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

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.

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.

From a partial to the complete crystal structure. II. The procedure and its applications

Acta Crystallographica Section A Foundations of Crystallography, 1985

2~p, 2~q, 2~t¢ = ~ f2 A multisolution procedure, based on the probabilistic formulas obtained by Giacovazzo [Acta Cryst. (1983). A39, 685-692] is described, which aims at recovering the complete crystal structure from a partial one. A new weighted tangent formula develops starting phases: the correct solution among others is found by means of two revised figures of merit. The procedure is successfully applied to some practical cases. Symbols and abbreviations Throughout the paper a number of symbols will find frequent application. For most of them the reader is referred to the first paper of this series (Giacovazzo, 1983), from now on referred to as paper I. Other symbols not used in I are listed below.

WinCSD: software package for crystallographic calculations (Version 4)

Journal of Applied Crystallography, 2014

The fourth version of the program packageWinCSDis multi-purpose computer software for crystallographic calculations using single-crystal and powder X-ray and neutron diffraction data. The software environment and the graphical user interface are built using the platform of the Microsoft .NET Framework, which grants independence from changing Windows operating systems and allows for transferring to other operating systems. Graphic applications use the three-dimensional OpenGL graphics language.WinCSDcovers the complete spectrum of crystallographic calculations, including powder diffraction pattern deconvolution, crystal structure solution and refinement in 3 + dspace, refinement of the multipole model and electron density studies from diffraction data, and graphical representation of crystallographic information.

CURVIS : a program to study and analyse crystallographic structures and phase transitions

Journal of Applied Crystallography, 2005

The visualization of scientific data is, nowadays, of extreme importance. Phase transitions, the topology of a crystallographic system, the electron density distribution inside a lattice or the changes in crystal structure during phase transitions cannot be fully investigated without the help of proper visualization. The program CURVIS (downloadable free of charge upon request) was developed as a tool for investigating crystal structures and occurring transitions. In this tool, some features are implemented to analyse, display and manage the three-dimensional structure of crystals and single molecules. More importantly, CURVIS can generate and handle hyperbolic surfaces in three dimensions, and provide specific routines to perform calculations of curvature and energy of such surfaces. The most important features are (i) file format conversion (with assignment of the atom types and atomic charges), (ii) surface calculation and (iii) curvature and surface-energy analysis.

SIR 97: a new tool for crystal structure determination and refinement

Journal of Applied Crystallography, 1999

SIR97 is the integration of two programs, SIR92 and CAOS, the ®rst devoted to the solution of crystal structures by direct methods, the second to re®nement via least-squares±Fourier procedures. Several new features have been introduced in SIR97 with respect to the previous version, SIR92: greater automatization, increased ef®ciency of the direct methods section, and a powerful graphics interface. The program also provides publication tables and CIF ®les.

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.

REFMAC 5 for the refinement of macromolecular crystal structures

Acta Crystallographica Section D Biological Crystallography, 2011

This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the diffraction data employed (amplitudes or intensities), the presence of twinning and the availability of SAD/SIRAS experimental diffraction data. To ensure chemical and structural integrity of the refined model, REFMAC5 offers several classes of restraints and choices of model parameterization. Reliable models at resolutions at least as low as 4 Å can be achieved thanks to low-resolution refinement tools such as secondarystructure restraints, restraints to known homologous structures, automatic global and local NCS restraints, 'jelly-body' restraints and the use of novel long-range restraints on atomic displacement parameters (ADPs) based on the Kullback-Leibler divergence. REFMAC5 additionally offers TLS parameterization and, when high-resolution data are available, fast refinement of anisotropic ADPs. Refinement in the presence of twinning is performed in a fully automated fashion. REFMAC5 is a flexible and highly optimized refinement package that is ideally suited for refinement across the entire resolution spectrum encountered in macromolecular crystallography.