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Algorithms for deriving crystallographic space-group information. II: Treatment of special positions

Description: Algorithms for the treatment of special positions in 3-dimensional crystallographic space groups are presented. These include an algorithm for the determination of the site-symmetry group given the coordinates of a point, an algorithm for the determination of the exact location of the nearest special position, an algorithm for the assignment of a Wyckoff letter given the site-symmetry group, and an alternative algorithm for the assignment of a Wyckoff letter given the coordinates of a point directly. All algorithms are implemented in ISO C++ and are integrated into the Computational Crystallography Toolbox. The source code is freely available.
Date: October 5, 2001
Creator: Grosse-Kunstleve, Ralf W. & Adams, Paul D.
Partner: UNT Libraries Government Documents Department

On macromolecular refinement at subatomic resolution withinteratomic scatterers

Description: A study of the accurate electron density distribution in molecular crystals at subatomic resolution, better than {approx} 1.0 {angstrom}, requires more detailed models than those based on independent spherical atoms. A tool conventionally used in small-molecule crystallography is the multipolar model. Even at upper resolution limits of 0.8-1.0 {angstrom}, the number of experimental data is insufficient for the full multipolar model refinement. As an alternative, a simpler model composed of conventional independent spherical atoms augmented by additional scatterers to model bonding effects has been proposed. Refinement of these mixed models for several benchmark datasets gave results comparable in quality with results of multipolar refinement and superior of those for conventional models. Applications to several datasets of both small- and macro-molecules are shown. These refinements were performed using the general-purpose macromolecular refinement module phenix.refine of the PHENIX package.
Date: November 9, 2007
Creator: Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.; Lunin, Vladimir Y. & Urzhumtsev, Alexandre
Partner: UNT Libraries Government Documents Department

Improved Statistics for Determining the Patterson Symmetry fromUnmerged Diffraction Intensities

Description: We examine procedures for detecting the point-group symmetryof macromolecular datasets and propose enhancements. To validate apoint-group, it is sufficient to compare pairs of Bragg reflections thatare related by each of the group's component symmetry operators.Correlation is commonly expressed in the form of a single statisticalquantity (such as Rmerge) that incorporates information from all of theobserved reflections. However, the usual practice of weighting all pairsof symmetry-related intensities equally can obscure the fact that thevarious symmetry operators of the point-group contribute differingfractions of the total set. In some cases where particular symmetryelements are significantly under-represented, statistics calculatedglobally over all observations do not permit conclusions about thepoint-group and Patterson symmetry. The problem can be avoided byrepartitioning the data in a way that explicitly takes note of individualoperators. The new analysis methods, incorporated into the programLABELIT (cci.lbl.gov/labelit), can be performed early enough during dataacquisition, and are quick enough, that it is feasible to pause tooptimize the data collection strategy.
Date: January 9, 2006
Creator: Sauter, Nicholas K.; Grosse-Kunstleve, Ralf W. & Adams, Paul D.
Partner: UNT Libraries Government Documents Department

cctbx news

Description: The 'Computational Crystallography Toolbox' (cctbx, http://cctbx.sourceforge.net/) is the open-source component of the Phenix project (http://www.phenix-online.org/). Most recent cctbx developments are geared towards supporting new features of the phenix.refine application. Thus, the open-source mmtbx (macromolecular toolbox) module is currently being most rapidly developed. In this article we give an overview of some of the recent developments. However, the main theme of this article is the presentation of a light-weight example command-line application that was specifically developed for this newsletter: sequence alignment and superposition of two molecules read from files in PDB format. This involves parameter input based on the Phil module presented in Newsletter No. 5, fast reading of the PDB files with the new iotbx.pdb.input class, simple sequence alignment using the new mmtbx.alignment module, and use of the Kearsley (1989) superposition algorithm to find the least-squares solution for superposing C-alpha positions. The major steps are introduced individually, followed by a presentation of the complete application. The example application is deliberately limited in functionality to make it concise enough for this article. The main goal is to show how the open-source components are typically combined into an application. Even though the example is quite specific to macromolecular crystallography, we believe it will also be useful for a small-molecule audience interested in utilizing the large open-source library of general crystallographic algorithms (see our previous articles in this newsletter series) to build an application. We describe recent developments of the Computational Crystallography Toolbox.
Date: November 22, 2006
Creator: Grosse-Kunstleve, Ralf W.; Zwart, Peter H.; Afonine, Pavel V.; Ioerger, Thomas R. & Adams, Paul D.
Partner: UNT Libraries Government Documents Department

Robust indexing for automatic data collection

Description: We present improved methods for indexing diffraction patterns from macromolecular crystals. The novel procedures include a more robust way to verify the position of the incident X-ray beam on the detector, an algorithm to verify that the deduced lattice basis is consistent with the observations, and an alternative approach to identify the metric symmetry of the lattice. These methods help to correct failures commonly experienced during indexing, and increase the overall success rate of the process. Rapid indexing, without the need for visual inspection, will play an important role as beamlines at synchrotron sources prepare for high-throughput automation.
Date: December 9, 2003
Creator: Sauter, Nicholas K.; Grosse-Kunstleve, Ralf W. & Adams, Paul D.
Partner: UNT Libraries Government Documents Department

Automated Structure Solution with the PHENIX Suite

Description: Significant time and effort are often required to solve and complete a macromolecular crystal structure. The development of automated computational methods for the analysis, solution and completion of crystallographic structures has the potential to produce minimally biased models in a short time without the need for manual intervention. The PHENIX software suite is a highly automated system for macromolecular structure determination that can rapidly arrive at an initial partial model of a structure without significant human intervention, given moderate resolution and good quality data. This achievement has been made possible by the development of new algorithms for structure determination, maximum-likelihood molecular replacement (PHASER), heavy-atom search (HySS), template and pattern-based automated model-building (RESOLVE, TEXTAL), automated macromolecular refinement (phenix.refine), and iterative model-building, density modification and refinement that can operate at moderate resolution (RESOLVE, AutoBuild). These algorithms are based on a highly integrated and comprehensive set of crystallographic libraries that have been built and made available to the community. The algorithms are tightly linked and made easily accessible to users through the PHENIX Wizards and the PHENIX GUI.
Date: June 9, 2008
Creator: Zwart, Peter H.; Zwart, Peter H.; Afonine, Pavel; Grosse-Kunstleve, Ralf W.; Hung, Li-Wei; Ioerger, Tom R. et al.
Partner: UNT Libraries Government Documents Department