Version 2004 for Windows
User Guide

1. How to use this guide

   Using this book
   Who should use this book
   What does FELIX do?
      Feature list
   Starting FELIX
   Related books
   Typographical conventions

2. Theory

      Linear prediction
   Automatic phase correction
      Basis of the assignment strategy
   2D/3D homonuclear assignment strategy
      3D/4D heteronuclear assignment strategy
      Assign building blocks
   Autoscreen module
      Autoscreen scoring strategy

3. Tasks

   Task: Importing data
      Transferring data
   Task: Modifying the quick-access (context) menu
   Task: Working with 1D data
      Reading data files
      Saving data
      Displaying 1D spectra
      Changing 1D limits
      Adjusting plot parameters
      1D data buffers
      Adjusting stack and buffer display
      Axes and referencing
      Finding data values in spectra
      Correlated cursors
      Spectrum separation
      Zero-filling and removing DC offset
      Linear prediction
      Solvent signal suppression
      Viewing and applying window functions
      Fourier transforms
      Correcting baseline distortions
      Baseline point entities and files
      Spectrum display for baseline correction
      Adding and deleting baseline points
      Applying baseline-correction functions
      Miscellaneous work tools
   Task: 1D peak picking and integration
      1D peak entities and files
      Working with picked peaks
      1D line fitting
   Task: Processing 2D data
      General processing steps
   Task: Analysis of relaxation data
      Evaluate peak heights or peak volumes
      Estimate signal-to-noise ratio
      Fit data to exponential function
      Analysis of heteronuclear NOE data
      Preparing input data files for Modelfree
   Task: Working with assignment databases
   Task: Adding modified residues to the Assign database
   Task: Peak picking
   Task: Using connected frames to navigate among multiple spectra within Assign
   Spin systems
      Task: Manual spin-system collection
      Task: Automated spin-system detection
      Task: Semiautomated spin-system detection
      Task: Spin-system extension
      Task: Spin-system promotion
      Task: Spin-system identification
   Task: Establishing connectivities
   Task: Sequential assignment
   Task: Resonance assignment
   Task: Peak assignment
   Task: Restraint generation
   Task: Checking and redefining restraints

4. Introduction to the menu interface

   About this chapter
   About FELIX
   Software license
   Program modules
   Getting started
   Completing a session
   Initialization macro
      Some FELIX initialization options
      1D workspace (work)
      Additional 1D workspaces (buffers)
      N-dimensional matrix workspace (matrix)
   Memory allocation
   File directories and prefix definitions
   Menu interface
      Control panels (dialog boxes)
      Pointer types
      Accessing the FELIX command interface
   Graphics frame layouts
      Other graphics frame features
      Database editor
      Database contents viewer

5. Processing, visualization, and analysis interface (1D/2D/ND)

   File pulldown
      File/Save As
      File/Print Setup
      File/Print Preview
      File/Log File
   View pulldown
      View/Tile and Strip Plot
      1D vector views
      2D plane views
      View/Export Limits
      2D plane exporting
      View/Draw Peaks
      View/Draw Frequencies
      View/Draw Integrals
      View/Draw Basepoints
      View/Draw Annotations
      View/Draw 1D Slices
      View/Draw Multiple 1D Slices
      View/Draw Thick 1D Slice
      View/Draw 2D Slices
      View/Tile Plot
      View/Strip Plot
      View/Command Input
   Edit pulldown
      Edit/Delete Table
      Edit/3J Restraints
      Edit/Prototype Patterns
      Edit/Spin Systems
   Preference pulldown
      Preference/Plot Parameters
      Preference/1D Scale
      Preference/2D/ND Levels
      Preference/Pick Parameters
      Preference/Peak Display
      Preference/DQF Parameters
      Preference/Frame Layout
      Preference/Frame Connection
      Preference/Multiple Cursor
      Preference/Macro Debug
   Process1D pulldown
      Process1D/DC Offset
      Process1D/Zero Fill
      Process1D/Solvent Suppression
      Process1D/Window Function
      Process1D/Linear Prediction
      Process1D/Phase Correction
      Process1D/Baseline Correction
      Process1D/Open Process
   ProcessND pulldown
      ProcessND/Open and Process 2D
      ProcessND/Open and Process 3D
      ProcessND/Open and Plane Process 3D
      ProcessND/Open and Process 4D
      ProcessND/Phase Correct
      ProcessND/Baseline Correct
      ProcessND/Reverse Matrix
   Tools pulldown
      List contents
      List action
      Tools/Generate Spectrum/FID
   Peaks pulldown
      Peaks/Pick One
      Peaks/Pick Region
      Peaks/Pick All
      Peaks/Remove One
      Peaks/Remove Region
      Peaks/Remove All
      Peaks/Example Peak
      Peaks/Brother Peak
      Peaks/Name One Peak
   Measure pulldown
      Measure/Cursor Position
      Measure/Correlated Cursors
      Measure/J Coupling
      Measure/DISCOVER Restraints
      Measure/X-PLOR Restraints
   Window pulldown
      Window/Tile Horizontally
      Window/Tile Vertically
      Window/Add New Window
      Window/New Layout
   Help pulldown

6. Assign user interface

   Project menu items
      The Experiments table-Assign/Experiment
      Assign/Define Library
      Assign/Read Coordinates
   Manual spin-system picking-the Assign/Frequency Clipboard menu items
      Assign/Frequency Clipboard/Zero Clipboard
      Assign/Frequency Clipboard/Add One
      Assign/Frequency Clipboard/Delete One
      Assign/Frequency Clipboard/Swap Two
      Assign/Frequency Clipboard/Remove Duplicates
      Assign/Frequency Clipboard/Compare Frequencies
      Assign/Frequency Clipboard/Copy Clipboard To Pattern
      Assign/Frequency Clipboard/Copy Clipboard To Proto
      Assign/Frequency Clipboard/Copy Pattern To Clipboard
      Assign/Frequency Clipboard/Copy Proto To Clipboard
      Assign/Frequency Clipboard/View Clipboard
      Assign/Frequency Clipboard/Sort Clipboard
      Assign/Frequency Clipboard/Tile Clipboard
      Assign/Frequency Clipboard/Strip Plot Clipboard
      Assign/Frequency Clipboard/Draw Clipboard
   Prototype Pattern menu items
      Assign/Collect Prototype Patterns
      Assign/Edit Prototype Pattern
      Assign/Promote Prototype Patterns
      Assign/Zoom Prototype Pattern
   Pattern (Spin Systems) menu items
      Assign/Spin System
      Spin System Extension-Assign/Extend Spin Systems
      Residue Type Probability-Assign/Residue Type
      Neighbor Probability-Assign/Neighbor
      Search for Sequential Assignment -Assign/Sequential
      Spin System Assignment-Assign/Assign Spin System
      Assign/Chemical Shift Index (CSI)
      Reporting Spin Systems-Assign/Report Spin System
      Assign/Zoom Spin System
      Spin System Table-Edit/Spin Systems
      Stretches of Spin Systems-Edit/Stretches
      Assign Residue Table-Edit/Residues
   Peak Assignment menu items
      Assign/List Peak
      Assign/Peak Assign
      Pattern/List Membership
   Pattern/List Frequency

7. Autoscreen user interface

   Project menu items
      Processing and scoring menu items
      ROI menu items
      Display and print menu items
      Menu items for presenting results

A. References

B. Keyboard shortcuts and accelerator keys

   Accelerator keys
   Pulldown-independent functions

C. FELIX startup

   The felixrc.ini file
      The felixrc.ini file format
   The initialization macro

D. Data files

   File types
   File format for ASCII data files
      ASCII data file example