Dear Vivian, Thank you for your feedback. OneDep deposition system uses mmCIF framework for archival data consistency. In this case, it follows the enumeration list defined in the mmCIF dictionary which is based on beamline information at BNL. We will look into front end implementation for possible future improvement. 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 5:02 PM, Stojanoff, Vivian wrote: > Dear Jasmine > > Thanks for getting back to us so fast and clarifying some of the > selection means. However, if we choose 'nsls ii' without the dash the > beam lines do not come up. Most users seem to use "nsls ii" instead of > "nsls-ii". Is it possible to allow for the two notations? > > Thank you > > Vivian > > ------------------------------------------------------------------------ > *From:* Jasmine Young <jasmin@rcsb.rutgers.edu> > *Sent:* Wednesday, March 17, 2021 4:30 PM > *To:* Stojanoff, Vivian <stojanof@bnl.gov>; pdb-l@sdsc.edu > <pdb-l@sdsc.edu> > *Subject:* Re: Question on NSLS II deposits > > 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!SirRoEWt3vCd4KBaLbniZwZAUQMoljoUxNxyFI4jWn9EbbbaBBhoI2Vp58U8Lg4$ > <https://urldefense.com/v3/__https://www.bnl.gov/ps/beamlines/beamline.php?r=17-ID-1__;!!Mih3wA!SirRoEWt3vCd4KBaLbniZwZAUQMoljoUxNxyFI4jWn9EbbbaBBhoI2Vp58U8Lg4$ >. > > > 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 <mailto: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!SirRoEWt3vCd4KBaLbniZwZAUQMoljoUxNxyFI4jWn9EbbbaBBhoI2VpWL9DgCU$ >> <https://urldefense.com/v3/__https://www.bnl.gov/ps/lifesciences/__;!!Mih3wA!SirRoEWt3vCd4KBaLbniZwZAUQMoljoUxNxyFI4jWn9EbbbaBBhoI2VpWL9DgCU$ > >> >> >> 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 <mailto:pdb-l-bounces@sdsc.edu> >> <pdb-l-bounces@sdsc.edu> <mailto:pdb-l-bounces@sdsc.edu> on behalf of >> Jasmine Young <jasmin@rcsb.rutgers.edu> <mailto:jasmin@rcsb.rutgers.edu> >> *Sent:* Wednesday, March 17, 2021 11:12 AM >> *To:* pdb-l@sdsc.edu <mailto:pdb-l@sdsc.edu> <pdb-l@sdsc.edu> >> <mailto: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$ >> > >> <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 <mailto: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$> >> .