What the CcpNmr suite is for
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 CCPN authored software has components that come under the open-source GPL, LGPL and special CCPN licenses. In essence CCPN software is free for academic and non-profit organisations. For-profit organisations must subscribe to join CCPN. Full details of the CCPN licensing can be found here
An overview of the different software components
CcpNmr Analysis is a graphics-based interactive NMR assignment and project management program. It has been partly 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.
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, .mol and .mol2, but ChemBuild is special in its ability read and write CCPN chemical component XML files, which store NMR-aware information.
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.
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.
CCPN currently provides a few software services via the web. More details about these services can be found here.
- CcpNmr FormatConverter: Convert between 30+ NMR data formats. Import data into a CCPN project.
- CcpNmr ACPYPE: Create topology parameter files for arbitrary organic compounds.
- CcpNmr Grid: Structure calculation grid server. Currently running ARIA 2.
- CCPN Project Upgrade:Convert version 1.0 projects to version 2.0.
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. From this CCPN autogenerates interfaces (APIs) for various languages, format description and I/O routines, and documentation.
CcpNmr FormatExchange lets you read entire NmrView or Sparky projects into CCPN in a simple manner. it is not yet ready for release, but you can test it for us, or request us to read in data for you.
CcpNmr Workflow Management System is a prototype server that lets you run Cyana, Aria, Unio and CS-Rosetta jobs starting and ending directly on a CCPN project. You can launch several different programs from a single input selection. This is an alpha test prototype and is not yet ready for release, but expert users and eager testers may find it interesting.