BMRB Deposition Systems

Notice: Effective starting 6-December-2010, depositions going to PDB now require assigned chemical shift data. Starting on that date, ADIT-NMR will begin enforcing that policy. More information about this policy can be found at the BMRB news page.

ADIT-NMR A single tool that allows you to deposit at both PDB and BMRB.
     (Most new depositions start here.)
     An overview of ADIT-NMR is available for new users.

Note: previous version of ADIT-NMR data deposition system has been taken off-line. To retrieve unfinished depositions created before December 6, 2010 contact bmrbhelp@bmrb.wisc.edu

SMSDep Small Molecule Structure Deposition System.
    Only those structures which are too small for PDB to accept may be deposited here.
     Please read the PDB Entry requirements page for the precise purpose and criteria for the SMSDep deposition 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-delineated 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 one large NMR-STAR file. An excellent example of an NMR-STAR file with a number of types of data is bmr4267.str, Apo-HNGAL Human Neutrophil Gelatinase-Associated Lipocalin.

Time domain data (raw spectral data) is uploaded separately via ftp. These are 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.

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 with ADIT-NMR. - BMRB

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

LACS report generator will create LACS validation report for NMR-STAR 2.1 assigned chemical shifts table.

CheckShift - Chemical Shift Reference Check - Center of Applied Molecular Engineering, the University of Salzburg, Austria. It works on NMR-STAR 2.1, SHIFTX or TALOS files. (Firefox is recommended for CheckShift)

Formatting tools, References, etc.

• 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.
  See these for examples of NMR-STAR files.
• Ambiguity code assignment interface: simplifies assignment of chemical shift ambiguity codes.
• 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.

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.