How to Use This Book

This book provides an introduction to the use of QUANTA's X-Ray crystallography applications. The first chapter contains an overview of the crystallographic process and the components of Accelrys' crystallographic software applications that facilitate each activity in the process. The remaining chapters describe the applications in detail.

How to find information

If you want to know about... Read...

Managing maps and using the Maps Management table

Managing Maps

General information about fitting coordinates to maps

Introduction to X-AUTOFIT/X-BUILD/X-POWERFIT (X-FIT)

Background and tips for skeletonizing and fitting coordinates to electron density maps

Using X-AUTOFIT

Model building

Using X-BUILD

Generate Ca traces from electron density maps

Using X-POWERFIT

Using the commands on the X-AUTOFIT or X-BUILD palettes

X-AUTOFIT:X-BUILD Tools

Fitting ligand coordinates automatically into electron density maps

Using X-LIGAND

Searching electron density maps for water peaks

Using X-SOLVATE

Controlling the 3D pointer

Using the 3D Pointer

Creating databases to be used by Search Fragment Database.

Creating a Fragment Database

Using the cnx.bat file

The cnx.bat File

Searching a specialized database to locate a suitable set of fragments for modeling undefined regions of a protein

Searching for Fragments

Using RTF and PSF modes

Using RTF and PSF Modes

An extension of the mbkall program

Extend

If you want to know about...	Read...
Managing maps and using the Maps Management table	Managing Maps
General information about fitting coordinates to maps	Introduction to X-AUTOFIT/X-BUILD/X-POWERFIT (X-FIT)
Background and tips for skeletonizing and fitting coordinates to electron density maps	Using X-AUTOFIT
Model building	Using X-BUILD
Generate Ca traces from electron density maps	Using X-POWERFIT
Using the commands on the X-AUTOFIT or X-BUILD palettes	X-AUTOFIT:X-BUILD Tools
Fitting ligand coordinates automatically into electron density maps	Using X-LIGAND
Searching electron density maps for water peaks	Using X-SOLVATE
Controlling the 3D pointer	Using the 3D Pointer
Creating databases to be used by Search Fragment Database.	Creating a Fragment Database
Using the cnx.bat file	The cnx.bat File
Searching a specialized database to locate a suitable set of fragments for modeling undefined regions of a protein	Searching for Fragments
Using RTF and PSF modes	Using RTF and PSF Modes
An extension of the mbkall program	Extend

Typographical conventions

Unless otherwise noted in the text, this manual uses the typographical conventions described below:

Words in italic represent variables. For example:

The application saves the file to filename.msf

In this example, the name of the MSF that you want to use replaces the value filename.

Sample syntax and the examples illustrating the contents of files are presented in a fixed-width font. For example, the following illustrates a line in an input file:

	ACAM_HAMMH.CRD

Names of items in the interface or presented on the screen are presented in bold. For example:

Select X-AUTOFIT on the Applications menu.