Frequently Asked Questions

1.Deposition and update of BMRB entries

1-1 How do I deposit NMR experiment and/or NMR structure data?
You can obtain that information on the front page.
* Overview of the Submission Process
* Submission Manual
1-2 Is there a tutorial available on how to use ADIT-NMR?
Click Submitting data on the front page, you can obtain that information.

* Step1 Preparation for Data Deposition
* Step2 Create of an ADIT-NMR Session
* Step3 Upload of Deposition Data Files
* Step4 Entering Relevant Data
* Step5 Preview and Deposition of your Entry

1-3 I want to know NMR-STAR format in detail.
The following rows are NMR-STAR format.

#############################################
# Molecular system (assembly) description # -->Supergroups
#############################################
save_assembly -->Saveframe categories
_Assembly.Sf_category assembly -->Tag categories
_Assembly.Sf_framecode assembly

There are more information in NMR-STAR Format. Please check.
* Supergroups
* Saveframe categories
* Tag categories (tables)
1-4 I want to deposit the NMR experiment data to BMRB. The NMR structure data derived from it has been deposited to PDB.

A1. If you know the ADIT-NMR Session Restart ID of your PDB entry which has been deposited:
1. Please input the Restart ID to "Continue Previous Session" box on ADIT-NMR and click "CONTINUE SESSION" button.
The previous session will be available.
2. Please click "BMRB" of "View Mode" menu. You can upload your NMR experiment data file(s) and input additional information for BMRB entry.
3. Please click "Deposit to BMRB" button to submit your entry to BMRB.

A2. If you don't know the ADIT-NMR Session Restart ID of your PDB entry which has been deposited:
1. Please click "BEGIN" button of "New ADIT-NMR Session" on ADIT-NMR.
2. Please upload the mmCIF file of your PDB entry. The information of the uploaded file will be imported into the session.
3. Please upload your NMR experiment data file(s) and input additional information for BMRB entry.
4. Please click "Deposit to BMRB" button to submit your entry to BMRB.

1-5 I want to deposit the NMR structure data to PDB. It derived from the NMR experiment data which has been deposited to BMRB.

A1. If you know the ADIT-NMR Session Restart ID of your BMRB entry which has been deposited:
1. Please input the Restart ID to "Continue Previous Session" box on ADIT-NMR and click "CONTINUE SESSION" button. The previous session will be available.
2. Please change the View Mode from BMRB to PDB. You can upload your atomic coordinates and restraints files, and input additional information for PDB entry.
3. Please click "Deposit to PDB" button to submit your entry to PDB.

A2. If you don't know the ADIT-NMR Session Restart ID of your BMRB entry which has been deposited:
1. Please click "BEGIN" button of "New ADIT-NMR Session" on ADIT-NMR.
2. Please upload the NMR-STAR(Ver.3) file of your previous BMRB entry. The information of the uploaded file would be imported into the session.
3. Please upload your atomic coordinates and restraints files, and input additional information for PDB entry.
4. Please click "Deposit to PDB" button to submit your entry to PDB.

1-6 I want to deposit new NMR structure using previous BMRB entry which has been deposited to BMRB.

A1. If you know the ADIT-NMR Session Restart ID of your previous BMRB or PDB entry:
1. Please input the Restart ID to "New Session Copied From Previous Deposition" box on ADIT-NMR and click "NEW SESSION" button. New session will be copied from the previous session.
2. Please upload new NMR data file(s), verify the input information and modify the data to update.
3. Please click "Deposit to BMRB/PDB" button to submit your new entry. New BMRB accession number or PDB ID will be assigned.

A2. If you don't know the ADIT-NMR Session Restart ID of your previous BMRB or PDB entry:
1. Please click "BEGIN" button of "New ADIT-NMR Session" on ADIT-NMR.
2. Please upload the NMR-STAR(Ver.3) file or the mmCIF file of your previous BMRB/PDB entry. The information of the uploaded file will be imported into the session.
3. Please upload new NMR data file(s), verify the input information and modify the data to update.
4. Please click "Deposit to BMRB/PDB" button to submit your new entry. New BMRB accession number or PDB ID will be assigned.

