Changelog

Metabolomics features

Assignment Inspector Navigation

Backbone Assignment Module can use multiple Display Groups to separate aliphatic and carbonyl regions

Show line widths in ppm - change to PeakTables Settings

Save traces as 1D now in Selected Peak Context Menu

Centre Z-planes on peak

Residue Info now includes picture with AA structure and atom nomenclature

Interactive scaling of 1D traces

Auto-colour spectra in SpectrumGroup with a spectrum colour scheme

1D traces are auto-scaled

Re-added single/double-cursor toggling from menu and shortcuts

Restraints in collections will now be grouped in the restraint-analysis inspector

Copy peaks options improved

Changing font sizes in Preferences now updates axes

Font sizes during printing

Crash in 1D SpectrumDisplay when stacking spectra

Code cleanup

bug fixes

Automated carbon atom assignment in Pick & Assign module

Pick & Assign module now works from Peak Lists as well as NmrResidue lists

AnalysisScreen: PowerPoint reports from HitAnalysis module

Easy renumbering of NmrChains and Chains

Easy reloading of spectra

Sequence prediction includes the i-1 chemical shifts

AnalysisStructure: Integration with ARTINA

Backbone Assignment Tutorial

bug fixes

bug fixes

Table columns can now be saved

bugs

new table column header pop-up for Restraint Analysis Table

bug fixes

New equations for Kd calculations

Global fitting

bug fixes

bug fixes

Various updates and fixes

Addition of "Don't show this again" tick box in various places

Simultaneous Pick & Assign in multiple SpectrumDisplays

1D display can be flipped to vertical

Improved handling of paths when loading data

Restraint Analysis Table improvements

speed-up of table searching

DQ cursor improvements

out-of-plane peaks now selectable

set dark / light theme in Preferences / Appearance

bug fixes

AnalysisMetabolomics ProfileByReference: Overlay simulations of metabolite standards to identify and quantify substances in mixtures

AnalysisMetabolomics ProfileByReference: Linking of spectrum displays to active simulations

AnalysisMetabolomics ProfileByReference: Multiple active simulations

AnalysisMetabolomics ProfileByReference: Profile state saveable and recoverable in project files

AnalysisMetabolomics ProfileByReference: Supports reading from multiple database directories simultaneously

AnalysisMetabolomics ProfileByReference: Improved control of active simulations and sample-spectrum focus

AnalysisMetabolomics ProfileByReference: Improved robustness of sum-spectra recording

AnalysisMetabolomics ProfileByReference: Improved user interface logic

AnalysisMetabolomics CreateDatabaseReference: Export simulation parameters for spin-system and peak-list based spectra as NEF files

AnalysisMetabolomics CreateDatabaseReference: Improved user interface logic

mmCIF Reader

CCPN Macro: Assignment Statistics (beta version)

Propagate Assignments feature (also from single source peak)

Copy Assignments feature (also from single source peak)

CANCOCX Reference Experiment Type and synthetic PeakList simulation

Peptides: Macro to create a Noesy PeakList from a PeakList containing multiplets

Peptides: Macro to pick/place peaks for whole NmrResidue

Peptides: Documentation

Ability to “Pick and Assign” on multiple rows in one go

Improvements to loading/saving read-only handling

More “don't show again” options

Added code to all classes to aid macro-writing

Tables: hidden columns can now be saved/restored

Creation of marks from nmrAtoms/nmrResidues with multiple ChemicalShiftLists

Inconsistent new naming

Simulated Spectra are now called synthetic PeakLists

Macro Editor

Right-mouse menu options for multiplets

Update mechanism, now with a changelog in the user popup

New sequence editors in the Create Chain pop-up

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

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

New resources framework for Reference Chemical Shifts and more

New Tips of the Day

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

Assign: New Decay model for the Dynamics module

Screen: Prescreening inspection

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

Metabolomics: Unknown substance simulations

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

Screen: HitAnalysis module general bug fixes

Screen: QBind analysis module general bug fixes

Improved some figures with larger text font sizes.

