Index of CcpNmr Analysis V3 Video Tutorials and Manual

General

General Information

V3 Highlights
A short introduction to some of the new features in V3 of CcpNmr Analysis

FAQs
Frequntly Asked Questions on all aspects of CcpNmr Analysis V3

Installation

Information about downloading and installing CcpNmr Analysis V3

Installation on Mac or Linux
How to download and install CcpNmr Analysis V3 for Mac or Linux

Installing Updates
How to keep CcpNmr Analysis updated with all the latest Updates

Using Analysis with NMRbox
How to use Analysis with NMRbox rather than installing it yourself

Basic Usage

Basic tasks to get you started with the programme

Getting Started Demo
Some basics to get you started

Mouse Usage
Mouse function within Analysis

Keyboard Shortcuts
Using two-letter keyboard shortcuts

Working with Modules
How to add modules to the drop area and rearrange them

Zooming
How to change and store zoom levels

Visualising 3D Spectra
How to visualise and navigate through 3D spectra

Working with Strips
How to create, remove and manipulate strips

Working with Tables
How to display, search and export tables

Peak Lists and Tables
How to work with peak lists and tables

Working with 1D Spectra
How to work with 1D spectra and integrate peaks

Project

Opening, importing and other project related tasks

Importing a V2 Project
How to import a project save in CcpNmr Analysis V2.4

Importing a Sparky Project
How to import a Sparky project

BMRB Import
How to import a chemical shift list from a BMRB NmrStar file

NEF Export for BMRB Deposition
How to export data in a NEF file for deposition with the BMRB

Search Box
How to find data quickly using the Search Box

Spectrum

Opening, displaying and working with your spectra

Loading Spectra
How to load different types of spectra into CcpNmr Analysis

Customise Spectrum Display
How to change the way your spectra are displayed

Organise Spectra with Spectrum Groups
How to use the Spectrum Groups feature to organise your spectra in the sidebar

Peak Picking
How to pick peaks in 2D and 3D spectra

Multiplets
How to use the multiplet feature

Customising Peak Labels
How to change the way you display your peak lables and symbols

Flipping Spectra
How to change the axis arrangement of a spectrum

Phasing Spectra
How to phase 2D and 3D spectra to obtain phasing parameters for your processing script

Adding 1D Traces
How to show horizontal or vertical traces in your ND spectra

Creating Strip Plots
Ways to generate strip plots automatically

Setting Experiment Types
How to set the experiment types of your spectra

Aliasing
How to change the aliasing of peaks in your spectra

Molecules

Using molecules within your project

Adding Sequences
How to add a protein or DNA/RNA sequence to your project

Assign

Making and changing assignments manually and using automated routines

NmrResidues
How NmrResidues, NmrAtoms and NmrChains are used as an aid to assignment

Setting Up NmrResidues
How to create and assign new NmrResidues and NmrAtoms to your HSQC (or other base) spectrum

Pick and Assign
Peak pick your 3D spectr and transfer assignments from a 2D

Pick and Assign: Assessing your data
Ways to investigate your data if you are struggling with the Pick & Assign module

Backbone Assignment
How to make sequential backbone assignments for a protein

Quick Assignments
How to assign your peaks quickly from NmrResidues or NmrAtoms in the sidebar

Transferring Assignments
Ways to copy assignments from one spectrum to another

Macros

Writing and Running your own Macros in CcpNmr Analaysis

Running Macros
How to run and save a macro you have written yourself or copied from elsewhere

V3 Environment
List of external packages included in the V3 environment

NMR Exchange Format (NEF)

Information about the NMR Exchange Format

NEF
Format and specifications for NEF files

NEF Atom Names
Specifications for atom naming in NEF files

NEF Export for BMRB Deposition
How to export data in a NEF file for deposition with the BMRB

V2 to V3 transition

Information for those switching from CcpNmr Analysis V2 to V3

V2 to V3 translation
Tables showing the V3 equivalent for V2 commands

Popular V2 features in V3
List of whether and how V2 features have been implemented in V3

Metabolomics

How to use V3 of CcpNmr Analysis for Metabolmics Applications

Getting Started: Importing Spectra
How to import Bruker format spectra

Creating Stacked Plots
How to create stacked plots of multiple 1D spectra

Renaming Spectra
How to rename a single spectrum or multiple spectra in one go

Printing to PDF
How to customise your spectrum display and print to PDF

Pipeline Processing
How to create a pipeline to process several 1D spectra at once

Principal Component Analysis (PCA)
How to conduct a Principal Component Analysis (PCA) Decomposition

Overlaying Reference Spectra
How to overlay experimental with reference spectra

Picking Peaks
How to pick peaks

Annotating Peaks
How to annotate peaks

Exporting Peak Lists
How to export your peak lists to an Excel file

Molecule Assignment Tips
How to make correlations between spectra to help with making assignments

Forum Help

Guidance on the CCPN Forum

Forum Sign Up
How to sign up to the forum and set your email preferences

Forum Usage
How to post on the forum and more