Converter

Contents

Release 2000, March 2000

1. Introduction

What Does Converter Do?

Starting Converter

Using This Guide

Additional Information

Note on Command Names

2. Theory

Two- to Three-Dimensional Conversion

Distance Geometry

Describing Molecular Conformation

Covalent Distance Constraints

Vicinal Distance Constraints

Chirality Constraints

Steric Distance Constraints

Triangle Bound Smoothing

Metrization

Embedding

Optimization of the Coordinates

The Error Function

Computation of Distances in Four Dimensions

Minimization and Analysis

3. Command Summary

Sketch Pulldown

DB_Convert

4. Methodology

Using Converter in the Insight II Environment

Conformational Sampling

Generating Multiple Stereoisomers

Converting Multiple-Piece Sketches

Running Converter as a UNIX Job

3D Conversion Errors In Sketch and Converter

Insufficient Disk Space to Run DGII

Invalid License for DGII_Pgm

Unusual Chemical Structure

Invalid Command

A. References

B. Glossary

C. File Formats

Sketch Files

Converter Files

D. Utilities

db_convert Utility