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Translation Search (translation + search)
Selected AbstractsBulk-solvent correction for fast translation search in molecular replacement: service programs for AMoRe and CNSJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 2 2003Andrei Fokine A new software package, BULK, was developed to allow fast and easy use of low-resolution data for the translation problem in molecular replacement. When the search model is relatively complete but not precise, or when its orientation is imprecisely determined, low-resolution data contribute very favourably to the solution of the translation-search problem. BULK comprises a specially developed program and a set of procedures complementary to the program AMoRe, as well as an input file for the CNS suite. [source] Molecular replacement: the probabilistic approach of the program REMO09 and its applicationsACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2009Rocco Caliandro The method of joint probability distribution functions has been applied to molecular replacement techniques. The rotational search is performed by rotating the reciprocal lattice of the protein with respect to the calculated transform of the model structure; the translation search is performed by fast Fourier transform. Several cases of prior information are studied, both for the rotation and for the translation step: e.g. the conditional probability density for the rotation or the translation of a monomer is found both for ab initio and when the rotation and/or the translation values of other monomers are given. The new approach has been implemented in the program REMO09, which is part of the package for global phasing IL MILIONE [Burla, Caliandro, Camalli, Cascarano, De Caro, Giacovazzo, Polidori, Siliqi & Spagna (2007). J. Appl. Cryst.40, 609,613]. A large set of test structures has been used for checking the efficiency of the new algorithms, which proved to be significantly robust in finding the correct solutions and in discriminating them from noise. An important design concept is the high degree of automatism: REMO09 is often capable of providing a reliable model of the target structure without any user intervention. [source] On the use of low-resolution data for translation search in molecular replacementACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2002Andrei Fokine Low-resolution reflections (approximately 15,Å and lower) are very useful for the translation search in molecular replacement because they are less sensitive to model errors compared with the traditionally used reflections of resolution 4,10,Å. At low resolution, however, the contribution from the bulk solvent is quite significant and corresponding structure factors calculated from a macromolecular model cannot be compared with experimental values if this contribution is neglected. The proposed method provides a way of fast translation searches where low-resolution reflections are taken into account. Test calculations using several experimental data sets show a dramatic improvement in the signal after the bulk-solvent correction and low-resolution reflections were included in the calculation; this improvement allowed unambiguous identification of the solution. [source] The restriction enzyme SgrAI: structure solution via combination of poor MIRAS and MR phasesACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2009Pete W. Dunten Uninterpretable electron-density maps were obtained using either MIRAS phases or MR phases in attempts to determine the structure of the type II restriction endonuclease SgrAI bound to DNA. While neither solution strategy was particularly promising (map correlation coefficients of 0.29 and 0.22 with the final model, respectively, for the MIRAS and MR phases and Phaser Z scores of 4.0 and 4.3 for the rotation and translation searches), phase combination followed by density modification gave a readily interpretable map. MR with a distantly related model located a dimer in the asymmetric unit and provided the correct transformation to use in averaging electron density between SgrAI subunits. MIRAS data sets with low substitution and MR solutions from only distantly related models should not be ignored, as poor-quality starting phases can be significantly improved. The bootstrapping strategy employed to improve the initial MIRAS phases is described. [source] | ||||||||||