Part I. Usage

Table of Contents

1. Introduction

2. Installation

3. Quick User's Guide

Overview

Helpful Concepts

Clicking

Guide Nomenclature

Viewing and Plotting a 2D Spectrum

Presumptions

Start NMRView

Orient Yourself

Set Preferences

Open and Draw a Dataset

Opening and drawing datasets and spectrum windows as separate steps

Using Spectrum Windows

Familiarize yourself with the Spectrum Window

Familiarize yourself with the cursors

The Spectrum Window buttons

Plotting your spectrum

Practice zooming in and out

Orient yourself with respect to the window menus

4. Control Panel

The File Menu

The Dataset Menu

The Windows Menu

The Assign Menu

The Analysis Menu

The Molecule Menu

The Help Menu

5. Datasets

Datasets

Dataset Formats

Adding File Formats

Loading Datasets

Changing Reference Information

Dataset Parameter File

Datasets Table

Manage Datasets

6. Creating and Using Spectral Display Windows

Adding Spectral Display Windows

Using the Graphical Interface

Using Tcl Commands

Using Spectral Windows

Display Modes

The Spectrum Icon Bar

Cursors

Crosshair Correlation

Keypad Navigation

Spectral Attributes Dialog

The File Panel

The View Panel

The Graph Panel

The Plot Panel

The PeakPick Panel

The Peak Display Panel

The Peak Attributes Panel

The Analysis Panel

Spectral Display Menu

Managing Spectral Display Windows

Spectrum Synchronization

Preserving the Spectral Window State between Sessions

7. Peaks

The Peak Inspector

The Peak Table

Peak Filtering

Systematic Peak Examination

Peak Menu Commands

Measuring Peak Volumes

Identifying Peaks

Transferring assignments to peaks

Linking peak lists together

Interactive peak link viewing and adjustment

The Resonance Table

8. STAR Files for Data Storage and Archival

STAR Format

The NMRViewJ STAR Editor

Retrieving STAR Files

9. Molecular Structures

10. Strips

11. RunAbout

General Description

Required Data

Preparing the Spectra, PeakLists, and Sequence File

Checking out your Spectrum Levels

RunAbout Parameters Panel - Selecting Peaklists

Details of RunAbout's peak list patterns

Runabout -Edit Peaks Mode

Peak Registration

Automatic Peak Actions

RunAbout -Edit Clusters (HN-C)

Enter into Edit Clusters Mode

Orientation - Helm's Left:

Orientation - Helm's Right

Editing Clusters

RunAbout - Edit Links

Edit Links Overview

Orientation and sketch of actions

Automation

Semi-automated Assignment Strategy

Continuing and Finishing

Sidechain Assignments

TocsyCONNH Assignment Mode

HCCH Assignment Mode

12. CSI Display

13. Rate Analysis

14. Titration Analysis

15. Tables

16. Charts