AFITT User Manual

Release version 1.3.1
January 23, 2008

OpenEye Scientific Software, Inc.

9 Bisbee Ct, Suite D
Santa Fe, NM 87508
www.eyesopen.com
support@eyesopen.com

Front Matter
Contents
1. Introduction
2. Installation
- 2.1 Microsoft Windows
- 2.2 UNIX/Linux
- 2.3 Mac OS X
  - 2.3.1 Platform differences
  - 2.3.2 Launching from the command line
- 2.4 Licenses
3. Getting Started
- 3.1 Why Another Modelling Program?
- 3.2 General Concepts
- 3.3 Object States
- 3.4 Scope
  - 3.4.1 Annoyances with Scope
- 3.5 Layout
  - 3.5.1 Main Windows
  - 3.5.2 Peripheral Windows
- 3.6 Undo/Redo
- 3.7 3D Window Usage
- 3.8 Spreadsheet Usage
- 3.9 2D Preview Usage
- 3.10 How to Center
- 3.11 Tasks
- 3.12 Ligand Task
- 3.13 Protein Task
- 3.14 Refinement
4. File I/O
- 4.1 Opening Files
- 4.2 Closing Files
- 4.3 Saving Files
- 4.4 Importing Files
- 4.5 Exporting Files
- 4.6 Drag and Drop
5. 3D Display
- 5.1 User Interaction
  - 5.1.1 Mouse
  - 5.1.2 Style Control
- 5.2 Rendering
- 5.3 Stereo
- 5.4 Viewpoint
- 5.5 Bookmarks
- 5.6 Tiled Display
- 5.7 Toolbars
- 5.8 Display Widgets
- 5.9 Molecular Visualization
- 5.10 Grid Visualization
  - 5.10.1 Grid Types
  - 5.10.2 Reentrant Grids
- 5.11 Surface Visualization
- 5.12 Symmetry
- 5.13 Symmetry menu
- 5.14 Custom Views
6. Modeling Basics
- 6.1 Tasks
  - 6.1.1 Task Menu
- 6.2 File menu
- 6.3 Edit menu
- 6.4 Popup menus
- 6.5 Real Space Refinement
7. Ligand Modeling
- 7.1 Ligand Modeling Window
- 7.2 3D window
- 7.3 Spreadsheet
- 7.4 2D Preview
- 7.5 Locating ligand density
- 7.6 Filtering Ligand Density Based on Distance to a residue
- 7.7 Working With Poor Density
- 7.8 Writing Refinement Dictionaries
8. Protein Modeling
- 8.1 List Window
- 8.2 3D Window
- 8.3 Style Window
- 8.4 Protein Modeling Operations
- 8.5 Appending, Prepending or Mutating Residues or Rotamers
- 8.6 Bond Specific Operations
  - 8.6.1 Adding Covalent Bonds
- 8.7 Mouse Mode Toolbars
- 8.8 2D Sequence View
- 8.9 Ramachandran plot
- 8.10 Modeling toolbar
9. Protein Refinement
- 9.1 Setting Up Refmac5
- 9.2 Altering Refmac5 Parameters
10. 2D Display
- 10.1 Preview vs. Viewer
- 10.2 Interaction
11. Spreadsheet
- 11.1 Basic Usage
- 11.2 Sorting
- 11.3 Displaying Data
- 11.4 Organizing Columns
- 11.5 Creating New Columns
  - 11.5.1 Math Functions
  - 11.5.2 OEChem Functions
- 11.6 Filtering
- 11.7 Statistics
- 11.8 Formatting Columns
- 11.9 Importing/Exporting
  - 11.9.1 Importing
  - 11.9.2 Exporting
12. List Management
- 12.1 Introduction
- 12.2 Browsing
- 12.3 Views
- 12.4 List Columns
- 12.5 List Manipulation
  - 12.5.1 Creating Lists
  - 12.5.2 Deleting from Lists
- 12.6 List Toolbar
13. Process Management
- 13.1 Processes
- 13.2 Pipes
14. Scripting
- 14.1 Journal File
- 14.2 Startup File
- 14.3 Scripting Manual
- 14.4 Scripting Window
- 14.5 OEChemLite
15. Query language
- 15.1 Introduction
- 15.2 Operators
- 15.3 Lists and Ranges
- 15.4 Properties
- 15.5 Macros/Pre-defined sets
- 15.6 Scripting with ScratchScope
16. Preferences
- 16.1 Useful Preferences
17. Example Data
18. Example Scripts
19. Automation
- 19.1 Getting Started With Automation
- 19.2 Advanced Automation
- 19.3 Platform Differences
  - 19.3.1 Windows
  - 19.3.2 OS X
20. Mouse Maps
- 20.1 AFITT Mouse Map
21. Release Notes
- 21.1 Version 1.3.1
- 21.2 Version 1.3.0
- 21.3 Version 1.2.2
- 21.4 Version 1.2.1
- 21.5 Version 1.2.0
Bibliography
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