1-7 I want to update my BMRB entry which has been deposited to BMRB.
You can not modify in ADIT-NMR Session.
Please contact us using left green "Feedback" tab. (clearly stating BMRB accession number and revised points.)
1-8 I want to update my PDB entry.
Please contact PDBj Deposition and Annotation staff. (clearly stating PDB ID or RCSB ID in the subject.)

2.Released data and various search service at BMRB

2-1 How can I set the release date of my entry?
When you deposit your entry using ADIT-NMR, you can choose the release date of your entry as follows: (Please set "Release status for NMR experimental data" in Entry information.)

As for NMR experiment data, atomic coordinates and restraints:
* RELEASE NOW
* HOLD FOR PUBLICATION
* HOLD FOR 4 WEEKS
* HOLD FOR 8 WEEKS
* HOLD FOR 6 MONTHS
* HOLD FOR 1 YEAR

As for the sequence data of your studied molecule:
* RELEASE NOW
* HOLD FOR RELEASE

You are, of course, welcome to ask us to release your entry at any time.
Please contact us using left green "Feedback" tab or PDBj Deposition and Annotation staff.
2-2 How do I check the processing status of the entry ?
You can use Access to BMRB Biological NMR Data.
Please enter BMRB accession number you want to check. The processing status of the entry will be displayed.

The following pages are available to check the entry status.
* Entries Received and Being Processed at BMRB
* Entries 'On Hold' at BMRB
* Listing of New BMRB NMR-STAR files released in the last month

2-3 BMRB entry which was presented papers has not been published yet. When will it be released?
Please let us know update on citation status by return mail.
2-4 I have withdrawn PDB entry. Should I also withdraw BMRB entry which has relation to that?

A1. No,you don't need to withdraw your BMRB entry.
Of course, if you want to do it, please let us know.

A2. If PDB entry was withdrawn due to replace with new PDB entry, please let us know.
(clearly stating BMRB accession number, updated PDB information and new PDB ID.)

2-5 How do I find BMRB entry of NMR experiment data that relates to other databases.
You can use Access to BMRB Biological NMR Data.
Please select the database and enter the ID that you want to search.
The list of related BMRB entries will be displayed.
´╝ŐDatabase: DBj, EMBL, GenBank, PDB, PIR, PRF, REF, SWISS-PROT
2-6 How do I search for BMRB entries by experimental conditions?
You can make use of the various BMRB search archives as follows:

* NMR Browse : search entries by pH and/or temperature condition(s).
* Chemical Shift Search : find the chemical shifts for any given residue or residue atom.
* BMRB FASTA search : search entries by protein and nucleic acid sequence.

2-7 How do I find the data derived from the solid state NMR?
Please click Solid-state NMR Entries.

3.About chemical shift

3-1 How can I extract NMR experiment data in NMR-STAR format?
You can use various BMRB software as follows:

* STARch file converter (Note: Preparation Method of Chemical Shift)
* NMR-STAR template Generator: It produces NMR-STAR 3.1 formatted tables for NMR data.
* Ambiguity code assignment interface: It insert default ambiguity codes to assigned chemical shifts table.

Click Tool List on the front page, you can obtain more information.
3-2 Where can I get the chemical shift statistics?
Please click BMRB Database Statistics.
3-3 What does it mean, Assembly and Entity?
Molecular "Entity" is chemically unique molecule.
"Assembly" that is present in the sample tube is composed of one or more molecular entities.

For example:
About molecule studies Zinc finger protein (Assembly).
It is composed of alpha domain (1st entity), beta domain (2nd entity) and Zinc ion (3rd entity) in the NMR tube.

* Examples and Instructions for Describing the Molecular System in an ADIT-NMR Deposition
3-4 How do I describe the chemical shift reference of each observed nucleus?
BMRB recommends NMR Measurements which using Chemical Shift Referencing of IUPAC.

