Releases: PINT-NMR/PINT
Releases · PINT-NMR/PINT
PINT v2.1.0
This release includes binaries for 64-bit versions of Windows, Linux and macOS.
--Changelog--
General changes:
- Added support for fitting line shapes and performing downstream analysis of 3D spectra. As a result, all parts of PINT have been updated to accommodate for this feature; returning users should quickly feel used to the GUI changes.
- Added two video tutorials on analyzing 3D spectra.
- A global change to all spin boxes to accept '.' as a separator instead of ','.
- It is now possible to update the default directory used for loading projects. This is done in the "Load project" interface.
- The project name is now displayed in the window title.
Project files:
- Fixed a bug that disabled tabs in the workspace when files were removed.
- Added an error check for transposed spectra, which are currently not compatible for usage with PINT.
- Added a button, "Project description", that opens a text browser where detailed project descriptions can be written.
Spectra:
- Corrected a calculation error when trimming the spectral width by altering the downfield chemical shift. In prior versions the imported spectrum could be slightly off in ppm values when trimmed, this has been corrected in this version. Please note that this only affected the visualization of rendered spectra in the "Spectra" tab and had no effect on line shape or downstream fitting results.
- It is now possible to print a high quality .pdf file of the contour plot.
- If the spectral width of a spectrum is trimmed in PINT, the settings are saved and loaded everytime the spectrum or a different plane of the spectrum is loaded. To change the spectral width further or restore prior settings, the user must tick the "Trim spectral width before loading spectrum" box before loading the spectrum.
- Fixed a bug causing PINT to crash when picking peaks (>500 peaks) in the "3D view".
- Added the button "Shift peaks" that allows all or a selection of peaks to be shifted in any dimension. This is useful for TROSY experiments.
Integration:
- Increased the number of visible items in the auto-completer.
- Added the option "fitIndividual", which will fit unique peak positions for each spectrum or plane in a pseudo-3D spectrum. This is useful for spectra where peaks are moving slightly in between experiments. It is not intended for usage with titration data.
- Added the lineshape "SUMMATION", which can be used as a last resort for fitting peaks with low signal to noise ratio. The reported intensity is extracted from the data point closest to the peak position and the volume is calculated from the signal integral. The volume is then used instead of the intensity in downstream fitting to increase accuracy. Note that this lineshape is NOT suitable for analyzing overlaps and volumes depend on the peak radii.
- Added the option "cpmgPValue" that specifies the p-value that is used in the F-test performed in 2D fits for CPMG RD analysis. Note that this value also can be specified directly from 2D fits.
- Added the option "cpmgDim" that specifies the dimension of CPMG RD experiments.
- Changed the defined unit of Δω from /s2 to ppm. Note that the options "cpmgDeltaOmega" and "defineCpmgDeltaOmega" are affected by this change. This will affect prior CPMG RD projects in PINT using these options.
- Added the options "defineMaxIterationDownstream" and "defineMaxIterationLineshape".
3Dfits:
- For failed fits, the axes have been updated to always be scaled to the experimental data.
2Dfits:
- The "Exchange" boxes (fitCPMG routine) can be toggled. Peaks with toggled boxes can be added to the "Parameter browser" by clicking the button "Add checked to Parameter browser". This is useful for only analyzing peaks with chemical exchange.
PINT v2.0.5
This release includes binaries for 64-bit versions of Windows, Linux and macOS.
--Changelog--
General changes:
- Integration speed has been improved. Benchmark tests revealed an approximate 66% time reduction.
- Tables and lists now have grid lines to increase readability.
- GUI design and functionality has been slightly modified, but should be intuitive to returning PINT users.
- Font size of GUI elements has been increased (macOS only) to increase readability.
- The "User_manual.pdf" and seven tutorial videos have been updated.
- Increased the support for high DPI screens (4k resolution and Mac retina screens). Please contact a developer if you are experiencing any issues with the display of any GUI elements or cramped up areas of the interface.
Spectra:
- The spin box used for browsing the planes of a pseudo-3D spectrum has been changed into a slider and moved below the spectrum.
- The mouse pointer in the contour plot viewport has been changed to show vertical and horizontal lines instead of a crosshair.
- It is now possible to adjust the width of the peaklist table.
- Contour levels are now applied on a logarithmic scale.
- Changes in contour levels, factors, cutoffs and colors will be saved and loaded on a per spectrum basis.
- A button that hides the tools below the spectrum has been added. This is useful when running PINT on smaller computer screens and laptops.
Integration:
- Fixed a multi-threading issue that occasionally caused the application to crash or freeze.
- The "overlap auto" algorithm, detecting intersection of ellipses, has been replaced. The new algorithm is significantly better at detecting overlaps and can be used for detecting intersection of ellipsoids as well (currently not supported).
