BMRB Deposition Systems
After September 30th 2016 wwPDB structure depositions started on the "joint" ADIT-NMR system can no longer be submitted.
NMR (not structure) data depositions can be migrated to the current BMRB deposition server, e-mail firstname.lastname@example.org
OneDep: wwPDB Deposition & Annotation System
ADIT-NMR system for
depositing NMR data (not structures) to BMRB
BMRB accepts the following kinds of data:
- NMR spectral parameters
(chemical shifts, coupling constants, time-domain data, spectral peak lists, and RDCs),
- Relaxation data (R1/T1, R2/T2, R1rho/T1rho, heteronulear NOEs),
- Other kinetic data (H-exchange, chemical rates)
- Thermodynamic data (pKa, binding constants,order parameters).
(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
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: email@example.com, or to BMRB help alias:
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.
NMR-STAR to other formats: 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.
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 (firstname.lastname@example.org) that a pulse sequence has been deposited. Please indicate
in the e-mail the names of all the files included in the submission.
- 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.
- 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 (email@example.com)
that a program macro has been deposited. Please include the following information in the e-mail:
- 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.
- 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.