2022-08-17 : 21807 EMDB map entries, 12166 PDB coordinate entries RCSB PDB | PDBe

EM-specific metadata template to help with OneDep depositions

A new time-saving EM-specific template for metadata input is now available at the PDB_EXTRACT website.

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 the mmCIF-based EM-specific template by clicking the green highlighted 'EM' at the top of the PDB_EXTRACT website home 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:

https://pdbj.org/cif-editor/#filterErroneousData=false,url=https://pdb-extract.wwpdb.org/help/data_template_em.cif

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 separately in either PDB or CIF format, with EM as the chosen method and refinement software specified. After 'Run' is clicked,a second page will appear that allows users to upload the filled-in template. The mmCIF output from PDB_EXTRACT will include model coordinates, as well as the metadata from the template, which when uploaded to the wwPDB 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@deposit.rcsb.org.

Source: April 6 [3DEM] post by Justin Flatt

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National Institute of General Medical Sciences

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