CcpNmr FormatConverter

About

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.

Development

FormatConverter was written by Wim Vranken, then at the Molecular Structure Database group, European Bioinformatics Institute, and first released in 2003. 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 CCPN and FormatConveerter is based on the internal PDBe database and to reference information from AQUA and the BioMagResBank.

Relationship to other applications

FormatConverter serves as the standard route for moving data between the CCPN data model and external formats, and so is an entry route to the CcpNmr Suite. It uses the CCPN data model API, but is independent of the rest of the CcpNmr Suite. It had a key role in the WeNMR project, transferring data between the various supported programs, and has been used for data clean-up and remediation in RECOORD and the BioMagResBank.

FormatConverter documentation

• Quick Start

• Tutorial

• Example Python Scripts