Screen: Peak snapping 1D algorithm

Screen: Peak matching 1D algorithm

Screen: Speed optimisation of the pipeline

Screen: QBind analysis now works independently from the hitAnalysis module

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

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

Metabolomics: Improved simulation speed for larger spin system matrices

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

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

Metabolomics: Added reset buttons for multiplet chemical shifts

Signal to noise calculation and Estimate Noise routines

Dynamics Tutorials

New simulated Experiment Types

New Tips of the Day

Macro Writers: project.newCollection() fixed

Tutorials and Macros

Macro Writers: newPeak() allows setting of ClusterID

Dedicated Relaxation Analysis module with several fitting models

New Chemical Shift Mapping Analysis module with new fitting models

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

Auto and manual arrangement of peak labels

Simulated 13C HSQC peak list

1D strips

Pinning for strips

Marks on individual strips

Metabolomics module: 1D spectrum simulator

Metabolomics module: Profile by Reference

Metabolomics module: Create Database Reference

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

2D multiplet picker

New core object Bonds

General GL bug fixes

Threading issues caused by the IPython console history manager

DataTable bug on tiny/huge numbers

Series editor popup

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

Auto backup settings

Read-only mode

Tables layout and formatting

Tip of the Day

Validate Paths: new features including Search & Replace

Navigation among displays

Tutorials: Introduction to NMR, Dynamics

Read-only mode

Autobackup

minor bugs

Tutorial: Chemical Shift Perturbations

Validate Paths: new features including Search & Replace

Project Backup

AnalysisScreen: Peak Snapping during Peak Copying

AnalysisScreen: Matching Scores

Edit Collections pop-up

Double-quantum diagonal and mouse cross-hairs

copyPeakAssignments CCPN Macro

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

Ubuntu 22 patches and distribution

NEF Tutorials

New Chemical Shift Mapping Module (alpha)

Relaxation Data Analysis Module (alpha)

NEF Import with wrongly defined IsotopeCode

Peak picking on scaled spectra

Printing: bug fixes and improvements

Several GUI and Core bugs

Minor bugs

Tutorials

Tables: appearance, speed and filtering options

Amino Acid Type Prediction

AnalysisAssign: Backbone Assignment Settings

AnalysisAssign: Peak Assigner

AnalysisAssign: AssignmentGraph

AnalysisStructure: Xplor NIH set up

AnalysisStructure: wwPDB xml report import

AnalysisScreen: HitAnalysis Module

AnalysisScreen: Pipelines Module

handling of pseudo-3D spectra

Collections - an easy way to organise data in a project

DataTables - an easy way to store any data analysis data

interactive shifting of 1D spectra

Tip of the Day

Key Concepts for new users

AnalysisStructure: Structure menu with various features

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

AnalysisStructure: Restraint Analysis Tables

AnalysisStructure: PDB Validation Report import

AnalysisScreen: spectrum scaling

AnalysisScreen: Mixture labelling by well plate numbers

AnalysisScreen: export of Mixtures to Bruker robot format

Bruker format spectra automatically scaled with NC_RPOC value

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

mouse context menus

CCPN macros menu

NEF Importer

PeakAssigner interface

Data Loaders

Reference Chemical Shifts module

BMRB Import and Peak List creation

AnalysisScreen: HitAnalysis interface

tutorial files and projects

html manual files

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

handling of Chemical Shifts and Chemical Shift Lists

organisation of underlying code

speed when dealing with large/many tables

copy peaks behaviour

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

AnalysisScreen: Peak Matching

AnalysisScreen: data filtering and labelling

AnalysisScreen: Mixture Analysis

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

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

New fonts for SpectrumDisplays and widgets

Various minor bug fixes on GUI items and core objects

Significant speed optimisation on opening and displaying spectra

Validating SSL certificates

Reading NMRStar files containing multiple chains

New and updated html video tutorial files

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

Improvements to Drag & Drop of NmrAtoms for ambiguous peak assignments

Macro to calculate Distance Restraints from a peak list

general bug fixes for improved stability

NEF parser general bug fixes

Academic licence extended to 2100 for usability

general graphical speed optimisations