BMRB

Biological Magnetic Resonance Data Bank


A Repository for Data from NMR Spectroscopy on Proteins, Peptides, Nucleic Acids, and other Biomolecules
Member of WWPDB

BMRB Deposition Systems

ADIT-NMR deposition system allows you to deposit at both PDB and BMRB.

BMRB accepts the following kinds of data:

(Click on the links above for complete listings.)
SMSDep: Small Molecule Structure Deposition system.
Only those structures which are too small for the PDB to accept may be deposited here. Please read the PDB entry requirements page for the precise purpose and criteria for the SMSDep system.

The prefered file format for NMR data files is NMR-STAR, a Self-defining Text Archival and Retrieval format (STAR). STARch is a software tool that can convert data files from various formats, including PIPP, XEASY, and tab-delimited files generated from common spreadsheets into NMR-STAR format.

Individual data files along with the information you enter about your study will be collated into a single NMR-STAR file. An excellent example of an NMR-STAR file with a number of types of data is entry 4267: Apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin.

Time domain data (raw spectral data) is uploaded separately via ftp. Please see the instructions on how to upload time domain data.

To submit additional or corrected data for an existing BMRB entry, please send the file(s) as e-mail attachment to BMRB annotators: annotators@bmrb.wisc.edu, or to BMRB help alias: bmrbhelp@bmrb.wisc.edu

Pre-deposition data validation services

Chemical Shift vs Coordinate nomenclature check A tool to check Assigned Chemical Shift nomenclature versus Coordinate file nomenclature. This tool runs the same checks as will be run later when you deposit atomic coordinates with ADIT-NMR.

Visualization server will generate DEVise visualizations for uploaded NMR-STAR 3.1 data tables.

Protein Structure Validation Suite (PSVS) is a useful tool for the assesment of protein structures generated by NMR and X-ray methods. PSVS is broadly applicable for structure quality assessment in structure biology projects.

iCing Validation Package is part of the Common Interface for NMR structure Generation (CING) package.

CheckShift - Chemical Shift Reference Check at Center of Applied Molecular Engineering, the University of Salzburg, Austria. It works on NMR-STAR 2.1, SHIFTX or TALOS files.

Format conversion tools

STARch file converter: 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.

NMR-STAR template generator: produces NMR-STAR 3.1 formatted tables for NMR data.
(Use these as examples of NMR-STAR data files.)

Ambiguity code assignment interface: simplifies assignment of chemical shift ambiguity codes.

Format Converter from PDBe: a set of Python scripts that can read NMR data files and output them into a number of different formats. Here is an introduction to its usage and the download page.

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.

FELIX to NMR-STAR: software for converting FELIX chemical shift files to NMR-STAR 2.1 format.

PIPP to NMR-STAR: software for converting PIPP chemical shift files to NMR-STAR 2.1 format.

NMR-STAR to TALOS+: script for converting chemical shift tables in BMRB entries to TALOS+ input files.

CYANA to XPLOR: script for converting CYANA formatted files to XPLOR/CNS/PDB files.

Reference information about atom nomenclature, standard chemical shifts, indirect chemical shift references, etc.

Submitting pulse programs.

ASCII text files containing pulse sequences, text files describing the experiments, and other ancillary files can be submitted by anonymous ftp to "deposit.bmrb.wisc.edu". Please place the files in the incoming/pulse_sequence directory and notify BMRB by e-mail (bmrbhelp@bmrb.wisc.edu) that a pulse sequence has been deposited. Please indicate in the e-mail the names of all the files included in the submission.

  • Required:
  • Brief title for the pulse sequence.
  • Suggested location for the pulse sequence in the library.
  • Concise description of what the pulse sequence is intended to provide.
  • Spectrometer manufacturer and model(s) on which the pulse sequence is known to operate.
  • Pulse sequence with phase cycling as an ASCII text file.
  • Literature reference, if appropriate.
  • Name(s) of author(s).

This information can be included as comments in the file containing the pulse sequence.

  • Optional:
  • File containing a figure describing the pulse sequence. Please indicate the format of the file (postscript, GIF, MPEG, etc.).
  • Files containing parameter lists used to execute the pulse sequence (shaped pulses, gradient programs, frequency lists, delay lists, etc.).

Sample Minimal Submission
Sample Fancy Submission

Submitting software and macros.

ASCII text files containing the software macro can be submitted by anonymous ftp to "deposit.bmrb.wisc.edu". Please place the files in the incoming/macro_definition directory and notify BMRB by e-mail (bmrbhelp@bmrb.wisc.edu) that a program macro has been deposited. Please include the following information in the e-mail:

  • Required:
  • Brief title for the processing macro.
  • Suggested location or category for the macro in the library.
  • Concise description of what the data processing macro is intended to provide.
  • Software vendor, software product, and software version number compatible with the macro.
  • A literature reference, if appropriate.
  • The name(s) of the author(s) of the macro.

The above information can be included as comments in the file containing the macro.

  • Optional:
  • If control parameters or other information required for the macro to function is contained in ancillary files, please supply an example of those files.
  • E-mail address, telephone number, or other contact information, if you are willing to provide assistance.