- Error estimation of line widths and peak positions are now calculated with Jackknife resampling. Please note that error estimation of line widths and peak positions are not calculated by default; the option "nLineShapeResample" must be added by the user.
- Added the option "nLineShapeResample" used to define the number of resampled data sets in line shape fitting. Integration times will increase if this flag is used, we recommend to add it once the fits have been optimized if you need errors in line widths and peak positions.
3Dfits:
- The default appearance of plots has been changed as it is often more valuable to inspect the total sum of intensities instead of fitted individual peaks. The appearance of plots from prior versions can still be toggled.
- A slider for browsing the planes of a pseudo-3D spectrum has been added. The option to view all planes at once has been removed.
- Added slice plots displaying F1/Intensity and F2/Intensity slices. Click any data point to update these plots. The plots show slices of the fitted total and experimental intensities. The plots are toggled by clicking a button.
2Dfits:
- It is now possible to adjust major and minor tick lengths, margins and tick label sizes.
Parameters:
- It is now possible to plot multiple data sets in one graph. It is also possible to plot parameters from different working directories within the same project. Read the user manual for more information.
- It is possible to name plotted data series.
Plots:
- Please note that any default settings for the Plots tab saved with an older version of PINT are incompatible with this version of PINT. Do not try to import old settings manually.
- It is now possible to reverse the ranges of the axes as well as to use logarithmic scales.
- It is now possible to adjust major and minor tick lengths.
- A legend has been added to the plot. It can be toggled and its position can be changed.
- Fixed a bug causing coloring of data points to not function properly when not plotting errorbars.
- Fixed a bug that caused deletion of data points to fail.
PINT v2.0.4
This release includes binaries for 64-bit versions of Windows, Linux and macOS.
--Changelog--
General changes:
- Fixed a bug that prevented the information messages to pop up when starting or loading a project, the bug was introduced in 2.0.3.
- Reduced the application size by compressing the video tutorials slightly.
- Minor UI changes.
Integration:
- Optimized the lineshape fitting for speed. The analysis of VOIGT and Galore lineshapes and overlapped peaks is much faster than before.
- It is now possible to use "fitR2FromR1rho" without using "r2fromr1rhoR1List" to supply a list with measured r1 values.
- We have redesigned how to add working directories. Now each working directory have their own Parameter browser that is saved when switching between different working directories.
- It is now possible to give your working directory a short comment that keeps track of its purpose.
- It is now possible to delete working directories from within PINT.
2Dfits:
- The plotting interface has been updated to include more customization options.
Parameters:
- R1rho analyses will now calculate and report the effective field and the carrier offset.
- Added greek symbols for header items of the Parameter table.
- It is now possible to correlate parameters of choice.
Plots:
- The plotting interface has been updated to include more customization options.
- Now you can customize the plot to your liking and save it as a default template for future sessions.
- Pearson correlation coefficient is calculated for correlated parameters.
PINT v2.0.3
This release includes binaries for 64-bit versions of Windows, Linux and macOS.
--Changelog--
General changes:
- Added a format check of directories when creating new projects as directories with illegal characters cause problems with peak integration.
- Directories and file names including white space are now supported.
Project files:
- The project will now be automatically saved if any file is added or removed.
Spectra:
- The peaklist table will only show frequencies using floating points and convert those with scientific notation to this format.
- Removed two unnecessary options from the Macro function.
- If a shortcut is used to define an option, e.g. defineOverlap, defineRadius or any Macro function, peaks that already have a similar flag in the Integration browser will be updated to the new flag. Modified options with too few parameters for the specific option will be removed.
- A blue contour showing the current radii for the selected peak(s) was added as well as a "Define radius" button that is equal to using the "Ctrl+D" shortcut.
- Added the option to define a custom region considered for line shape fitting by selecting peaks and pressing Ctrl+Shift+D; by adding anchors in the spectrum the custom region will be defined. See the tutorial "3-10 Manually define peak radii in the spectrum" for more information.
- Improved the rendering of contour plots by enabling multi-threading utilizing the maximum number of available cores of the CPU.
- Fixed a bug that caused peak selection to fail if the project was just opened.
Integration:
- Fixed a bug that caused errors in integration caused by peaks moving too much to be reported as failure to calculate line widths.
- Errors from the downstream fitting will be reported in the Integration status widget.
- Reported errors will be colored orange in the Integration status widget.
- Optimized the fitCPMG routine to become more robust.
- Optimized the lineshape fitting routine for speed.
- Added the options "maxIterationDownstream" and "maxIterationLineshape" that limit the number of iterations performed when trying to reach convergence for downstream and line shape fitting, respectively.
3Dfits:
- Fixed a bug causing 3D surface colors to be rendered incorrectly.
- Fixed a bug where peaks that failed downstream fitting were reported as having failed the successful line shape fitting.
2Dfits:
- For fits of CPMG dispersions the F-test statistics will be used to highlight dynamic residues in the interface.
