1,721,009 research outputs found
A robust tangent procedure
No full textThird-generation direct methods programs are based on a phasing algorithm (e.g. the tangent or the parameter shift method) and on dual space refinement techniques. The two spaces may be alternated during the phasing procedure or used in a sequential way: for example, first phase and after extend and refine. The tangent approach in SIR2011 belongs to the second category: phases are first estimated by the tangent formula, then their extension and refinement is performed in direct space via electron density modification techniques. In this article a number of new algorithms are described, with the aim of improving the SIR2011 tangent step and allowing more efficient phase extension and refinement. New criteria were chosen for defining the number of reflections to phase, for modifying the tangent weighting scheme, and for fixing the active use of the psi-0 triplets and of the quartet invariants. Each tangent trial may now be submitted to the RELAX procedure, a tool for moving to the correct position a well oriented but misplaced structural model. The resulting procedure shows surprising efficiency, testified by a wide set of applications. The experimental results have been compared with the tangent and VLD (vive la difference) approaches implemented in SIR2011
From a random to the correct structure: the VLD algorithm
No full textA recent probabilistic reformulation of the difference electron-density Fourier synthesis [Burla, Caliandro, Giacovazzo & Polidori (2010). Acta Cryst. A66, 347-361] suggested that the most suitable Fourier coefficients are the sum of the classical difference term (mF - DFp) with a flipping term, depending on the model and on its quality. The flipping term is dominant when the model is poor and is negligible when the model is a good representation of the target structure. In the case of a random model the Fourier coefficient does not vanish and therefore could allow the recovery of the target structure from a random model. This paper describes a new phasing algorithm which does not require use of the concept of structure invariants or semi-invariants: it is based only on the properties of the new difference electron density and of the observed Fourier synthesis. The algorithm is cyclic and very easy to implement. It has been applied to a large set of small-molecule structures to verify the suitability of the approach
The phantom derivative method when a structure model is available: about its theoretical basis
No full textThis study clarifies why, in the phantom derivative (PhD) approach, randomly created structures can help in refining phases obtained by other methods. For this purpose the joint probability distribution of target, model, ancil and phantom derivative structure factors and its conditional distributions have been studied. Since PhD may use n phantom derivatives, with n 1, a more general distribution taking into account all the ancil and derivative structure factors has been considered, from which the conditional distribution of the target phase has been derived. The corresponding conclusive formula contains two components. The first is the classical Srinivasan & Ramachandran term, relating the phases of the target structure with the model phases. The second arises from the combination of two correlations: that between model and derivative (the first is a component of the second) and that between derivative and target. The second component mathematically codifies the information on the target phase arising from model and derivative electron-density maps. The result is new, and explains why a random structure, uncorrelated with the target structure, adds useful information on the target phases, provided a model structure is known. Some experimental tests aimed at checking if the second component really provides information on ’ (the target phase) were performed; the favourable results confirm the correctness of the theoretical calculations and of the corresponding analysis
Refining a model electron-density map via the Phantom Derivative method
No full textThe Phantom Derivative (PhD) method [Giacovazzo (2015), Acta Cryst. A71, 483-512] has recently been described for ab initio and non-ab initio phasing. It is based on the random generation of structures with the same unit cell and the same space group as the target structure (called ancil structures), which are used to create derivatives devoid of experimental diffraction amplitudes. In this paper, the non-ab initio variant of the method was checked using phase sets obtained by molecular-replacement techniques as a starting point for phase extension and refinement. It has been shown that application of PhD is able to extend and refine phases in a way that is competitive with other electron-density modification techniques
SIR2001: Phase Extension and Refinement for Proteins Via a Partial Structure Based Tangent Formula
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