Will NIH 3D pipeline script work with new EMDB metadata format?

[phil.cruz@…]

Will the change to EMDB data model v3 effect how the NIH 3D ChimeraX pipeline script fetches the suggested contour level for maps?

​https://www.wwpdb.org/news/news?year=2021#610ad31fef055f03d1f222bb

[Tom Goddard]

Comparing the old metadata file

​https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/header/emd-1080-v19.xml

to the new file

​https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-1080/header/emd-1080-v30.xml

shows that the suggested contour level is put in a new location. So the code to obtain that contour level will have to be adjusted if it is not already using the v30 format.

[pett]

As far as I can tell, the script's fetching of the contour level is unaffected in any way by this announcement. The script fetches JSON information about the contour level from:

​https://www.ebi.ac.uk/pdbe/api/emdb/entry/map/EMD-<emdb ID>

It doesn't use any of the FTP tomfoolery mentioned in the announcement.

See: ​https://www.ebi.ac.uk/pdbe/api/doc/emdb.html

[goddard@…]

Good!  So the NIH 3D ChimeraX script is using an EMDB web service that returns JSON.  The underlying meta-data change is in XML metadata files and the JSON format appears to not mimic the XML.  So the script should be fine.