Modifications to support for SHEET and ligand SITE records at the PDB in June 2021
In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy
PDB file format was frozen
http://www.wwpdb.org/news/news?year=2014#5764490799cccf749a90cde3. In
addition to PDBx/mmCIF files for all entries, wwPDB produces PDB
format-formatted files for entries that can be represented in this
legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)
As the size and complexity of PDB structures increases, additional
limitations of the legacy PDB format are becoming apparent and need to
be addressed.
Defining complex sheet records
Restrictions in the SHEET record fields in legacy the PDB file format do
not allow for the generation of complex beta sheet topology. Complex
beta sheet topologies include instances where beta strands are part of
multiple beta sheets and other cases where the definition of the strands
within a beta sheet cannot be presented in a linear description. For
example, in PDB entry 5wln a large beta barrel structure is created from
multiple copies of a single protein; within the beta sheet forming the
barrel are instances of a single beta strand making contacts on one side
with multiple other strands, even from different chains.
This limitation, however, is not an issue in the PDBx/mmCIF formatted
file, where these complex beta sheet topology can be captured in
/_struct_sheet/, /_struct_sheet_order/, /_struct_sheet_range/, and
/_struct_sheet_hbond/.
Starting June 8th 2021, legacy PDB format files will no longer be
generated for PDB entries where the SHEET topology cannot be generated.
For these structures, wwPDB will continue to provide secondary structure
information with helix and sheet information in the PDBx/mmCIF formatted
file.
Deprecation of _struct_site (SITE) records
wwPDB regularly reviews the software used during OneDep biocuration. The
/_struct_site/ and /_struct_site_gen/ categories in PDBx/mmCIF (SITE
records in the legacy PDB file format) are generated by in-house
software and based purely upon distance calculations, and therefore may
not reflect biological functional sites.
Starting in June 2021, the in-house legacy software which produces
/_struct_site/ and /_struct_site_gen/ records will be retired and wwPDB
will no longer generate these categories for newly-deposited PDB
entries. Existing entries will be unaffected.
--
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
---==========================
Hello
We are not sure to whom send the following message:
"We have been observing that several members of our user community are having problems to deposit their structures collected on one of the NSLS II beam lines, AMX, FMX and NYX. The major hurdle encountered is in regard to the keyword "source type". If user is looking for "nsls ii" or "NSLS II" they are not able to find the source in the dropdown menu; only "NSLS-II" or "nsls-ii" with a hyphen is accepted. Is there a way that different spelling can be included? Most probably other sources in the future will be affected as well?"
We would appreciate any comment.
Sincerely,
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
e nsls.lifesciences@gmail.commailto:nsls.lifesciences@gmail.com
w https://urldefense.com/v3/https://www.bnl.gov/ps/lifesciences/;!!Mih3wA!QO9Am2NTTzYXpnKWpsNHKSUMHXeJlC8Ls4jHRpxWLnjokzDmi3UHle9FOWvAQCM$
Address:
Life Science Biomedical Technology Resource
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973
From: pdb-l-bounces@sdsc.edu pdb-l-bounces@sdsc.edu on behalf of Jasmine Young jasmin@rcsb.rutgers.edu
Sent: Wednesday, March 17, 2021 11:12 AM
To: pdb-l@sdsc.edu pdb-l@sdsc.edu
Subject: pdb-l: Modifications to support for SHEET and ligand SITE records at the PDB in June 2021
In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy
PDB file format was frozen
<https://urldefense.com/v3/http://www.wwpdb.org/news/news?year=2014*5764490799cccf749a90cde3;Iw!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHuBU0Hj$ >. In
addition to PDBx/mmCIF files for all entries, wwPDB produces PDB
format-formatted files for entries that can be represented in this
legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)
As the size and complexity of PDB structures increases, additional
limitations of the legacy PDB format are becoming apparent and need to
be addressed.
