New, significantly improved, BMRBDep deposition system. (Still in beta.)
Traditional ADIT-NMR system.
BMRB accepts the following kinds of data:
Note that unfinished depositions started before 2016 are not available on the current ADIT-NMR server. They have been archived and can be migrated to it, please contact email@example.com for details.
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: 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 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.
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
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.
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.
This information can be included as comments in the file containing the pulse sequence.
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:
The above information can be included as comments in the file containing the macro.