wwPDB NMR restraint remediation conforms to standard NMR-STAR and NEF format
Dear PDB-l,
NMR data files are standardized in NEF
https://www.nature.com/articles/nsmb.3041 and NMR-STAR format [Ulrich,
2019 https://link.springer.com/article/10.1007/s10858-018-0220-3] for
the PDB entries which have NMR data in many different software specific
formats. This remediation project provides unified NMR data in single
NMR-STAR/NEF file for the PDB entries. wwPDB is moving forward single
file upload for NMR data (restraints, chemical shifts and possibly peak
list) in NMR-STAR/NEF format and will eventually phase out the upload of
software specific format in OneDep in future. During transition period,
OneDep converts certain restraint formats into NMR-STAR/NEF at the
deposition and provides users with NMR restraint validation
https://www.wwpdb.org/news/news?year=2020#5fc8e8ab09ae2a096d081e27 in
wwPDB validation reports for NMR entries having assigned chemical shifts
and reasonable restraints in following supported formats:
AMBER, BIOSYM, CHARMM, CNS, CYANA, DYNAMO/TALOS/PALES, GROMACS, ISD,
ROSETTA, SYBYL, and XPLOR-NIH
Depending on complexity of restraints and whether spectral peak lists
have been deposited, the first rollout includes NMR entries with simple
restraints in the supported formats and without spectral peak lists. The
next rollout will include entries with spectral peak lists. Entries
which met the following criteria are the scope for remediation:
- Both assigned chemical shifts and restraints have been deposited to
the PDB - A valid topology file or specific comments must be present to
interpret restraint files in a specific format (i.e. AMBER, CHARMM,
GROMACS) - All atoms described in NMR data (assigned chemical shifts and
restraints) are consistent with model’s atoms - Sequence alignment between the model and restraints matches,
allowing terminal sequence extensions
NMR-STAR format is the master format used to handle wide variety of
restraints in this NMR restraint remediation project. Data items
starting with “Auth_asym_ID”, “Auth_seq_ID”, “Auth_comp_ID”, and
“Auth_atom_ID” terms, i.e. “_Gen_dist_constraint.Auth_seq_ID_1”, point
to equivalent data items in mmCIF, “_atom_site.auth_asym_id”,
“_atom_site.auth_seq_id”, “_atom_site.auth_comp_id”,
“_atom_site.auth_atom_id”, respectively. Complete atom name mapping
information is incorporated using “_Assembly” and “_Entity” categories.
NMR constraints used by structure determination software but not covered
by the NMR-STAR ontology, such as chemical planarity, equilibrium bond
angle, non-crystallographic symmetry, etc., are stored as JSON data
under "_Other_constraint_list.text_data" tag to ensure no information is
lost during remediation. Furthermore, statistics on remediated
restraints are available. NEF data files are provided as best effort
conversions from the master NMR-STAR data files.
New unified NMR data files in NEF and NMR-STAR formats of existing NMR
entries are distributed in the “nmr_data” directory of the PDB archive
in the same manner for entries accompanied by the single NMR data file
(https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/) and
at BMRB archive
(https://bmrb.io/ftp/pub/bmrb/nmr_pdb_integrated_data/coordinates_restraints_chemshifts/remediated_restraints).
The existing data files in the PDB archive directories
“nmr_chemical_shifts” and “nmr_restraints” are remained as is.
To retrieve NMR data, users should primarily obtain unified NMR data
files at ../nmr_data directory. Conventional chemical shifts and
restraints can be used only if unified NMR data are not available.
For newly deposited NMR entries with conventional separated NMR data
files, OneDep now unifies assigned chemical shifts and restraints into a
single data file, which can be accessed from OneDep upload summary page.
After submission, depositors can not roll back to the conventional formats.
wwPDB validation reports are re-calculated to provide NMR restraint
validation for the target entries. NMR restraints can be interpreted and
weighted differently by various software during structure calculation.
The NMR restraints validation software employs a more general approach
recommended by NMR-VTF, independently verifying the satisfaction of each
restraint in every model. This can occasionally result in a large number
of violations when the actual structure determination software adopts a
different approach or assigns less weight during structure calculation.
For any further information about NMR data remediation, please contact
us at deposit-help@mail.wwpdb.org.
See wwPDB news at
https://www.wwpdb.org/news/news?year=2023#64875a3cd78e004e766a967c.
--
Regards,
Jasmine
---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
---==========================
Hi there,
Okay thank you, Will be waiting for your response, always happy to help,
hoping to receive a bounty for finding this vulnerability and reporting it
ethically to you.
