| Xsight |
Xsight is a fully integrated suite of software for the elucidation of macromolecular structures from single crystal X-ray diffraction data. It provides tools for phasing from heavy-atom derivative and anomalous dispersion data, molecule replacement, phase improvement by density modification, model fitting, refinement, analysis, and graphical representation.
Xsight is the collective name for a set of software components that can be used for macromolecular crystallographic analysis within the Insight II environment. Xsight includes the XtalView package for MIR analysis and density fitting, the MADSYS program for MAD phase determination, the REPLACE molecular replacement package, a graphical interface to the CNX package for structure refinement, the ProLSQ95 least-squares refinement package, and RotLSQ, a rigid-body refinement program. In addition, density modification routines, structure validation routines, and facilities to create crystal packing diagrams and to render solid electron density surfaces are contained within Xsight. Insight II functions that are applicable to X-ray analysis are also available.
XtalView (McRee 1993) is an extensive package of software that contains numerous routines to aid in the analysis of multiple isomorphous replacement data. In addition, it contains a powerful graphics package Xfit, which is primarily used in fitting models to electron density maps but also contains useful routines for generating presentation graphics.
MADSYS (Hendrickson 1991) is a program for carrying out all aspects of phase determination from multiple wavelength anomalous scattering data. This system includes facilities for scaling of multiple data sets, extracting anomalous scattering differences, refining anomalous scatterers, and calculating protein phases. To run the MADSYS program from within Xsight requires a separate MADSYS license.
REPLACE (Tong 1993) is a suite of computer programs that was developed for crystal structure determination by the method of molecule replacement. It includes a rotation function program as well as a translation function program.
CNX is a program for structure determination, which incorporates crystal structure refinement by simulated annealing and least-squares minimization. A graphical dictionary is provided for including stereochemical parameters for ligands in the CNX system. The graphical interface to CNX in this version of Xsight is compatible with CNX 2000 from Molecular Simulations Inc. The scripts written by this interface are not compatible with X-PLOR program scripts. To run the CNX program from within Xsight requires a separate CNX license.
ProLSQ95 (Hendrickson 1985) is a modified set of the computer programs for restrained least-squares refinement of protein structures. Modifications include the incorporation of a bulk solvent-scattering model, automatic handling of discretely disordered conformations, free R-value calculations, and the FFT algorithm for fast calculations. A graphical dictionary is available for adding new ligands to the ProLSQ95 stereochemical dictionary.
RotLSQ (Hendrickson, unpublished) is a program for carrying out rigid-body refinements of protein structures.
XtalView, MADSYS, REPLACE, CNX, ProLSQ95, and RotLSQ can all be accessed from the Xsight module within Insight II (see Getting started). The density modification routines, structure validation routines, routines for creating crystal packing diagrams, and routines for solid electron density rendering capability are also accessed from the Xsight module. The ability to generate Richardson-style secondary renderings is included the Molecule pulldown of the Viewer module.
To access the Xsight software, first start the Insight II® software, then click the logo in the upper left corner and select Xsight from the pulldown. Alternatively, Xsight can be accessed by entering the command Xsight at the system prompt. See Chapter 4, Methodology, for more detailed information about getting started.
In referring to commands that are accessed when using Xsight from within Insight II, this guide uses the format Pulldown/Command, since you use the mouse to select the pulldown first, before the command name appears. However, if you enter commands on the command line near the bottom of the Insight II window, the names must be entered in the format Command Pulldown or Command (whichever appears at the top of the equivalent parameter block).
This guide contains both theoretical and practical information for using Xsight functionalities. Chapter 2, Theory, contains explanations of the mathematical and chemical principles underlying the Xsight software. Chapter 3, Implementation, describes how the theory was put into practice to create this software. Chapter 4, Methodology, explains how to solve certain general types of problems using the software. Chapter 5, Tutorial, takes you through specific examples of solving problems using Xsight. The appendices list the references cited in the text and provide detailed keyword descriptions for the component packages.
Online help for the commands and parameters in Xsight as accessed through the Insight II program is available by using the mouse to click the ? at the bottom of the icon bar in Insight II. To print online help, click the PostScript button, then the appropriate button for the file you want to print.