Defining complex sheet records
Restrictions in the SHEET record fields in legacy the PDB file format do
not allow for the generation of complex beta sheet topology. Complex
beta sheet topologies include instances where beta strands are part of
multiple beta sheets and other cases where the definition of the strands
within a beta sheet cannot be presented in a linear description. For
example, in PDB entry 5wln a large beta barrel structure is created from
multiple copies of a single protein; within the beta sheet forming the
barrel are instances of a single beta strand making contacts on one side
with multiple other strands, even from different chains.
This limitation, however, is not an issue in the PDBx/mmCIF formatted
file, where these complex beta sheet topology can be captured in
/_struct_sheet/, /_struct_sheet_order/, /_struct_sheet_range/, and
/_struct_sheet_hbond/.
Starting June 8th 2021, legacy PDB format files will no longer be
generated for PDB entries where the SHEET topology cannot be generated.
For these structures, wwPDB will continue to provide secondary structure
information with helix and sheet information in the PDBx/mmCIF formatted
file.
Deprecation of _struct_site (SITE) records
wwPDB regularly reviews the software used during OneDep biocuration. The
/_struct_site/ and /_struct_site_gen/ categories in PDBx/mmCIF (SITE
records in the legacy PDB file format) are generated by in-house
software and based purely upon distance calculations, and therefore may
not reflect biological functional sites.
Starting in June 2021, the in-house legacy software which produces
/_struct_site/ and /_struct_site_gen/ records will be retired and wwPDB
will no longer generate these categories for newly-deposited PDB
entries. Existing entries will be unaffected.
--
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
---==========================
TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
https://urldefense.com/v3/https://lists.sdsc.edu/mailman/listinfo/pdb-l;!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHs_oQ8H$ .
Dear Vivian,
The beamline information in the source details is a pull-down
enumeration. It provides auto-suggestion when a depositor starts typing.
For example, when one types "nsls" as shown in the screenshot of OneDep
deposition interface, the system provides a suggested list which
includes both NSLS and NSLS-II for depositor to select. The NSLS
beamline enumeration is based on beamline sector as described at BNL,
e.g., AMX is 17-ID-1
https://urldefense.com/v3/https://www.bnl.gov/ps/beamlines/beamline.php?r=17-ID-1;!!Mih3wA!TVvBjus-bpVEFFi1N648VYUTAqL1qH20OQcrlMQbCTnou2PxrSp9Dug0jvzydD4$ .
Feel free to contact me if you have further question regarding this.
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
---==========================
On 3/17/21 12:04 PM, Stojanoff, Vivian wrote:
Hello
We are not sure to whom send the following message:
"We have been observing that several members of our user community are
having problems to deposit their structures collected on one of the
NSLS II beam lines, AMX, FMX and NYX. The major hurdle encountered is
in regard to the keyword "source type". If user is looking for "nsls
ii" or "NSLS II" they are not able to find the source in the dropdown
menu; only "NSLS-II" or "nsls-ii" with a hyphen is accepted. Is there
a way that different spelling can be included? Most probably other
sources in the future will be affected as well?"
We would appreciate any comment.
Sincerely,
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
ensls.lifesciences@gmail.com mailto:nsls.lifesciences@gmail.com
w https://urldefense.com/v3/https://www.bnl.gov/ps/lifesciences/;!!Mih3wA!TVvBjus-bpVEFFi1N648VYUTAqL1qH20OQcrlMQbCTnou2PxrSp9Dug0OOt0adw$
<https://urldefense.com/v3/https://www.bnl.gov/ps/lifesciences/;!!Mih3wA!TVvBjus-bpVEFFi1N648VYUTAqL1qH20OQcrlMQbCTnou2PxrSp9Dug0OOt0adw$ >
Address:
Life Science Biomedical Technology Resource
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973
From: pdb-l-bounces@sdsc.edu pdb-l-bounces@sdsc.edu on behalf of
Jasmine Young jasmin@rcsb.rutgers.edu
Sent: Wednesday, March 17, 2021 11:12 AM
To: pdb-l@sdsc.edu pdb-l@sdsc.edu
Subject: pdb-l: Modifications to support for SHEET and ligand SITE
records at the PDB in June 2021
In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy
PDB file format was frozen
<https://urldefense.com/v3/http://www.wwpdb.org/news/news?year=2014*5764490799cccf749a90cde3;Iw!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHuBU0Hj$
. In
addition to PDBx/mmCIF files for all entries, wwPDB produces PDB
format-formatted files for entries that can be represented in this
legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)
As the size and complexity of PDB structures increases, additional
limitations of the legacy PDB format are becoming apparent and need to
be addressed.
