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Index of CcpNmr Analysis V3 Video Tutorials and Manual

General | Installation | Basic Usage | Project | Spectrum | Molecules | Assign | Background | Macros | Screen | NMR Exchange Format | V2 to V3 transition | Metabolomics | Forum Help

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
Command Line 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
Backups
How your project is backed up and how you can restore backed up versions

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 and Fitting
How to pick and fit peaks in your spectra
Copy Peak List
How to copy a peak list
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
Synchronising Axes
How to link axes in different SpectrumDisplays so moving/scaling one will also affect the other(s)
Phasing Spectra
How to phase 2D and 3D spectra to obtain phasing parameters for your processing script
Signal to Noise
Understanding and estimating spectrum noise levels and peak signal/noise ratios
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
Working with Pseudo 3D Spectra
How to open, view and peak pick Pseudo 3D spectra
Shifting Spectra Interactively
How to move 1D spectra relative to one another
Printing to File
How to create images of your spectra

Molecules
Using molecules within your project
Adding Sequences
How to add a protein or DNA/RNA sequence to your project
Small Molecules
Find out how you can adapt NmrChains, NmrResidues and NmrAtoms to label and assign small molecules
Creating Non-canonical Amino Acid ChemComp Files
Using ChemBuild to create your own ChemComp .xml files for bespoke amino acids
Creating Chains with Non-canonical Amino Acids
How to add ChemComp files to your project and then create a Chain with non-canonical amino acids

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 spectra and transfer assignments from a 2D
Pick and Assign: Working with difficult data
Ways to investigate and work with your data if you are struggling with the Pick & Assign module
Backbone Assignment
How to make sequential backbone assignments for a protein
Using the Peak Assigner
How to use the Peak Assigner to assign and de-assign peaks and manipulate your NmrAtoms
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
Assignment Statistics Tables
How to create and use statistics on your level of assignment

Background
Understanding some of the principles underlying CCPNMR Analysis
Chemical Shifts
Understanding how Analysis uses Chemical Shifts
NmrResidues
How NmrResidues, NmrAtoms and NmrChains are used as an aid to assignment
Titrations
Some background on the theory and practice of how to carry out quantitative titrations

Macros
Writing and Running your own Macros in CcpNmr Analysis
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

Screen
Using CcpNmr AnalysisScreen
AnalysisScreen Nomenclature
An overview of the terminology used in AnalysisScreen
AnalysisScreen Pipelines
How to build Pipelines to analyse many spectra in one go
AnalysisScreen Pipes
A description of the Pipes used in AnalysisScreen
AnalysisScreen Screening Datasets
What is a Screening Dataset?
AnalysisScreen Hit Analysis Tables
Different types of Tables in the Hit Analysis module
AnalysisScreen Peak Matches
Creating and editing Peak Matches in the Hit Analysis module
AnalysisScreen Hit Analysis Linked SpectrumDisplays
Customising Spectrum Displays linked to the Hit Analysis module
AnalysisScreen Hit Analysis Scores
What scores are there and how are they calculated?
AnalysisScreen Hit Analysis Filtering
Filtering tools for your Hit Analysis tables
AnalysisScreen Hit Analysis Plots
Inspecting and using the plots in the Hit Analysis module
AnalysisScreen Hit Analysis Flags
Setting and removing flags on your Screening Data

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 Import
How to import data contained in a NEF file
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