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CcpNmr Analysis
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cjc core concepts diagrams
Nmr Experiment Nomenclature - Obsolete
Highlighted features
General usage
HowTos
Add a peak list to a spectrum
Add a small molecule
Analyse restraints and violations for a generated structure
Analyse structures
Arrange peak labels
Assign a peak
Assign groups
Assign NOEs based on structural information
Calculate 3J H-Ha coupling constants
Calculate heteronuclear NOE values from peak intensities
Calculate T1, T2 or T1rho relaxation constants
Centos 5.x standard installation
Centos 5.x Tcl/Tk 8.5 Python 2.7
Centos 7.x standard installation
Change Molecule Sequence
Check for assignment errors
Copy assignments between molecular chains
Copy assignments between peaks
Copy peaks between or within spectra
Create a new molecule from a sequence
Create a new project
Create a sequence with unusual residues or a mixed-type sequence
Create and import a residue template
Create disulfide bridges in a molecule
Create duplex DNA
Deal with multiplications of spectrum contours
Export data
Find matching peaks
Generate restraint lists
Get more assignment possibilities
Get updates
How to get help with CCPN analysis, FormatConverter and the data model API
Import data
Inspect and modify spin systems and resonances
Load spectra
Make an automatic sequential assignment
Make synthetic peak lists
Merge and split restraint lists
Move data between projects
Navigate between windows
Pick and assign 3D peaks from 2D root peaks
Pick peaks
Predict a spin system type
Predict the residue type of a spin system and the optimal arrangement of residue types
Propagate assignments
Run CING from Analysis
Run MARS from Analysis
Run structure calculation programs
Separate peaks and estimate peak volumes using the Peak Separator
Set 1D slice range
Set aspect ratio
Set contour colors
Set contour levels
Set crosshairs
Set fonts
Set keyboard shortcuts
Set peak annotations
Set peak box size
Set spectrum display options
Set the window background color
Set up multimers: dimers and homodimers
Set window names
Transfer assignments and compare frequencies when peaks have moved
Transpose the axes in a multidimensional window
Unaliase a peak
Windows 10 - WSL installation
Write a macro
Tutorials
Basic Tutorial
Data Management in CCPN
Experiment types and prototypes
Extension to the basic tutorial
Format Converter
Popup basics
Prodecomp-Integration
Programmers Overview Tutorial
Protein assignment
Protein structure calculation
Python API Course
Relaxation data analysis
Solid-state NMR Course
Three Day Course
15N-HSQC peak picking
3D peak picking (1)
3D peak picking (2)
Assigning non-root resonances
Assigning peaks to resonances and spin systems
Assigning resonances to atom types
Assigning resonances to atoms
Assigning root resonances (1)
Assigning root resonances (2)
Assigning side chain resonances
Assignment & Structure Validation
Assignment quality control
Automatic sequential assignment
Basic Peak Picking & NOE Assignment
Browse files
CCPN Tkinter Graphical Objects
CcpNmr Analysis Macros
CcpNmr Analysis Windows
Copying peaks between related spectra
Course Day 1 of 3
Course Day 2 of 3
Course Day 3 of 3
Create and edit an experiment prototype
Customizing project settings
Defining sequences and molecular systems
Dihedral constraints
Efficient resonance assignment
Entering non-standard molecules
Example CCPN Graphical Interface
Experiment Prototypes
Explanatory Diagrams
Failure
Filter Options
Following chemical shifts (1)
Following chemical shifts (2)
Identifying spin system types
Importing Structure Calculation Results
Introduction to protein backbone assignment
Isotope labelling schemes
Loading existing projects and save options
Loading the spectra
Making Dihedral Restraints from Chemical Shifts
Making Distance Restraints
Molecular Description
Molecules: Molecule Setup
Navigation and strips
NMR Experiments and Spectra
NMR Restraints
Opening an NOE spectrum
Peak & Peak Lists
Peak picking and manipulation
refData changed
Relaxation analysis
Resonance Assignment
Restraints
Restraints & Violations
Scalar couplings
Sequential assignment (1)
Sequential assignment (2)
Sequential protein backbone assignments
Setting experiment types
Setting reference dimensions
Setting up the tutorial project
Solid-state NMR Course - Part One
Solid-state NMR Course - Part Two
Spectrum windows
Start a new project and load the spectra
Structures
Structures & Ensembles
Submitting a Structure Calculation to CCPN Grid
Table menu
Top-level Projects