Defining complex sheet records
Restrictions in the SHEET record fields in legacy the PDB file format do
not allow for the generation of complex beta sheet topology. Complex
beta sheet topologies include instances where beta strands are part of
multiple beta sheets and other cases where the definition of the strands
within a beta sheet cannot be presented in a linear description. For
example, in PDB entry 5wln a large beta barrel structure is created from
multiple copies of a single protein; within the beta sheet forming the
barrel are instances of a single beta strand making contacts on one side
with multiple other strands, even from different chains.
This limitation, however, is not an issue in the PDBx/mmCIF formatted
file, where these complex beta sheet topology can be captured in
/_struct_sheet/, /_struct_sheet_order/, /_struct_sheet_range/, and
/_struct_sheet_hbond/.
Starting June 8th 2021, legacy PDB format files will no longer be
generated for PDB entries where the SHEET topology cannot be generated.
For these structures, wwPDB will continue to provide secondary structure
information with helix and sheet information in the PDBx/mmCIF formatted
file.
Deprecation of _struct_site (SITE) records
wwPDB regularly reviews the software used during OneDep biocuration. The
/_struct_site/ and /_struct_site_gen/ categories in PDBx/mmCIF (SITE
records in the legacy PDB file format) are generated by in-house
software and based purely upon distance calculations, and therefore may
not reflect biological functional sites.
Starting in June 2021, the in-house legacy software which produces
/_struct_site/ and /_struct_site_gen/ records will be retired and wwPDB
will no longer generate these categories for newly-deposited PDB
entries. Existing entries will be unaffected.
--
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
---==========================
TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
https://urldefense.com/v3/https://lists.sdsc.edu/mailman/listinfo/pdb-l;!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHs_oQ8H$
https://urldefense.com/v3/__https://lists.sdsc.edu/mailman/listinfo/pdb-l__;!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHs_oQ8H$
.
Dear Vivian,
The beamline information in the source details is a pull-down
enumeration. It provides auto-suggestion when a depositor starts typing.
For example, when one types "nsls" at OneDep deposition interface, the
system provides a suggested list which includes both NSLS and NSLS-II
beamlines for depositor to select. The NSLS beamline enumeration is
based on beamline sector as described at BNL. For example, AMX is
17-ID-1 https://urldefense.com/v3/https://www.bnl.gov/ps/beamlines/beamline.php?r=17-ID-1;!!Mih3wA!VdVSi2V2LmDCUscfjiVmWF9WAOyWE5yKwevy4QF-fzBv1W19Fl7ttOOK9klxJT4$ .
Feel free to contact me if you have further question regarding this.
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
---==========================
On 3/17/21 12:04 PM, Stojanoff, Vivian wrote:
Hello
We are not sure to whom send the following message:
"We have been observing that several members of our user community are
having problems to deposit their structures collected on one of the
NSLS II beam lines, AMX, FMX and NYX. The major hurdle encountered is
in regard to the keyword "source type". If user is looking for "nsls
ii" or "NSLS II" they are not able to find the source in the dropdown
menu; only "NSLS-II" or "nsls-ii" with a hyphen is accepted. Is there
a way that different spelling can be included? Most probably other
sources in the future will be affected as well?"
We would appreciate any comment.
