BMRB accepts the following kinds of data:
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@example.com with your ADIT-NMR restart ID for support.
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) 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: firstname.lastname@example.org, or to BMRB help alias: email@example.com. Large datasets can be uploaded via FTP using the same procedure as for the timedomain data.
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.
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.
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.
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.
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.
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 (firstname.lastname@example.org) for instructions.
This information can be included as comments in the file containing the pulse sequence.
ASCII text files containing the software macro can be submitted to BMRB. Please contact us by e-mail at (email@example.com) for instructions.
The above information can be included as comments in the file containing the macro.