Volumic omit maps inab initiodual-space phasing

2016 ◽  
Vol 72 (4) ◽  
pp. 480-488
Author(s):  
Gábor Oszlányi ◽  
András Sütő

Alternating-projection-type dual-space algorithms have a clear construction, but are susceptible to stagnation and, thus, inefficient for solving the phase problemab initio. To improve this behaviour new omit maps are introduced, which are real-space perturbations applied periodically during the iteration process. The omit maps are calledvolumic, because they delete some predetermined subvolume of the unit cell without searching for atomic regions or analysing the electron density in any other way. The basic algorithms of positivity, histogram matching and low-density elimination are tested by their solution statistics. It is concluded that, while all these algorithms based on weak constraints are practically useless in their pure forms, appropriate volumic omit maps can transform them to practically useful methods. In addition, the efficiency of the already useful reflector-type charge-flipping algorithm can be further improved. It is important that these results are obtained by using non-sharpened structure factors and without any weighting scheme or reciprocal-space perturbation. The mathematical background of volumic omit maps and their expected applications are also discussed.

2015 ◽  
Vol 71 (6) ◽  
pp. 592-598 ◽  
Author(s):  
Rick P. Millane ◽  
Romain D. Arnal

Uniqueness of the phase problem in macromolecular crystallography, and its relationship to the case of single particle imaging, is considered. The crystallographic problem is characterized by a constraint ratio that depends only on the size and symmetry of the molecule and the unit cell. The results are used to evaluate the effect of various real-space constraints. The case of an unknown molecular envelope is considered in detail. The results indicate the quite wide circumstances under whichab initiophasing should be possible.


Author(s):  
K. Chowdhury ◽  
S. Ghosh ◽  
M. Mukherjee

AbstractThe direct method program SAYTAN has been applied successfully to redetermine the structure of cytochrome c


2011 ◽  
Vol 326 ◽  
pp. 012026 ◽  
Author(s):  
K Müller ◽  
M Schowalter ◽  
O Rubel ◽  
D Z Hu ◽  
D M Schaadt ◽  
...  

2000 ◽  
Vol 2 (17) ◽  
pp. 3743-3751 ◽  
Author(s):  
Graham S. Chandler ◽  
Brian N. Figgis ◽  
Zucheng Li

1994 ◽  
Vol 225 (4-6) ◽  
pp. 421-426 ◽  
Author(s):  
G.S. Chandler ◽  
B.N. Figgis ◽  
P.A. Reynolds ◽  
S.K. Wolff

1995 ◽  
Vol 408 ◽  
Author(s):  
D. J. Sullivan ◽  
E. L. Briggs ◽  
C. J. Brabec ◽  
J. Bernholc

AbstractWe have developed a set of techniques for performing large scale ab initio calculations using multigrid accelerations and a real-space grid as a basis. The multigrid methods permit efficient calculations on ill-conditioned systems with long length scales or high energy cutoffs. We discuss the design of pseudopotentials for real-space grids, and the computation of ionic forces. The technique has been applied to several systems, including an isolated C60 molecule, the wurtzite phase of GaN, a 64-atom cell of GaN with the Ga d-states in valence, and a 443-atom protein. The method has been implemented on both vector and parallel architectures. We also discuss ongoing work on O(N) implementations and solvated biomolecules.


2021 ◽  
Vol 54 (6) ◽  
Author(s):  
Navjot Kaur ◽  
Atul Khanna ◽  
Alex C. Hannon

High real-space resolution neutron diffraction measurements up to 34 Å−1 were performed on a series of xCuO–(100 − x)TeO2 (x = 30, 40 and 50 mol%) glasses that were synthesized by the melt-quenching technique. The Fourier transformation of neutron diffraction structure factors was used to generate the pair distribution functions, with the first peak at 1.90 Å due to the overlapping Te–O and Cu–O atomic pairs. Reverse Monte Carlo (RMC) simulations were performed on the structure factors and the six partial atomic pair distributions of Cu–Cu, Cu–Te, Cu–O, Te–Te, Te–O and O–O were calculated. The Te–O and Cu–O distributions are very similar and asymmetrical, which revealed that there is a significant short-range disorder in the tellurite network due to the existence of a wide range of Te—O and Cu—O bond lengths. A high-Q (magnitude of momentum transfer function) neutron diffraction study revealed that the average Te–O coordination number decreases steadily from 3.45 to 3.18 with an increase in CuO concentration from 30 to 50 mol% in the glass network. Similar coordination number modifications were earlier found by the RMC analysis of neutron diffraction data sets of copper tellurite glasses that were performed up to lower Q maximum values of 9.5 Å−1. The comparison of high-Q and low-Q neutron diffraction studies reveals that RMC is a powerful and possibly the only technique that is available to elucidate the glass short-range and medium-range structural properties when diffraction data are available up to low Q values of, say, 9.5 Å−1, and when cation–oxygen bond lengths are strongly overlapping and cannot be resolved by Fourier transformation. In situ high-temperature (473 K) neutron diffraction studies of 50CuO–50TeO2 glass revealed that significant distortion of the tellurite network occurs with heating.


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