method. A variety of algorithms [Patterson deconvolution, superposition techniques, a cross-correlation function (C map), the VLD (vive la difference) approach, the FF function, a nonlinear iterative peak-clipping algorithm (SNIP) for defining the background of a map and the free lunch extrapolation method] have been combined to over- come the lack of experimental information at non-atomic resolution. The method has been applied to a large number of protein diffraction data sets with resolutions varying from ̊ , with the condition that S or heavier atoms are atomic to 2.1 A present in the protein structure. The applications include the use of ARP/wARP to check the quality of the final electron- density maps in an objective way. The results show that resolution is still the maximum obstacle to protein phasing, ̊ but also suggest that the solution of protein structures at 2.1 A resolution is a feasible, even if still an exceptional, task for the combined set of algorithms implemented in the phasing program. The approach described here is more efficient than the previously described procedures: e.g. the combined use of the algorithms mentioned above is frequently able to provide phases of sufficiently high quality to allow automatic model building. The method is implemented in the current version of SIR2014

Separated and aligned molecular fibres in solid state self-assemblies of cyclodextrin [2]rotaxanes

The original publication can be found at www.springerlink.comThe conformations of two [2]rotaxanes, each comprising α-cyclodextrin as the rotor, a stilbene as the axle and 2,4,6-trinitrophenyl substituents as the capping groups, have been examined in solution and in the solid state, using ¹H NMR spectroscopy and X-ray crystallography, respectively. In solution, introducing substituents onto the stilbene prevents the cyclodextrin from being localized over one end of the axle. Instead the cyclodextrin moves back and forth along the substituted stilbene. In the solid state, the axles of the rotaxanes form extended molecular fibres that are separated from each other and aligned along a single axis. The molecular fibres are strikingly similar to those formed by the axle component of one of the rotaxanes in the absence of the cyclodextrin, but in the latter case they are neither separated nor all aligned.Hideki Onagi, Benedetta Carrozzini, Giovanni L. Cascarano, Christopher J. Easton, Alison J. Edwards, Stephen F. Lincoln and A. David Ra

Benzophenone Photophore Flexibility and Proximity: Molecular and Crystal Structure of a Bpa-Containing Trichogin Dodecapeptide Analogue

An X-ray diffraction analysis of a Bpa-containing analogue of the lipopeptaibol trichogin GA IV strongly points to the conclusion that caution should be exercised in utilizing this highly flexible, benzophenone-based photoprobe acritically in biochemical and biophysical studies. As a result of the different side-chain conformations adopted by the Bpa residue, the distance of its ketone carbonyl carbon from the midpoint of the N-O bond of the nitroxide-containing side chain of the TOAC residue in the two crystallographically independent peptide molecules differs by as much as 11 \uc5

EXPO. A package for full pattern decomposition and for solving crystal structures by direct methods. User's manual

Printed from http://www.ic.cnr.it target=NewWindow>www.ic.cnr.it (March 2005)Consiglio Nazionale delle Ricerche - Biblioteca Centrale - P.le Aldo Moro, 7 , Rome / CNR - Consiglio Nazionale delle RichercheSIGLEITItal