Felix User Guide

Contents

Release 98.0, December 1998

How to Use This Book

Using this book

Who should use this book

What does Felix do?

Feature list

Starting Felix

Related books

Typographical conventions

1. 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 the Felix and Insight programs together

Communication between Felix and Insight II

Starting Felix from Insight II/NMRchitect

Sharing data between Felix and Insight II

Importing coordinates from Insight II to Felix

Reading IRMA files into Felix

Exporting restraints to the Insight II environment

Using Insight II for molecular 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 spectral data values

Correlated cursors

Spectral 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

Spectral 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 2-dimensional 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 in 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

2. 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 system mode

Graphics frame layouts

Other graphics frame features

Macros

The database

The database editor

DBA contents viewer

User interface widgets

Buttons

Sliders

Input fields

Option menus

3. 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

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

Process pulldown

Process/DC Offset

Process/Zero Fill

Process/Solvent Suppression

Process/Window Function

Process/Linear prediction

Process/Transform

Process/Phase Correct

Process/Baseline correction

Process/1D Data Processing

Process/2D Data Processing

Process/3D Data Processing

Process/3D Plane Processing

Process/4D Data Processing

Process/Phase Correct Matrix

Process/Baseline Correct Matrix

Process/Reverse Matrix

Process/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

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

4. Assign User Interface

Project commands

Assign/Project

The Experiments table--Assign/Experiment

Assign/Define Library

Assign/Read Coordinates

Manual spin system picking--the Assign/Frequency Clipboard commands

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 commands

Assign/Collect Prototype Patterns

Assign/Edit Prototype Pattern

Assign/Promote Prototype Patterns

Assign/Zoom Prototype Pattern

Pattern (Spin Systems) Commands

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 Commands

Assign/List Peak

Assign/Peak Assign

Pattern/List Membership

Pattern/List Frequency

5. Model Interface

Getting started

Coordinate information

NMR cross peak information

Calculation of theoretical nuclear overhauser effects (NOE's)

Model pulldown commands

Model/Setup/Connect

Model/Matrix Doubling

Model/Set Scale

Model/Draw Experimental

Model/Draw Theoretical

Model/Draw Molecule

Molecule commands

General commands

Preference/Plot Parameters

Measure/Cursor Position

6. Analytical User Interface

Project commands

Analytical/Project

The Experiments table--Analytical/Experiment

Analytical/Read Coordinates

Analytical/Label

Analytical/Color

Manual spin system picking--the Analytical/Frequency Clipboard commands

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 commands

Analytical/Collect Prototype Patterns

Analytical/Edit Prototype Pattern

Analytical/Zoom Prototype Pattern

Peak Commands

Analytical/List Peak

7. Theory

About this chapter

Processing

Linear prediction

Assign

Basis of the assignment strategy

Assign building blocks

Model

Calculation of theoretical Nuclear Overhauser Effects (NOE's)

A. References

B. 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 >

Help pulldown < Alt-h >

Pulldown-Independent commands

If the active display is a one-dimensional slice

C. Felix Startup

The .Xdefaults file

The initialization macro

The init.mac file format

The .felixrc97 file

The .felixrc97 file format

D. 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

E. Data Files

File Types

File Format for ASCII Data Files

ASCII Data File Example

Index