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Bulk-solvent Correction (bulk-solvent + correction)
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] 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] A smooth and differentiable bulk-solvent model for macromolecular diffractionACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2010T. D. Fenn Inclusion of low-resolution data in macromolecular crystallography requires a model for the bulk solvent. Previous methods have used a binary mask to accomplish this, which has proven to be very effective, but the mask is discontinuous at the solute,solvent boundary (i.e. the mask value jumps from zero to one) and is not differentiable with respect to atomic parameters. Here, two algorithms are introduced for computing bulk-solvent models using either a polynomial switch or a smoothly thresholded product of Gaussians, and both models are shown to be efficient and differentiable with respect to atomic coordinates. These alternative bulk-solvent models offer algorithmic improvements, while showing similar agreement of the model with the observed amplitudes relative to the binary model as monitored using R, Rfree and differences between experimental and model phases. As with the standard solvent models, the alternative models improve the agreement primarily with lower resolution (>6,Å) data versus no bulk solvent. The models are easily implemented into crystallographic software packages and can be used as a general method for bulk-solvent correction in macromolecular crystallography. [source] A robust bulk-solvent correction and anisotropic scaling procedureACTA CRYSTALLOGRAPHICA SECTION D, Issue 7 2005Pavel V. Afonine A reliable method for the determination of bulk-solvent model parameters and an overall anisotropic scale factor is of increasing importance as structure determination becomes more automated. Current protocols require the manual inspection of refinement results in order to detect errors in the calculation of these parameters. Here, a robust method for determining bulk-solvent and anisotropic scaling parameters in macromolecular refinement is described. The implementation of a maximum-likelihood target function for determining the same parameters is also discussed. The formulas and corresponding derivatives of the likelihood function with respect to the solvent parameters and the components of anisotropic scale matrix are presented. These algorithms are implemented in the CCTBX bulk-solvent correction and scaling module. [source] Flat bulk-solvent model: obtaining optimal parametersACTA CRYSTALLOGRAPHICA SECTION D, Issue 9 2002Andrei Fokine A bulk-solvent correction is regularly used for macromolecular refinement. The flat model of the bulk solvent is considered to be the most reliable. It is shown that the standard procedure does not always result in the optimal values of the bulk-solvent correction parameters. A method to obtain the best values for parameters ksol and Bsol of the flat-solvent model is discussed. The values of correctly determined parameters for crystallographic structures deposited in the Protein Data Bank are clustered around ksol = 0.35,e,Å,3 and Bsol = 46,Å2, which have a reasonable physical meaning. Such a distribution allows the use of these mean values of solvent parameters for many practical applications when refined parameters cannot be obtained, especially when an atomic model in the unit cell is not yet known. [source] | ||||||||||