CcpNmr Analysis Version-3 software

This Changelog shows the major changes made to the CcpNmr Analysis Version-3 software for each release.

3.2.2
April 11, 2024

You can update to this version using the update server, though we have also provided new builds for a direct download of the full program for those who haven't previously installed the program.

Added

Update mechanism, now with a changelog in the user popup

Added

New sequence editors in the Create Chain pop-up

Added

Drag and drop of custom ChemComps and ability to use them in new Chains

Added

New Macro: setUpCustomNmrResidues macro for use on e.g. CANCO

Added

New resources framework for Reference Chemical Shifts and more

Added

New Tips of the Day

Added

Assign: SyncSpectrumDisplays macro to enable synchronisation of axes between different spectrumDisplays

Added

Assign: New Decay model for the Dynamics module

Added

Screen: Prescreening inspection

Added

Screen: Pipeline can run in a separate thread with a progress bar (experimental feature!)

Added

Metabolomics: Unknown substance simulations

Added

Metabolomics: CreateDatabaseReference: a plugin that allows users to make their own simulated 1H spectra

Fixed

Screen: HitAnalysis module general bug fixes

Fixed

Screen: QBind analysis module general bug fixes

Improved

Improved some figures with larger text font sizes.

Improved

Screen: Peak snapping 1D algorithm

Improved

Screen: Peak matching 1D algorithm

Improved

Screen: Speed optimisation of the pipeline

Improved

Screen: QBind analysis now works independently from the hitAnalysis module

Improved

Screen: QBind analysis includes now the “Qbind Error” and other features.

Improved

Metabolomics: Simulations can now shift multiplets together to adapt to reference offset

Improved

Metabolomics: Improved simulation speed for larger spin system matrices

Improved

Metabolomics: ProfileByReference now uses integration rather than just scale for measuring metabolite relative concentrations

Improved

Metabolomics: Peak width is properly represented as Hz rather than a factor of ppm

Improved

Metabolomics: Added reset buttons for multiplet chemical shifts

Updated

Signal to noise calculation and Estimate Noise routines

Updated

Dynamics Tutorials

3.2.1
November 23, 2023
Added

New simulated Experiment Types

Added

New Tips of the Day

Fixed

Macro Writers: project.newCollection() fixed

Updated

Tutorials and Macros

Improved

Macro Writers: newPeak() allows setting of ClusterID

3.2.0
July 6, 2023

A new release with plenty of new features! (Requires a fresh download)

Added

Dedicated Relaxation Analysis module with several fitting models

Added

New Chemical Shift Mapping Analysis module with new fitting models

Added

New scientific packages to the environment (RDKit, EMCEE etc)

Added

Auto and manual arrangement of peak labels

Added

Simulated 13C HSQC peak list

Added

1D strips

Added

Pinning for strips

Added

Marks on individual strips

Added

Metabolomics module: 1D spectrum simulator

Added

Metabolomics module: Profile by Reference

Added

Metabolomics module: Create Database Reference

Added

Tutorials: intro to NMR, Dynamics, CSM, BRMB/NMR-STAR, NEF-Pipelines

Added

2D multiplet picker

Added

New core object Bonds

Fixed

General GL bug fixes

Fixed

Threading issues caused by the IPython console history manager

Fixed

DataTable bug on tiny/huge numbers

Fixed

Series editor popup

Updated

Conda environment with the latest updates (Python 3.10, Numpy, Scipy, QT etc.)

Improved

Auto backup settings

Improved

Read-only mode

Improved

Tables layout and formatting

Improved

Tip of the Day

Improved

Validate Paths: new features including Search & Replace

Improved

Navigation among displays

3.1.1.updates
April 21, 2023
Added

Tutorials: Introduction to NMR, Dynamics

Added

Read-only mode

Fixed

Autobackup

Fixed

minor bugs

Updated

Tutorial: Chemical Shift Perturbations

Improved

Validate Paths: new features including Search & Replace

Improved

Project Backup

Improved

AnalysisScreen: Peak Snapping during Peak Copying

Improved

AnalysisScreen: Matching Scores

3.1.1
January 18, 2023

Small improvements and additions along with some new alpha functionality

Added

Edit Collections pop-up

Added

Double-quantum diagonal and mouse cross-hairs

Added

copyPeakAssignments CCPN Macro

Added

Reading of complex NmrPipe time domain (unprocessed) data (experimental feature)

