For depositing NMR data (not structures) to BMRB:

BMRBDep deposition system.

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.)

Note that unfinished depositions started on the previous ADIT-NMR deposition system can usually be manually migrated to BMRBdep by BMRB staff. Please contact [email protected] with your ADIT-NMR restart ID for support.

OneDep: wwPDB Deposition & Annotation System

• X-ray, EM, NMR
• Overview of the new wwPDB deposition system
• Tutorials

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 preferred 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) can now be uploaded as part of a standard deposition.

To submit additional or corrected data for an existing BMRB entry, please send the file(s) as e-mail attachment to BMRB support: [email protected]. Large datasets can be uploaded and associated with the entry via BMRbig. Timedomain data files can be added to existing entries easily by using the time domain data upload tool.

Note that the above applies to NMR structure depositions submitted via OneDep system as well. Once you have deposited an NMR structure to OneDep and received the BMRB ID, please use the above methods to send us additional data not collected by the OneDep system.

Pre-deposition data validation services

wwPDB ValidationService will check your model and experimental files prior to submitting a structure to wwPDB.

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

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

PIPP to NMR-STAR: software for converting PIPP chemical shift files to NMR-STAR 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 to BMRB. Please contact us by e-mail ([email protected]) for instructions.

• 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 to BMRB. Please contact us by e-mail at ([email protected]) for instructions.

• 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.