The CcpNmr software suite is a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model. Between programs written by the CCPN, external contributions, and ‘outside’ programs integrated with the data model, it is the intention to provide one suite of programs to carry out all tasks needed in macromolecular NMR spectroscopy. The nature of the data model guarantees that any other program or suite that interfaces with the data model can be used alongside or instead of the CcpNmr suite.

The CcpNmr suite currently consists of:

• Process, for processing of raw experimental data (not yet available)
  

• Analysis, for interactive analysis, spectrum display, and assignment
• FormatConverter for reading and writing between the data formats of existing programs
• ECI/PDB deposition for submitting CCPN data to PDBe and BMRB
  

Chemical compound reference information in addition to the defaults that are included in the CcpNmr distributions can be found at the EBI PDBe NMR pages.

For more information on the software development read the ‘Quick Guide’.
A CcpNmr mailing list has been set up for discussion of the software.

Format Converter

Overview

The FormatConverter is a package of scripts that allow import and export of existing NMR and related data formats into the CCP Data Model. It can also read/write/edit NMR acquisition and processing parameters/scripts. It is written in Python and originally developed by Wim Vranken (Molecular Structure Database group, European Bioinformatics Institute).

The format converter package can be accessed by individual python function calls or from a GUI. All code is subject to the GPGL licence.

Development

Particular thanks with regard to development go to Wayne Boucher (who provided much of the GUI code and for discussions), Rasmus Fogh (for discussions and Data Modelling), Aart Nederveen (for extensive testing), Jurgen Doreleijers (for providing his Python STAR reader/writer), and Peter Guentert (for allowing the use of his CYANA library). The reference data used within CCP and this package is based on the internal MSD database and to reference information from AQUA and the BMRB.

CcpNmr Analysis

The Idea

CcpNmr Analysis is a graphics-based interactive NMR assignment and project management program. It has been inspired by NMR assignment applications like ANSIG and Sparky. The program contains all new computer code and while it continues some of the strong traditions of other assignment programs it also provides novel ways to approach the analysis of NMR data. CcpNmr Analysis is not just an assignment program; it can be considered a platform for all the NMR data described by the Data Model. For example you can use it to measure relaxation rates, calculate distance constraints, co-ordinate structure generation, edit molecular information and use it as a starting point to develop new software and algorithms for NMR.

Development

Most of the computer code for Analysis is written in Python. Only speed-critical functions are performed by code written in the fast, compiled language C. Such C functions include the calculation of contours and mathematically intensive algorithms. The Python part of the program consists of a series of integrated graphical windows ("Popups") and an underlying layer of Python library functions. The graphical elements allow the user to enter information and to view the status of the data, while the library functions manipulate the Data Model objects to record the scientific information.

Data Model

CcpNmr Analysis has its own Data Model package, which means it uses CCPN technology to create a program-specific part of the Python API and thus allows program information (colours, window positions etc.) to be recorded and stored as XML files.