For example:
loop_
_Chem_shift_ref.Atom_type
_Chem_shift_ref.Atom_isotope_number
_Chem_shift_ref.Mol_common_name
_Chem_shift_ref.Atom_group
_Chem_shift_ref.Chem_shift_units
_Chem_shift_ref.Chem_shift_val
_Chem_shift_ref.Ref_method
_Chem_shift_ref.Ref_type
_Chem_shift_ref.Indirect_shift_ratio

Case 1:
H 1 DSS "methyl protons" ppm 0.0 internal direct 1.0
C 13 DSS "methyl protons" ppm 0.0 n/a indirect 0.251449530
N 15 DSS "methyl protons" ppm 0.0 n/a indirect 0.101329118
Case 2:
H 1 water protons ppm 4.773 internal direct 1.0
C 13 water protons ppm 4.773 internal direct 0.251449530
N 15 water protons ppm 4.773 internal indirect 0.101329118
3-5 How do I describe the nomenclature for proteins and nucleic acids?
The nomenclature of BMRB is based on IUPAC rules.
Following lists are available:
* Proton nomenclature for proteins and nucleic acids
* Correlation of hydrogen atom naming systems, including diastereotopic protons.
* Correlation of hydrogen pseudoatom naming systems
3-6 What does it mean, the chemical shift ambiguity code?

The codes mean the ambiguity of your chemical shift assignment for each atoms.
* Assign ambiguity codes is available to insert default ambiguity codes to assigned chemical shifts table.

Chemical Shift Ambiguity Index Value Definitions
1
Unique (including isolated methyl protons, geminal atoms, and geminal methyl groups with identical chemical shifts)
(e.g. ILE HD11, HD12, HD13 protons)
2
Ambiguity of geminal atoms or geminal methyl proton groups
(e.g. ASP HB2 and HB3 protons, LEU CD1 and CD2 carbons, or LEU HD11, HD12, HD13 and HD21, HD22, HD23 methyl protons)
3
Aromatic atoms on opposite sides of symmetrical rings
(e.g. TYR HE1 and HE2 protons)
4
Intra-residue ambiguities
(e.g. LYS HG and HD protons or TRP HZ2 and HZ3 protons)
5
Inter-residue ambiguities
(LYS 12 vs. LYS 27)
6
Intermolecular ambiguities
(e.g. ASP 31 CA in monomer 1 and ASP 31 CA in monomer 2 of an asymmetrical homodimer, duplex DNA assignments, or other assignments that may apply to atoms in one or more molecule in the molecular assembly)
9
Ambiguous, specific ambiguity not defined
3-7 Which tags are mandatory for the assigned chemical shifts ?
The mandatory tags for the deposition are listed below:

loop_
_Atom_chem_shift.Comp_index_ID
_Atom_chem_shift.Comp_ID
_Atom_chem_shift.Atom_ID
_Atom_chem_shift.Val
_Atom_chem_shift.Val_err -->if possible
_Atom_chem_shift.Ambiguity_code -->if possible

1   ALA  H 8.19     0.01   1
1 ALA HA  4.26 0.01 1
1 ALA C 177.76 0.1 1
1 ALA CA 53.17 0.1 1
1 ALA N 128.18 0.02 1
2 ARG H 8.29 0.01 1
2 ARG HA 4.29 0.01 1
2 ARG C 176.44 0.1 1
2 ARG CA 56.80 0.1 1
2 ARG N 120.80 0.02 1
stop_

4.Troubleshooting

4-1 I encounter "Internal server error" when starting an ADIT-NMR session with Previous Session Restart ID.
When we released the current ADIT-NMR system in 2007, we changed the ADIT-NMR server.
If your previous session was generated before 2007, the ADIT-NMR will fail to start.
Please contact us using left green "Feedback" tab. (clearly stating Session Restart ID, BMRB accession number, PDB ID.)
4-2 I can't complete my deposition with a warning "Your deposition cannot be submitted".
Please click "Return to Input Tool" button above of the web page and check the status check boxes of each items listed in the left menu of the input page. To complete your deposition, all check boxes should be checked check mark. Please complete the unchecked item(s) exclamation mark, then click "Deposit To BMRB/PDB" button again.

5.Other inquiries

5-1 Frequently Asked Questions on PDB
Please see PDBj Frequently Asked Questions.