The CcpNmr Version-2 software suite is a series of programs for macromolecular NMR spectroscopy integrated with the CCP data model. Between programs written by the CCPN team, external contributions, and ‘outside’ programs integrated with the data model, it has been 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.
CcpNmr Analysis is a graphics-based interactive NMR assignment and project management program. It was partly inspired by NMR assignment applications like ANSIG and Sparky. The program was written from the ground up 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.
CcpNmr ChemBuild is a graphical tool to construct chemical compound definitions for NMR. While there are many chemical structure drawing packages available ChemBuild was especially created to handle concepts like protonation variants and magnetic equivalence which are required for NMR resonance assignment. Several different chemical file formats are supported, including PDB, Smiles, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information. We are continuing to develop ChemBuild as part of our Version 3 software suite.
CcpNmr Format Converter
The FormatConverter is a menu-driven program to import sequences, peak lists, chemical shift lists, constraint lists etc. to the CCPN data model and re-export them to other formats. It can read in entire projects or fragments of them, and can connect atoms, assignments etc. from different files to a consistent whole (‘link resonances’). FormatConverter can also read in Bruker and Varian NMR spectra and set up processing for NMRPipe and Azara. The program is written in Python, and individual functionalities are accessible to direct function calls, bypassing the user interface. It was originally developed by Wim Vranken while in the Molecular Structure Database group at the European Bioinformatics Institute.
The CCPN Data Model
The CCP Data Model for macromolecular NMR is intended to cover all data needed for macromolecular NMR spectroscopy from the initial experimental data to the final validation. It serves for exchange of data between programs, for storage, data harvesting, and database deposition. The data model proper is an abstract description of the relevant data and their relationships – it is implemented in the modeling language UML. From this CCPN autogenerates interfaces (APIs) for various languages, format description and I/O routines, and documentation.
Protein NMR – A Practical Guide
A website written by Vicky Higman, which contains experiment descriptions and tutorials covering assignment strategy for both solution and solid state spectra with V2.