Using Structures to Assign NOE Contributions
Window
Working with variable chemical shifts
Entering non-standard molecules
Entering sequences and molecular information
Finding side chain resonances using TOCSY data
Initialsing HSQCs
Loading Projects and Spectra
Making Dihedral Angle and Distance Restraints
Multiple Shift Lists and Copying Assignments
NOE assignment & protein structure calculation using ARIA
Picking peaks
Program Organization
Relaxation rate analysis
Simple Python Scripts for CCPN
Spectrum Window Navigation
Triple-resonance protein sequence assignment
Violation analysis and structure validation
Solid-state MAS NMR
1D Spectra
Double Quantum Axes
Isotopic Labelling
Side Bands
ssNMR Experiment Types
Strip Plots
Menu reference
Other menus
Top menu
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Windows
Peaks
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Charts
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Window menus
Assign
Peak
View
Navigate
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Window
Macros
Columns Graph menu
Structure viewer menu
Popup reference
Add existing contour file
Add peak
Assignment: Assignment Panel
Assignment: Automated Backbone Sequence
Assignment: Copy Assignments
Assignment: Initialise Roots
Assignment: Link NOEs
Assignment: Link Peak Lists
Assignment: Link Sequential Spin Systems
Assignment: Quality Reports
Backup changed
BACUS Control Module
CcpNmr Software Updates
Charts: Assignment Graph
Charts: Chemical Shifts Table
Charts: Ramachandran Plot
Charts: Residue Interaction Matrix
Charts: Secondary Structure Chart
CING Setup
Cloud Threader
Columns Graph
Confirm
Create axis type
Create axis unit
Create panel type
Create spectrum contour file
DANGLE
Data Analysis: 3J H-Ha Coupling
Data Analysis: Follow Shift Changes
Data Analysis: Heteronuclear NOE
Data Analysis: Measurement Lists
Data Analysis: Rates Analysis
Data Analysis: Shift Differences
Delete Object
Dimension number
Directory does not exist
Edit Analysis Profiles
Edit peak
Edit Peak Aliasing
Edit Project Spectrum & Data Paths
Edit spectrum contour files
Edit spectrum contour levels
Experiments: Edit Experiments
Experiments: Edit Spectra
Experiments: Experiment Prototypes
Experiments: NMR Series
Experiments: Open Spectra
Export data
Export PDB file
Filter Clouds
generalData changed
Highest scoring mappings
Hydrogen Cloud Molecular Dynamics
Import CSI file
Import PDB file
Input text
Molecules: Atom Browser
Molecules: Isotopomer Schemes
Molecules: Residue Information
New directory
Peak Details
Peak Groups
Peaks: Draw Parameters
Peaks: Peak Finding
Peaks: Peak Lists
Peaks: Selected Peaks
Print canvas to file
Print Structure
Project moved
Project valid
Project: Backup
Project: Close
Project: New
Project: Open
Project: Save as
Project: Validate
Quit CcpNmr Analysis
Read sequence file
Reference By Peak
Relaxation Matrix Optimisation
Resonance: Reference Chemical Shifts
Resonance: Resonance Table
Resonance: Spin System Types
Resonance: Spin Systems
Save project
Save table as plain text
Set spectrum referencing
Spin System Type Scores
Structure: Make Distance Restraints
Structure: Restraints and Violations
Structure: Structure Ensembles
Structure: Structure Viewer
Text Entry
Update file details
Verify Spectra
Warning
Window
Window group name
Windows: Axes
Windows: Edit Windows
Windows: Marks and Rulers
Windows: New Window
Windows: Print Window
Query
FAQs
Data Analysis
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Installation
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Items not documented
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Users and Contributors guide
CcpNmr FormatConverter
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Quick Start
CCPN Deposition
ADIT-NMR
AutoDep
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Python utility functions for I/O
Quick Guide to the CCPN Data Model for Software Development
Resonances and Assignment
Memops Generation Machinery
Connected Software
ARIA
ARIA HowTos
ARIA disulphides
AUREMOL
CING
CYANA
HADDOCK
ISD
MARS
MDD
NMR Deposition
PRODECOMP
TOPSPIN
ACYPYPE
A Comparative Test for ACEPYPE
Results for Ligands
User Charge Options
Contributed Software
Bruce D Ray Utility Programs
Readme
Clusterpose
Readme
Graeme Ball Analysis Macros
Readme
Jeremy Craven Utility Programs
Readme
Krystyna Bromek Utility Program
Readme
S Chandra Shekar NMRView Scripts
Readme
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Macromolecular NMR
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Relaxation Matrix Optimisation
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