How to O

‘How to O ’ is an attempt to bring my user manuals up to date. It is organised into broad areas of interest rather than dealing with detailed commands, all of which are described in my web-based ‘A-Z of O’. I plan to make these available on my home pages as they are completed, so at the moment you will find the following descriptions on HowTo:

• Get Started

• Use the Master-menu system

• Build your first model in an experimental electron density map

• Rebuild your molecule during crystallographic refinement


Each of these main topics will be split into numerous sub-topics as is needed, and some will include the necessary files for demonstration purposes. O users are encouraged to contact me if they have any problems using the program (alwyn @ xray.bmc.uu.se). Morten Kjeldgaard maintains the o-info bulletin board if you prefer to leave a question or comment. If all else fails, there is also my web site http://xray.bmc.uu.se/alwyn and various O-related publications that are referenced in the GetStarted page.



Contents

Chapter 1: Getting Started with O

1.1 Downloading O

1.2 Installing O

1.3. Running O

1.3.1 Unix-based OS’s

1.3.2 Microsoft Windows OS’s

1.4 User interaction

1.4.1 At the terminal

1.4.2 In 3D

1.4.3 Keyboard input

1.4.4 Interactive prompt (line 2)

1.4.5 ID message information (line 3)

1.4.6 Active commands (line 4)

1.4.7 O pull-down menu (line 5)

1.4.8 Input devices: Dials, Mouse and Keyboard

1.4.9 Three button mouse controls

1.4.10 Single button mouse

1.4.11 Keyboard

1.4.12 Gamepad/Dials/Pucks

1.5 Customisation

1.5.1 Environment variables

1.5.2 When starting O

1.5.3 ID message information

1.5.4 Changing OpenGL Variables

1.5.5 ID text

1.5.6 Default FastMap units in density slider windows.

1.5.7 Arcade and Spaceball actions

1.5.8 User menu

1.5.9 O system macros in ODB 


Chapter 2: Master Menus

2.0 History

2.1 Master Menu Overview

2.1.1 History

2.1.2 What do I do? 

2.1.3 What you don’t need to know.

2.2 Master Menu Rebuild

2.2.1 Getting Started

2.2.2 Symbols setup

2.2.3 Green Commands 

2.2.4 Simple Rebuild Blinds 

2.2.5 HKL blind

2.2.6 Averaging maps blind

2.2.7 Grab guide blind

2.3 Master Menu Skeleton

2.3.1 Getting Started

2.3.2 Setup & Making the skeleton blind

2.3.3 Auto build blind

2.3.4 Edit skeleton blind

2.3.5 SSTs blind

2.3.6 Decorate blind 

2.3.7 Rebuild loops blind 

2.4 Master Menu Make a Ligand (QDS)

2.5 Master Menu Font Selection


Chapter 3: Interactive Map Interpretation

3.0 Introduction

3.1 Getting started

3.2 Localising the molecule

3.3 Editing the skeleton

3.4 Directionality

3.5 Secondary Structure Templates

3.6 Decorating the TRACE