[3dem] EM-specific metadata template to help with PDB OneDep depositions

Justin Flatt 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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