MacroModel Quick Start Guide - ISP

ContentsDocument Conventions .................................................................................................... viiChapter 1: Getting Started............................................................................................... 11.1 About MacroModel .................................................................................................... 11.2 About this Manual ..................................................................................................... 11.3 Preparing for the Exercises..................................................................................... 21.3.1 Creating a Working Directory and Copying Files ................................................ 21.3.2 Starting Maestro ................................................................................................. 31.3.3 Setting the Maestro Working Directory ............................................................... 4Chapter 2: Using Maestro................................................................................................. 52.1 Importing a Structure ............................................................................................... 52.2 Identifying, Labeling, and Deleting Structure Elements .................................... 72.3 Using the Find Atoms Panel to Identify Molecules ............................................. 92.4 Displaying and Undisplaying Atoms ................................................................... 102.5 Applying and Removing Atom Labels................................................................. 122.6 Adjusting Bond Orders, Atom Types, and Formal Charges............................ 132.7 Adding Hydrogens to a United Atom Structure................................................. 142.8 Creating and Viewing Surfaces ............................................................................ 152.8.1 Creating a Molecular Surface of a Complex ..................................................... 152.8.2 Limits to a Surface ............................................................................................ 172.8.3 Generating a Surface for One Molecule in a Complex...................................... 182.8.4 Creating a Map of the Binding Site ................................................................... 192.9 Creating and Manipulating Atom Sets ................................................................ 212.9.1 Defining an Atom Set by Selecting Atoms ........................................................ 222.9.2 Defining an Atom Set with the Atom Selection Dialog Box ............................... 232.9.3 Defining Atom Sets With Boolean Operations .................................................. 242.10 Filtering Structures: Sorting ............................................................................... 252.10.1 Generating Data.............................................................................................. 26MacroModel 9.7 Quick Start Guideiii