Search_Compare - Introduction

What Does Search_Compare Do?

The Search_Compare module contains the pulldowns Volume, Overlap, SC_Search, Vector_Map, Conformer, Distance_Map, Spreadsheet, Graph, and Background_Job. The commands in Search_Compare enable you to calculate and operate on molecular volumes, to superimpose two or more molecules, to search systematically for the sterically allowed conformations of a molecule, and to quickly find and examine conformations of interest after they have been generated.

The Volume pulldown contains the commands for calculating and operating on molecular volumes--the space enclosed by a molecule's van der Waals surface. You can also change how a volume is displayed.

The Overlap pulldown enables you to simultaneously superimpose multiple flexible molecules using two approaches:

Generating an overall rms best fit of all atoms that have been selected for superimposition.
Optimizing the molecular field similarity, based on electrostatic potentials and steric shape.

You may specify certain bonds in the molecules as rotatable. During superimposition, these torsions will be rigidly rotated in the process of finding the best fit. No limit is imposed on the number of molecules, atom pairs, or torsions specified.

The SC_Search and Background_Job pulldowns are used to set up and run a systematic conformational search and to load the search results into Insight® II for viewing and analysis. The search is a systematic exploration of the conformational space accessible to a molecule and is determined by continuously rotating one or more bonds through desired ranges.

You can now use both distance constraints and a more powerful distance mapping facility in searches, for example, to find common conformations among a series of molecules having similar activity or to see whether a drug candidate molecule can adopt some desired conformation.

In addition, the energy evaluators and minimizers of Discover are directly accessible from Search_Compare. You can perform searches with energy calculation or minimization, thus screening out unstable conformers (and saving disk space). You can also subject the conformers resulting from previous searches to energy calculations without having to leave the Insight II environment.

The Vector_Map pulldown allows you to examine atomic movements that occurred during a conformational search so as to quickly find conformations in which pairs of atoms are located at specific points in space.

The Conformer pulldown is used to display conformations in the currently loaded trajectory associated with vector maps and graphs.

The Distance_Map pulldown contains commands that allow you to perform boolean operations on distance maps, and to construct distance map graphs either interactively or from a systematic search run with a distance map.

For more information on the Spreadsheet, Graph, and Background_Job pulldowns refer to the Insight II User Guide.

Starting Search_Compare

Search_Compare is invoked by selecting Search_Compare from the Module pulldown in Insight II.

Using This Guide

Chapter 2, Theory, in this User Guide presents the theories upon which the functionalities of Search_Compare are based. It is written mainly for the typical scientist-user of Search_Compare. Chapter 3, Implementation, presents some information on how the functionalities are implemented. Chapter 4, Command Summary, briefly summarizes the main functions of each command. Chapter 5, Methodology, explains how to use Search_Compare, while Chapter 6, Tutorial, shows how to use it in a series of tutorial lessons. Appendices A, References, and B, Glossary, contain the scientific references cited in this guide and a glossary of terms and symbols. The file formats and a utility are documented in Appendices C, File Formats, and D, Utilities.

Additional Information

In addition to this printed Search_Compare documentation, on-line help is available and activated by clicking the ? icon located on the icon bar in the Insight II window.

Technical information that is mainly of use to programmers and system administrators is contained in the System Guide.

Note on Command Names

In referring to commands that are used when running Search_Compare through the Insight II menus, this guide uses the format Pulldown/Command, since you use the mouse to select the pulldown first, before the command name appears. Note, however, that 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 simply Command (whichever appears at the top of the equivalent parameter block).

Last updated November 22, 2003.