Best Regards
Arslan
On Thu, Jun 15, 2023 at 12:59 AM Jasmine Young via pdb-l <
pdb-l@lists.wwpdb.org> wrote:
Dear PDB-l,
NMR data files are standardized in NEF
https://www.nature.com/articles/nsmb.3041 and NMR-STAR format [Ulrich,
2019 https://link.springer.com/article/10.1007/s10858-018-0220-3] for
the PDB entries which have NMR data in many different software specific
formats. This remediation project provides unified NMR data in single
NMR-STAR/NEF file for the PDB entries. wwPDB is moving forward single
file upload for NMR data (restraints, chemical shifts and possibly peak
list) in NMR-STAR/NEF format and will eventually phase out the upload of
software specific format in OneDep in future. During transition period,
OneDep converts certain restraint formats into NMR-STAR/NEF at the
deposition and provides users with NMR restraint validation
https://www.wwpdb.org/news/news?year=2020#5fc8e8ab09ae2a096d081e27 in
wwPDB validation reports for NMR entries having assigned chemical shifts
and reasonable restraints in following supported formats:
AMBER, BIOSYM, CHARMM, CNS, CYANA, DYNAMO/TALOS/PALES, GROMACS, ISD,
ROSETTA, SYBYL, and XPLOR-NIH
Depending on complexity of restraints and whether spectral peak lists
have been deposited, the first rollout includes NMR entries with simple
restraints in the supported formats and without spectral peak lists. The
next rollout will include entries with spectral peak lists. Entries
which met the following criteria are the scope for remediation:
- Both assigned chemical shifts and restraints have been deposited to
the PDB - A valid topology file or specific comments must be present to
interpret restraint files in a specific format (i.e. AMBER, CHARMM,
GROMACS) - All atoms described in NMR data (assigned chemical shifts and
restraints) are consistent with model’s atoms - Sequence alignment between the model and restraints matches,
allowing terminal sequence extensions
NMR-STAR format is the master format used to handle wide variety of
restraints in this NMR restraint remediation project. Data items
starting with “Auth_asym_ID”, “Auth_seq_ID”, “Auth_comp_ID”, and
“Auth_atom_ID” terms, i.e. “_Gen_dist_constraint.Auth_seq_ID_1”, point
to equivalent data items in mmCIF, “_atom_site.auth_asym_id”,
“_atom_site.auth_seq_id”, “_atom_site.auth_comp_id”,
“_atom_site.auth_atom_id”, respectively. Complete atom name mapping
information is incorporated using “_Assembly” and “_Entity” categories.
NMR constraints used by structure determination software but not covered
by the NMR-STAR ontology, such as chemical planarity, equilibrium bond
angle, non-crystallographic symmetry, etc., are stored as JSON data
under "_Other_constraint_list.text_data" tag to ensure no information is
lost during remediation. Furthermore, statistics on remediated
restraints are available. NEF data files are provided as best effort
conversions from the master NMR-STAR data files.
New unified NMR data files in NEF and NMR-STAR formats of existing NMR
entries are distributed in the “nmr_data” directory of the PDB archive
in the same manner for entries accompanied by the single NMR data file
(https://files.wwpdb.org/pub/pdb/data/structures/divided/nmr_data/) and
at BMRB archive
(
https://bmrb.io/ftp/pub/bmrb/nmr_pdb_integrated_data/coordinates_restraints_chemshifts/remediated_restraints).
The existing data files in the PDB archive directories
“nmr_chemical_shifts” and “nmr_restraints” are remained as is.
To retrieve NMR data, users should primarily obtain unified NMR data
files at ../nmr_data directory. Conventional chemical shifts and
restraints can be used only if unified NMR data are not available.
For newly deposited NMR entries with conventional separated NMR data
files, OneDep now unifies assigned chemical shifts and restraints into a
single data file, which can be accessed from OneDep upload summary page.
After submission, depositors can not roll back to the conventional formats.
wwPDB validation reports are re-calculated to provide NMR restraint
validation for the target entries. NMR restraints can be interpreted and
weighted differently by various software during structure calculation.
The NMR restraints validation software employs a more general approach
recommended by NMR-VTF, independently verifying the satisfaction of each
restraint in every model. This can occasionally result in a large number
of violations when the actual structure determination software adopts a
different approach or assigns less weight during structure calculation.
For any further information about NMR data remediation, please contact
us at deposit-help@mail.wwpdb.org.
See wwPDB news at
https://www.wwpdb.org/news/news?year=2023#64875a3cd78e004e766a967c.
--
Regards,
Jasmine
---==========================
Jasmine Young, Ph.D.
Biocuration Team Lead
RCSB Protein Data Bank
Research Professor
Institute for Quantitative Biomedicine
Rutgers, The State University of New Jersey
174 Frelinghuysen Rd
Piscataway, NJ 08854-8087
Email:jasmine@rcsb.rutgers.edu
Phone: (848)445-0103 ext 4920
Fax: (732)445-4320
---==========================
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