Sincerely,
Vivian Stojanoff, PhD
Education, Training, Outreach
User Program
p 1(631) 344 8375
ensls.lifesciences@gmail.com mailto:nsls.lifesciences@gmail.com
w https://urldefense.com/v3/https://www.bnl.gov/ps/lifesciences/;!!Mih3wA!VdVSi2V2LmDCUscfjiVmWF9WAOyWE5yKwevy4QF-fzBv1W19Fl7ttOOKgU-5DNI$
<https://urldefense.com/v3/https://www.bnl.gov/ps/lifesciences/;!!Mih3wA!VdVSi2V2LmDCUscfjiVmWF9WAOyWE5yKwevy4QF-fzBv1W19Fl7ttOOKgU-5DNI$ >
Address:
Life Science Biomedical Technology Resource
National Synchrotron Light Source II
Building 745
Brookhaven National Laboratory
Upton NY 11973
From: pdb-l-bounces@sdsc.edu pdb-l-bounces@sdsc.edu on behalf of
Jasmine Young jasmin@rcsb.rutgers.edu
Sent: Wednesday, March 17, 2021 11:12 AM
To: pdb-l@sdsc.edu pdb-l@sdsc.edu
Subject: pdb-l: Modifications to support for SHEET and ligand SITE
records at the PDB in June 2021
In 2014, PDBx/mmCIF became the PDB’s archive format and the the legacy
PDB file format was frozen
<https://urldefense.com/v3/http://www.wwpdb.org/news/news?year=2014*5764490799cccf749a90cde3;Iw!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHuBU0Hj$
. In
addition to PDBx/mmCIF files for all entries, wwPDB produces PDB
format-formatted files for entries that can be represented in this
legacy file format (e.g., entries with over 99,999 atoms or with
multi-character chain IDs are only available in PDBx/mmCIF)
As the size and complexity of PDB structures increases, additional
limitations of the legacy PDB format are becoming apparent and need to
be addressed.
Defining complex sheet records
Restrictions in the SHEET record fields in legacy the PDB file format do
not allow for the generation of complex beta sheet topology. Complex
beta sheet topologies include instances where beta strands are part of
multiple beta sheets and other cases where the definition of the strands
within a beta sheet cannot be presented in a linear description. For
example, in PDB entry 5wln a large beta barrel structure is created from
multiple copies of a single protein; within the beta sheet forming the
barrel are instances of a single beta strand making contacts on one side
with multiple other strands, even from different chains.
This limitation, however, is not an issue in the PDBx/mmCIF formatted
file, where these complex beta sheet topology can be captured in
/_struct_sheet/, /_struct_sheet_order/, /_struct_sheet_range/, and
/_struct_sheet_hbond/.
Starting June 8th 2021, legacy PDB format files will no longer be
generated for PDB entries where the SHEET topology cannot be generated.
For these structures, wwPDB will continue to provide secondary structure
information with helix and sheet information in the PDBx/mmCIF formatted
file.
Deprecation of _struct_site (SITE) records
wwPDB regularly reviews the software used during OneDep biocuration. The
/_struct_site/ and /_struct_site_gen/ categories in PDBx/mmCIF (SITE
records in the legacy PDB file format) are generated by in-house
software and based purely upon distance calculations, and therefore may
not reflect biological functional sites.
Starting in June 2021, the in-house legacy software which produces
/_struct_site/ and /_struct_site_gen/ records will be retired and wwPDB
will no longer generate these categories for newly-deposited PDB
entries. Existing entries will be unaffected.
--
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
---==========================
TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see
https://urldefense.com/v3/https://lists.sdsc.edu/mailman/listinfo/pdb-l;!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHs_oQ8H$
https://urldefense.com/v3/__https://lists.sdsc.edu/mailman/listinfo/pdb-l__;!!P4SdNyxKAPE!TMJ_sKC92iHD8D9rcMFAIhsAlGbNQXioeBnfMh8cqEdvm_BshRlCsnmZgHs_oQ8H$
.