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CcpNmr SpecView

About SpecView

CcpNmr SpecView is designed to provide a fast way to visualise NMR spectrum and peak data. It supports 2D and 3D graphical display modes for multidimensional and simple 1D spectra. SpecView can automatically import spectra and peaks from many different file formats without user intervention. Spectra may be frequency referenced and superposed within the program.

Download and installation:

Download SpecView as a beta-test version from the leading edge release.

 

Development

CcpNmr SpecView was initially written by Tim Stevens and Wayne Boucher with recent contributions from Magnus Lundborg. The program was created mostly using Python, PySide (the Python bindings to Qt) and PyQt (the Python bindings to OpenGl). Some of the more speed critical parts, like calculation of contours or the transfer of data to OpenGL, are written as C libraries with bindings to the Python word.

 

Relationship to Other CCPN Applications

CcpNmr SpecView forms part of the 'next-generation' of CCPN software and much of the spectrum display techniques it uses will be employed in other parts of the CcpNmr suite from version 3.0. The SpecView program may be used in isolation from other parts of the CCPN software and data model libraries, although an installation of the CCPN API (for Python) is naturally required to be able to read and write CCPN projects. From the version 1.0 release there is a special CCPN API release that can be extracted on top of the separate SpecView installation.

 

CcpNmr SpecView screenshot - contours

A screen-shot of CcpNmr SpecView.

Current Features

As of version 1.0 the basic features and capabilities of CcpNmr SpecView are as follows:

  • Loading of NMR spectra in multiple formats, including via drag-and-drop. Supported spectrum data formats include: Agilent (Varian), AZARA. Bruker, Felix, NMRPipe, NmrView, UCSF (Sparky) and XEasy.
  • Loading peak lists of multiple formats, including via drag-and-drop. Supported peak list formats include: ANSIG, AutoAssign, NmrDraw, NmrView, NmrStar (BMRB), Sparky and XEasy.
  • Display of 2D and 3D spectra as contours, 3D projected surfaces ('Mountain mode') and 3D contours ('Blob mode').
  • Peak picking with automated intensity and limited line-shape fitting.
  • Superposition of arbitrary numbers of spectra.
  • The ability to set the frequency referencing of spectra (while generally being indifferent to incorrect referencing) and data block interpretation.
  • Hz, ppm, data point and data fraction window axes.
  • Dedicated display of 1D spectra and slices of higher dimension data, with integration traces.
  • Stack plots for 1D and user specified X-Y offsets for 2+D contour displays.
  • Superposition of chemical structures on spectra from ChemBuild.

 

Three stacked 1D spectra in CcpNmr SpecView

Limitations and Future Features

In-keeping with its philosophy of being fast and simple SpecView will only ever have one spectrum window, although many spectra with similar axes may be superposed. For more complicated multi-panel work users should consider CcpNmr Analysis instead.

Re-export of spectra and peaks, in any of the supported import formats, will be added in the future, but is not ready at present.

There is no scope to do formal CCPN-style resonance assignments in SpecView, however there will be the ability to edit peak annotations, i.e. to use whatever style other programs use. In the future CcpNmr FormatExchange will likely be coupled to SpecView to make formal assignments if data is passed to the Analysis program.

At some stage SpecView will be expanded to include a few frequency-domain processing features, such as phasing and base-line correction.

 

CcpNmr SpecView screenshot - 3D contours
The 3D contour display mode of CcpNmr SpecView.

Bug Reporting

The currently available version is a beta test release and bug reports are welcome. Bug reports should be made via the CCPNMR mailing list at JISC.

As always, please be clear in your descriptions and give enough detail for the developers to be able to reproduce the problem from scratch. However, as SpecView is not yet part of the main CCPN release the bug fixing schedule will not necssarily be prompt and replies to small matters may not be issued. Once CcpNmr Analysis v3.0 is released SpecView  will be incorporated into the main CCPN distribution and will share the same bug reporting mechanism.