[3dem] EM-specific metadata template to help with PDB OneDep depositions
justin at rcsb.rutgers.edu
Wed Apr 6 14:45:51 PDT 2022
A new time-saving EM-specific template for metadata input is now
available at the PDB_EXTRACT website (https://urldefense.proofpoint.com/v2/url?u=https-3A__pdb-2Dextract.wwpdb.org-29-21&d=DwICAg&c=-35OiAkTchMrZOngvJPOeA&r=L7-zyQ-04fFCMRqzLIOnx7H0exGZHwIQe_wMPuY600I&m=WMLIKB6w7_Jp7IGyqlNW8hyd5sxXattIwnlCJCGRg3jIKyM8nW-51XBYs1UiuUfl&s=UK7u0a2kMUDpBfNkz4Z7FhHR0KNclOH4utKHhTSbfBc&e=
This template eases the burden of depositing multiple related structures
to the wwPDB OneDep System. The template captures authorship and
citation information, as well as associated EM metadata into a
downloadable and re-usable mmCIF file which can then be used by
PDB_EXTRACT to produce more complete and ready-to-deposit model files
for multiple structural models. In this way, users can avoid entering
the information over and over for each structure during deposition.
Access mmCIF-based EM-specific template at the PDB_EXTRACT website
(https://pdb-extract.wwpdb.org) by clicking the green highlighted 'EM'
at the top of the page where it states "Prepare a re-usable template
file of your metadata via PDBj's mmCIF Editor for Xray, NMR, EM". Or
visit the following URL:
The template is loaded and editable through PDBj's mmCIF editor. When
entering data into the form the editor will perform mmCIF data
validation to ensure that the provided information meets the wwPDB
OneDep deposition requirements. To save the completed form, click the
Editor's upper-left gear icon. This same icon enables users to download
and access help.
Upon completing and downloading the template, users must RUN PDB_EXTRACT
at the front page of the website (https://pdb-extract.wwpdb.org/). For
this final step, each structural model file will need to be uploaded in
either PDB or CIF format, EM is chosen as the method, refinement
software is specified and 'Run' is clicked. A second page will appear
that allows users to provide the filled-in template. The output mmCIF
will include model coordinates, as well as the metadata from the
template, which when uploaded to the OneDep system will be delivered to
the appropriate sections at the deposition user interface.
If you have questions or feedback regarding the procedure, please send
to deposit at deposit.rcsb.org.
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