SZMAP documentation

This is the documentation of SZMAP 1.0.0, the first public release.

For the complete list of features and bug fixes, please refer to the Release Notes chapter. You can find out more about our applications and toolkits in OpenEye Products

Contact support via email at support@eyesopen.com.

SZMAP

• Front Matter
• Installation and Platform Notes
  • Licenses
  • Installation
    • General Installation
    • Linux/Unix
    • Windows
    • Mac OS X
  • Uninstallation
    • Linux/Unix
    • Windows
    • Mac OS X
• Quick Start
  • Introduction
  • A Word About Pronunciation
  • SZMAP Workflow
    • Protein Preparation
    • Running SZMAP
    • Running SZMAP Stabilization Calculations
    • Running SZMAP at Coordinates
    • Analyze Results

Application

• Using SZMAP
  • Input File Preparation
  • Example Commands
• szmap
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Input File Options
    • Output File Options
    • Selection Options
    • Grid Options
    • Calculation Options
    • Other Options

Utilities

• fixdupatomnames
  • Example
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Other Options
• mkhetdict
  • Example
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Output Options
    • Other Options
• pch
  • Example
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Output Options
    • Other Options
• szmap_grid
  • Meta-data
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Grid Options
    • Interpolation Options
    • Other Options
• grid_comp
  • Example
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Grid Options
    • Parameter Options
    • Other Options
• szmap_report
  • Command Line Interface
    • Required Parameters
  • Command Line Options
    • Output Options
    • Molecule Display Options
    • General Options
    • Other Options

VIDA Extensions

• Installing VIDA Extensions
• WaterColor VIDA Extension
  • Tutorial
• Water Orientation VIDA Extension
• Color By Atom Properties VIDA Extension

Theory

• SZMAP Theory
  • Philosophy and Design
  • Technical Details
    • Energy Calculations
    • Water Charges
    • Neutral Water, Bubbles and Difference Grids

Appendix

• Appendix
  • Appendix 1: SZMAP Grids
    • Protein + Ligand Complex
    • Ligand Only
    • Protein Only
    • Complex - Protein - Ligand
  • Appendix 2: SZMAP Atom Properties
    • Complex, Apo or Ligand
    • Complex - Protein - Ligand

Release Notes

• Release Notes
  • SZMAP 1.0.0

Bibliography

• Bibliography

Indices

• Index
• Search Page

This documentation was updated on June 27, 2011.