Part I. Usage

Table of Contents

1. Introduction

2. Installation

Installation Overview

Java™

Mac OS X

Windows (XP, Vista, and 7)

Linux

NMRViewJ and dataChord Client Installers

Running the installer

Mac OS X

Linux, Windows, Solaris and Unix

Starting the Program

3. Quick User's Guide

Overview

Helpful Concepts

Clicking

Guide Nomenclature

Viewing and Plotting a 2D Spectrum

Datasets

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. Menus

File

Datasets

Windows

Canvas

Peaks

Assign

Analysis

Molecule

Help

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. Projects and Data

BMRB NMR-STAR Files

Projects

8. 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

Interactive Peak Assignment

The Resonance Table

9. Molecular Structures

Topology

Atom Nomenclature

Atom Specifiers

Structure Family Analysis

10. Strips

Strip Plot Overview

Strip Plot Configuration

Strip Plot Peaks

Sort Mode

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

Cluster Details

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. Atoms and Assignments

Atom Assignment Tables

File Menu

Reference Menu

LACS Plot

Seqeunce Display and CSI Analysis

Atom Assignments

Chemical Shift Index (CSI) Calculation

13. Rate Analysis

14. Constraint Generation, Evaluation and Export

Introduction

Distance Constraint Table

Generating Constraints from NOESY Peaks

Calibration

Inspecting Constraints

Constraint Peak Info

Constraint Map

Constraint Export/Import

15. Titration Analysis

16. Tables

17. Charts

Introduction

XY Plots

Fitting XY Chart Data

Bar Charts

Statistical Charts

Chart Menu

18. Appendix I Open Source Software