Search-Compare

Contents

Release 97.2, May 1998

Table of Contents

1. Introduction

What Does Search_Compare Do?

Starting Search_Compare

Using This Guide

Additional Information

Note on Command Names

2. Theory

Superimposing Molecules

RMS Fitting

Electrostatic Potential Similarity

Steric Shape Similarity

Field_Fit (Electrostatic & Steric Similarity)

Steric Clash-checking

Systematic Conformational Searching

Standard Searches

Use of Distance Constraints

Screening by Energy Criteria

Vector Maps

Screening Duplicate Conformations

3. Implementation

Volumes

Overlapping Molecules

Systematic Conformational Searching on Ring Systems

Use of Energy Criteria in Systematic Conformational Searching

Vector Mapping

Background Jobs

4. Command Summary

Volume Pulldown

Create

Boolean

Grid_Setup

Align

Color

Label

Display

List

Overlap Pulldown

Define

Field_Fit

Display

SC_Search Pulldown

Set_Ring_Closure

Set_Rot_Bond

Set_Distance

Set_Dist_Map

Scale_Radii

Set_Energy_Params

Set_Filter_Params

SCS_Run

Load

Vector_Map Pulldown

Create

Color

Label

Display_Vector

List

Conformer Pulldown

Display

Distance_Map Pulldown

Boolean

Construct_Graph

Spreadsheet Pulldown

Graph Pulldown

Background_Job Pulldown

5. Methodology

Using the Volume Pulldown

Aligning Molecules and Volumes

Specifying How Volumes will be Calculated

Creating Volumes

Displaying Information About the Volume

Boolean Operations on Volumes

Determining How Many Volumes Are Displayed after a Boolean Operation

Changing How Existing Volumes Are Displayed

Cancelling a Volume Calculation

Using the Overlap Pulldown

Using Highlights

Defining Atom Pairs

Setting Up Torsions

Checking the Specifications

Correcting Mistaken Entries

Executing the RMS Fitting Calculation

Executing the Field Fitting Calculation

Using the SC_Search Pulldown

Standard Searches

Advanced Searches

Using the Distance_Map Pulldown

Boolean Operations on Distance Maps

Setting up a Boolean Distance Map Calculation

Visualizing a Distance Map as a Graph

Constructing a Distance Map Graph of an N-Dimensional Distance Map

Constructing a Distance Map Graph From a Trajectory.

Using the Vector_Map Pulldown

Creating and Editing a Vector Map

Controlling the Display of a Vector Map

Using the Conformer Pulldown

6. Tutorial

Pilot Online Tutorials

A. References

B. Glossary

C. File Formats

Input Files

Search_Compare Parameter File (.scs_prm)

Output Files

Search_Compare Log File (.scs_log)

Files Used and Produced by Advanced Searches

D. Utilities

scs_xdrtor

Purpose

Syntax

Errors and Warnings

Figure 1. Construction of a Two-Dimensional Distance Map

Figure 2. Ring Closure Constraints

Table 1. Parameter Values for Various Types of Conformational Searches

Table 2. Input Files and Keywords Required and Output Files Produced in Various Types of Searches