- Fixed a bug that occasionally caused errors from a prior downstream analysis to be reported for the following analysis.
Parameters:
- The parameters tab will be displayed even without performing downstream fitting. This allows the user to inspect and plot fitted linewidths, positions, peak intensities and volumes from basic line shape fits.
- Fixed a bug where values were reported in wrong columns for failed downstream fits and where failed downstream fits would cause successful fits to not be reported at all.
- The parameter table will show values using floating points unless a set character limit is exceeded.
PINT v2.0.2
This release includes binaries for 64-bit versions of Windows, Linux and Mac OS X.
--Changelog--
General changes:
- Fixed a bug with the calculation of dof.
- It is now possible to sort the projects displayed in the "Load project" menu by name or date by clicking the header names.
- Searching in the "Parameter browser" will now highlight the text in blue.
- Fixed a bug related to Ubuntu causing TopSpin parameters to be incorrectly rounded during string to double conversion.
Spectra:
- Fixed a bug causing an infinite loop when folding peaks at an edge of the spectrum.
Integration:
- Fixed a bug that caused custom kex values for CPMG analyses to be ignored.
- Made the CPMG fitting routine more robust.
- Added a limit for maximum allowed distance a peak may move during integration based on its radii. Read the User_Manual.pdf for more information on this.
- Fixed a bug that caused integration to fail when the noise level was set to 0.
- Added the "-noise" option to override the automatically calculated and trimmed noise during integration.
3Dfits:
- Made evaluation of individual fits the default.
- Added an intensity range slider.
PINT v2.0.1
This release includes binaries for 64-bit versions of Windows, Linux and Mac OS X.
Note that projects created with v2.0 can be used directly in the updated version.
--Changelog--
General changes:
- Added support for Ubuntu and fixing bugs specifically related to this platform.
- When reading TopSpin data of pseudo-3D experiments, zerofilled planes will be omitted.
- Added the option "Save project as".
- Changed the layout of several workspace tabs to accomodate for smaller computer screens.
- Added the option to ignore prompts of choosing a dedicated directory for PINT projects.
- Fixed a bug that caused high CPU usage, even when being idle.
- Added the option to write the results of the peak integration and analysis to different directories.
- Additional minor bugs and typos were fixed.
- Updated and added video tutorials.
- Updated the user manual.
Project files tab:
- Now multiple folders of TopSpin data can be imported simultaneously through multiselection.
- Added a format check for spectra during import.
- 2D planes extracted from pseudo-3D spectra processed with NMRpipe are now supported. Read the User_Manual.pdf for more information on this.
Spectra tab:
- When interacting with single peaks, the zoom will now automatically center on the peak with the current level of magnification.
- When selecting peaks directly in the spectrum, the peaklist table will scroll to the selected item.
- Added the option to pick peaks by double clicking in the spectrum.
- Fixed a bug where files in out/ and plot/ directories would be deleted when centering peaks.
- Implemented continuous rendering of the contour plot while panning, which fixes a visual bug caused on Mac retina screens.
- The radii considered during integration and peak centering are now drawn in the contour plot and can be tailored to the analyzed spectra. Additional functionality and documentation for this function have been added as well.
- Added symbols to the mouse cursor to represent the current drag mode.
- Macro functionality was introduced, which will add custom syntax to the Parameter browser through a shortcut.
Integration:
- Arraying TopSpin data should now work as intended.
- It is now possible to analyze multiple TopSpin processed 2D spectra with different ##$NC_PROC scaling.
- Uncertainties in intensities and volumes are now calculated correctly for data sets without duplicates.
- Volumes and uncertainties in volumes for VOIGT line shapes are now reported correctly.
- Chi2 and dof are now reported correctly.
- The use of a vdlist has been set as default for TopSpin projects.
- Added the option to integrate all imported spectra in the project, useful for analysis of multiple 2D spectra.
- Volumes and intensities are now exported to text files.
- Integrating folded peaks should now work as intended.
- Added an option to perform a grid search during downstream analysis.
- Improved performance for the Levenberg-Marquardt algorithm.
- Fixed a bug that caused peak centering and integration to fail when using "fitOnly" in combination with "excludePlanes" flags.
- Added the options "cpmgGridSearch" and "defineCpmgGridSearch" to automatically aid fitting of CPMG dispersions.
3Dfits:
- When browsing "Single planes" in 3Dfits, if available, the last viewed peak will be shown for the new selected plane without having to browse the list.
- Added calculation of an average quality rating which is helpful for quickly evaluating applied global changes to the integration.
- Fixed a bug that occasionally caused plots and labels not to render correctly when changing inspected plane.
- All visual elements can now be toggled.
- Added plotting of fits for individual peaks, useful for analyzing overlaps.
2Dfits:
- Added plotting of residuals in the "2Dfits" tab.
Parameters & Plots:
- Added plotting of line widths, peak positions, volumes and intensities.