wARP : Improvement and Extension of Crystallographic Phases by Weighted Averaging of Multiple-Refined Dummy Atomic Models (original) (raw)

New Tricks of the Trade for Crystal Structure Refinement

ACS central science, 2017

Accurate crystal structures and their experimental uncertainties, determined by X-ray diffraction/neutron diffraction techniques, are vital for crystal engineering studies, such as polymorph stability and crystal morphology calculations. Because of differences in crystal growth and data measurement conditions, crystallographic databases often contain multiple entries of varying quality of the same compound. The choice of the most reliable and best quality crystal structure from many very similar structures remains an unresolved problem, especially for nonexperts. In addition, while crystallographers can make use of some professional software (i.e., Materials Studio) for structure refinement, noncrystallographers may not have access to it. In the present paper, we propose a simple method to study the sensitivity of the crystal lattice energy to changes in the structural parameters, which creates a diagnostic tool to test the quality of crystal structure files and to improve the low-q...

PRISM : automated crystallographic phase refinement by iterative skeletonization

Acta Crystallographica Section A - ACTA CRYSTALLOGR A, 1993

PATRICK AZAVANT AND ALBERT LICHANOT 97 ions are parameters that establish the almost fully ionic character of these compounds. The crystallinefield effect causes a contraction of the anions and a slight expansion of the cation. In the absence of recent and precise experimental data on structure factors, the values reported in this study may be used as a reference. They will be refined in the future by the exploration of the importance of polarization functions on the S 2-ion in order to improve the agreement factor for Li2S and to calculate its deformation accurately by the rigorous calculation of scattering factors by Fourier transform of the electron density on a 'per energy band occupied' basis and by taking thermal agitation into account.

Automatic solution and refinement of crystal structures by means of the package UNIQUE

Acta Crystallographica Section A Foundations of Crystallography, 1991

An automatic procedure for crystal structure solution and refinement has been devised. It is able to take decisions at each critical point of the analysis by taking careful account of all information available at that point. The procedure has been implemented into the package UNIQUE (CRYSTALS+SIR88) and has been applied successfully to a wide variety of crystal structures. In most cases, the complete structure is recovered and refined without any user intervention. R values usually lie in the range 0.08-0.15.

SIR2011 : a new package for crystal structure determination and refinement

Journal of Applied Crystallography, 2012

SIR2011, the successor of SIR2004, is the latest program of the SIR suite. It can solve ab initio crystal structures of small-and medium-size molecules, as well as protein structures, using X-ray or electron diffraction data. With respect to the predecessor the program has several new abilities: e.g. a new phasing method (VLD) has been implemented, it is able to exploit prior knowledge of the molecular geometry via simulated annealing techniques, it can use molecular replacement methods for solving proteins, it includes new tools like free lunch and new approaches for electron diffraction data, and it visualizes threedimensional electron density maps. The graphical interface has been further improved and allows the straightforward use of the program even in difficult cases.

From a partial to the complete crystal structure. III. A new procedure and its applications

Acta Crystallographica Section A Foundations of Crystallography, 1989

The procedure described in the first two papers of this series . Acta Cryst. A39, 685-692;. Acta Cryst. A41, 605-613] for recovering from a partial crystal structure the complete one has been reconsidered. Several modifications have been introduced which make the procedure more efficient. Furthermore, a new method is described which is able to combine prior information on a located fragment with the second representation formula P10. Experimental 0108-7673/89/110781-06503.00 tests show that very small fragments are sufficient to recover the complete crystal structure.

CrystTwiV: a webserver for automated phase extension and refinement in X-ray crystallography

Nucleic Acids Research, 2007

An important stage in macromolecular crystallography is that of phase extension and refinement when initial phase estimates are available from isomorphous replacement or anomalous scattering or other methods. For this purpose, an alternative method called the twin variables (TwiV) method has been proposed. The algorithm is based on alternately transferring the phase information between the twin variable sets. The phase extension and refinement is evaluated with the crystallographic symmetry test by deliberately sacrificing the spacegroup symmetry in the starting set, then using its re-appearance as a criterion for correctness. Here we present a software program (CrysTwiV) that runs on the web (freely available at: http://btweb.aua.gr/ crystwiv/) implementing the above-mentioned method.