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

1. Theory

   Processing
      Linear prediction
      Automatic phase correction
   Assign
      Basis of the assignment strategy
      Assign building blocks
   Model
      Calculation of theoretical nuclear Overhauser effects (NOEs)
   Autoscreen module
      Introduction
      Autoscreen strategy
      Scoring

2. Tasks

   Task: Importing data
      Step 1: Transferring data
      Step 2: Converting the data
      Step 3: Checking the data
      Converting processed data
      Other conversion options
   Task: Modifying the quick-access menu
   Task: Working with FELIX and Insight together
      Communication between FELIX and InsightII
      Starting FELIX from InsightII/NMRchitect
      Sharing data between FELIX and InsightII
      Importing coordinates from Insight II to FELIX
      Reading IRMA files into FELIX
      Exporting restraints to Insight II
      Using InsightII for molecule display
   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
      Window function descriptions
      Fourier transforms
      Phasing
      Correcting baseline distortions
      Baseline point entities and files
      Spectrum display for baseline correction
      Adding and deleting baseline points
      Applying baseline-correction functions
      Real-time baseline correction
      Automatic baseline flattening
      Miscellaneous work tools
   Task: 1D peak picking and integration
      1D peak entities and files
      Working with picked peaks
      1D line fitting
      Integration
   Task: Processing 2D data
      General processing steps
   Task: Analysis of relaxation data
   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
   Task: Spin systems
   Task: Manual spin-system collection
   Task: Automated spin-system detection
      Tolerances
      Two-dimensional systematic search method
      Two-dimensional simulated annealing method
      Double-resonance methods
      Triple-resonance methods
      User-definable 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
   Task: Back-calculating NOESY spectra

3. Introduction to the menu interface

   About this chapter
   About FELIX
   The software license
   The program modules
   Getting started
   Completing a session
   The initialization macro
      Some FELIX initialization options
   Workspaces
   Memory allocation
   File directories and prefix definitions
   The menu interface
      Dialog boxes
      Pointer types
      Command mode and operation-system mode
   Graphics frame layouts
      Other graphics frame features
   Macros
   The database
      The database editor
      DBA contents viewer
   User interface controls
      Buttons
      Sliders
      Entry boxes
      Option menus

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

   File pulldown
      File/New
      File/Open
      File/Save
      File/Save As
      File/Close
      File/Import
      File/Export
      File/Convert
      File/BMRB
      File/Print
      File/Licenses
      File/Exit
   View pulldown
      View/Plot
      View/Plottype
      View/Limits
      View/Export Limits
      View/Draw Peaks
      View/Draw Frequencies
      View/Draw Integrals
      View/Draw Basepoints
      View/Draw Annotations
      View/Draw 1D Slices
      View/Multiple 1D Slices
      View/Thick 1D Slice
      View/Draw 2D Slices
      View/Tile Plot
      View/Strip Plot
      View/Overlay
   Edit pulldown
      Edit/Table
      Edit/Peaks
      Edit/NOE_Distance
      Edit/3J Restraints
      Edit/Prototype Patterns
      Edit/Spin Systems
      Edit/Stretches
      Edit/Residues
      Edit/Atoms
      Edit/Delete Table
      Edit/Annotation
   Preference pulldown
      Preference/Plot Parameters
      Preference/Levels
      Preference/1D Scale
      Preference/1D Slice
      Preference/2D Slice
      Preference/Overlay
      Preference/Reference
      Preference/Pick Parameters
      Preference/Integral
      Preference/Peak Display
      Preference/DQF Parameters
      Preference/Frequency Display
      Preference/Keypad
      Preference/Frame Layout
      Preference/Frame Connection
      Preference/Multiple Cursor
      Preference/Table
      Preference/Directory
      Preference/Memory
   Process1D pulldown
      Process1D/DC Offset
      Process1D/Zero Fill
      Process1D/Solvent Suppression
      Process1D/Window Function
      Process1D/Linear Prediction
      Process1D/Transform
      Process1D/Phase Correct
      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
      ProcessND/Utilities
   Tools pulldown
      Tools/Buffers
      Tools/Lists
      Tools/Generate Spectrum/FID
      Tools/Functions
      Tools/Mathematics
   Peaks pulldown
      Peaks/Pick One
      Peaks/Pick Region
      Peaks/Pick All
      Peaks/Remove One
      Peaks/Remove Region
      Peaks/Remove All
      Peaks/Edit
      Peaks/Filter
      Peaks/Optimize
      Peaks/Brother Peak
      Peaks/List
      Peaks/Find
      Peaks/Name One Peak
      Peaks/Example Peak
   Measure pulldown
      Measure/Cursor Position
      Measure/Correlated Cursors
      Measure/Distance/Separation
      Measure/Integral/Volume
      Measure/Buildup
      Measure/J Coupling
      Measure/Relaxation
      Measure/Scalar/Normalize
      Measure/DISCOVER Restraints
      Measure/X-PLOR Restraints
   Help pulldown
      Help/About
      Help/Topic
      Help/Keypad
      Help/Command/Edit

