Validation tools

Pre-deposition data validation services

Downloadable data validation software

  • LACS 64-bit linux binary (requires Matlab runtime), Matlab source code, and python wrappers
  • Watto is a software package consisting of programs for analyzing, annotating, parsing, archiving, and disseminating experimental NMR data deposited by authors world wide into the PDB.

Deposit tools

Format conversion tools

  • Converts data files in various formats to NMR-STAR 3.1 for upload to ADIT-NMR. Input formats include NMRView, PIPP, Sparky, XEASY, as well as tab- and comma-delimited.
  • Generate data table produces NMR-STAR 3.1 formatted tables for NMR data. (Use these as examples of NMR-STAR data files.)
  • Assign ambiguity code simplifies assignment of chemical shift ambiguity codes.
  • NMR resources and services from PDBe: a set of Python scripts that can read NMR data files and output them into a number of different formats.
  • Convert NMR-STAR 3.1 table converts NMR-STAR 3.1 chemical shift tables to Sparky, NMRPipe/TALOS, XEASY, or NMR-STAR 2.1.

Conversion tools donated by the NMR community

  • tab2bmrb convert chemical shift tables between publication format and NMR-STAR 2.1 format. Also included are tools to calculate random coil chemical shifts and NMR experimental pulse lengths for experiments dependent on 3JHN(CA)HA coupling constants.
  • felix2bmrb software for converting FELIX chemical shift files to NMR-STAR 2.1 format.
  • pipp2nmrstar software for converting PIPP chemical shift files to NMR-STAR 2.1 format.
  • bmrb2talos script for converting chemical shift tables in BMRB entries to TALOS+ input files.
  • cyana2xplor script for converting CYANA formatted files to XPLOR/CNS/PDB files.

Utilities based on BMRB archive

  • nightshift program for plotting simulated 2D and 3D NMR spectra from assigned chemical shifts of BMRB archive.
  • Chenomx NMR Suite software suite to identify and quantify metabolites in NMR spectra.

BMRBj tools

Tools for NMR spectral analysis

  • NMR Tool Box includes MagRO-NMRView, SPARTA validation tool and FitRobot
  • SAS_CNS NMR assignment tool for solid-state NMR
  • Olivia Objective, chemical shift library based, stereo-view assignment software
  • xyza2pipe A cross conversion environment of multi dimensional NMR spectra

Tools for enhancing interoperability of BMRB