Added

Ubuntu 22 patches and distribution

Added

NEF Tutorials

Added

New Chemical Shift Mapping Module (alpha)

Added

Relaxation Data Analysis Module (alpha)

Fixed

NEF Import with wrongly defined IsotopeCode

Fixed

Peak picking on scaled spectra

Fixed

Printing: bug fixes and improvements

Fixed

Several GUI and Core bugs

Fixed

Minor bugs

Updated

Tutorials

Improved

Tables: appearance, speed and filtering options

Improved

Amino Acid Type Prediction

Improved

AnalysisAssign: Backbone Assignment Settings

Improved

AnalysisAssign: Peak Assigner

Improved

AnalysisAssign: AssignmentGraph

Improved

AnalysisStructure: Xplor NIH set up

Improved

AnalysisStructure: wwPDB xml report import

Improved

AnalysisScreen: HitAnalysis Module

Improved

AnalysisScreen: Pipelines Module

3.1.0
July 8, 2022

New release with significant changes to some of the underlying code

Added

handling of pseudo-3D spectra

Added

Collections - an easy way to organise data in a project

Added

DataTables - an easy way to store any data analysis data

Added

interactive shifting of 1D spectra

Added

Tip of the Day

Added

Key Concepts for new users

Added

AnalysisStructure: Structure menu with various features

Added

AnalysisStructure: export/import for structure calculation with XPLOR-NIH

Added

AnalysisStructure: Restraint Analysis Tables

Added

AnalysisStructure: PDB Validation Report import

Added

AnalysisScreen: spectrum scaling

Added

AnalysisScreen: Mixture labelling by well plate numbers

Added

AnalysisScreen: export of Mixtures to Bruker robot format

Fixed

Bruker format spectra automatically scaled with NC_RPOC value

Updated

main menus (now follow standard menu structure: File, Edit, View etc.)

Updated

mouse context menus

Updated

CCPN macros menu

Updated

NEF Importer

Updated

PeakAssigner interface

Updated

Data Loaders

Updated

Reference Chemical Shifts module

Updated

BMRB Import and Peak List creation

Updated

AnalysisScreen: HitAnalysis interface

Updated

tutorial files and projects

Updated

html manual files

Improved

speed of working with NmrPipe data (now uses and intermediate buffer file)

Improved

handling of Chemical Shifts and Chemical Shift Lists

Improved

organisation of underlying code

Improved

speed when dealing with large/many tables

Improved

copy peaks behaviour

Improved

bulk operations which alter many peaks or table entries are much faster (e.g. copy peaks etc.)

Improved

AnalysisScreen: Peak Matching

Improved

AnalysisScreen: data filtering and labelling

Improved

AnalysisScreen: Mixture Analysis

3.0.4
April 21, 2021

Stability Release with MacOS Big Sur and ARM compatibility

Added

Support for small molecules: new Chains can be defined and imported into AnalysisAssign

Added

Improvements to Drag & Drop of NmrAtoms for ambiguous peak assignments

Added

Macro to calculate Distance Restraints from a peak list

Fixed

general bug fixes for improved stability

Fixed

NEF parser general bug fixes

Updated

Academic licence extended to 2100 for usability

Improved

general graphical speed optimisations

3.0.3
January 11, 2021
Added

New context menu items on sidebar, including actions for cloning SpectrumGroups and ChemicalShiftLists

Added

New context menu items and toolbar shortcuts for 1D spectrum Display

Added

New fonts for SpectrumDisplays and widgets

Fixed

Various minor bug fixes on GUI items and core objects

Fixed

Significant speed optimisation on opening and displaying spectra

Fixed

Validating SSL certificates

Fixed

Reading NMRStar files containing multiple chains

Updated

New and updated html video tutorial files