5. Assign user interface

   Project menu items
      Assign/Project
      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

6. Model interface

   Getting started
      Coordinate information
      NMR cross peak information
      Calculation of theoretical nuclear Overhauser effects (NOEs)
   Model pulldown menu items
      Model/Setup/Connect
      Model/Matrix Doubling
      Model/Set Scale
      Model/Draw Experimental
      Model/Draw Theoretical
      Model/Draw Molecule
      Molecule menu items
   General menu items
      Preference/Plot Parameters
      Measure/Cursor Position

7. Analytical user interface

   Project menu items
      Analytical/Project
      The Experiments table-Analytical/Experiment
      Analytical/Read Coordinates
      Analytical/Label
      Analytical/Color
   Manual spin-system picking-The Analytical/Frequency Clipboard menu items
      Analytical/Frequency Clipboard/Zero Clipboard
      Analytical/Frequency Clipboard/Add One
      Analytical/Frequency Clipboard/Delete One
      Analytical/Frequency Clipboard/Swap Two
      Analytical/Frequency Clipboard/Remove Duplicates
      Analytical/Frequency Clipboard/Compare Frequencies
      Analytical/Frequency Clipboard/Copy Clipboard To Proto
      Analytical/Frequency Clipboard/Copy Proto To Clipboard
      Analytical/Frequency Clipboard/View Clipboard
      Analytical/Frequency Clipboard/Sort Clipboard
      Analytical/Frequency Clipboard/Tile Clipboard
      Analytical/Frequency Clipboard/Strip Plot Clipboard
      Analytical/Frequency Clipboard/Draw Clipboard
   Prototype Pattern menu items
      Analytical/Collect Prototype Patterns
      Analytical/Edit Prototype Pattern
      Analytical/Zoom Prototype Pattern
   Peak menu items
      Analytical/List Peak

8. Autoscreen user interface

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

A. References

B. FELIX startup

   The .Xdefaults file
   The initialization macro
      The init.mac file format
   The .felixrc99 file
      The .felixrc99 file format

C. Data transfer and conversion

   GE/Nicolet 1X80
   JEOL Alpha
   Varian VXR
   The FELIX data format
   Built-in data filters
   Gift data transfer and conversion filters

D. Keyboard shortcuts and accelerator keys

   Menu bar
   File pulldown <Alt>-f
   View pulldown <Alt>-v
   Edit pulldown <Alt>-e
   Preference pulldown <Alt>-p
   Process pulldown <Alt>-s
   Tools pulldown <Alt>-t
   Peaks pulldown <Alt>-k
   Measure pulldown <Alt>-u
   Model pulldown <Alt>-m
   Assign pulldown <Alt>-a
   Analytical pulldown <Alt>-l
   Autoscreen pulldown <Alt>-u
   Help pulldown <Alt>-h
   Pulldown-independent functions

E. Data files

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