[3dem] New PDB Beta Archive Available for Testing

[Justin Flatt]

Dear 3DEM community,

By 2028 4-character PDB IDs (e.g. 1abc) will be fully allocated. After 
that, all new entries will be assigned only extended PDB IDs.

The new extended PDB ID format [1] will be 12 characters, which includes 
a prefix pdb_ followed by 8 alphanumeric characters, e.g. pdb_1000axyz. 
This new ID format [1] will enable text mining detection of PDB entries 
in the published literature and allow for more informative and 
transparent delivery of revised data files. _When submitting extended 
PDB IDs to journals and citing extended PDB IDs in manuscripts, all 12 
characters including prefix pdb_ should be provided._

A PDB Beta Archive [2] is now available to help community adopt extended 
PDB ID and PDBx/mmCIF format during the transition phase. All files at 
this archive are re-organized with extended PDB ID (including file 
naming and directories) at entry level, mirroring the same data 
organization of the PDB Versioned Archive [3].

All data files for a particular entry are stored in a single directory, 
labeled based on a two-character hash generated from the penultimate two 
characters of the PDB code, i.e., 
https://urldefense.com/v3/__https://files-beta.wwpdb.org/pub/wwpdb/pdb/data/entries/__;!!Mih3wA!EvrDIpXI-3GmgIak1IYRDJzHQd0R4oD7DVcBLPA5qiuFcYd5wIfGcXKhIVF4fp3_y-5Y-PEsc3jUuB4Yli2ISXOA$ <two-letter-hash>/<pdb_accession_code>/<entry_data_File_names>. 
The two-letter hash will be based on the second and third characters 
from the last character. For example, PDB entry pdb_1abc5678 will be 
under /67/. This will maintain consistency with the current PDB archive: 
PDB entry 1abc is under /ab.

File naming is standardized such that the file type is used for the 
extension.
For example, file naming is changed from r116dsf.ent.gz to 
pdb_0000116d-sf.cif.gz for the structure factor file and from 
pdb318d.ent.gz to pdb_0000318d.pdb.gz for the legacy PDB formatted 
coordinate file.

When four character PDB IDs are about to be consumed, this PDB Beta 
Archive will replace the current PDB Archive (expect to be around 
mid-2027) and entries with extended PDB IDs issued are not compatible 
with PDB format. wwPDB encourages scientific journals, PDB community and 
users to transition to PDBx/mmCIF format and adopt new PDB ID format as 
earlier as possible.

For any further information please contact us at info at wwpdb.org.

Best wishes,
Justin Flatt on behalf of the wwPDB



Links:
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[1] https://urldefense.com/v3/__https://www.wwpdb.org/documentation/pdb-id-extension-faq__;!!Mih3wA!EvrDIpXI-3GmgIak1IYRDJzHQd0R4oD7DVcBLPA5qiuFcYd5wIfGcXKhIVF4fp3_y-5Y-PEsc3jUuB4YljhFGJ3Q$ 
[2] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-beta-ftp-sites__;!!Mih3wA!EvrDIpXI-3GmgIak1IYRDJzHQd0R4oD7DVcBLPA5qiuFcYd5wIfGcXKhIVF4fp3_y-5Y-PEsc3jUuB4YliaCcwEa$ 
[3] https://urldefense.com/v3/__http://files-versioned.wwpdb.org/__;!!Mih3wA!EvrDIpXI-3GmgIak1IYRDJzHQd0R4oD7DVcBLPA5qiuFcYd5wIfGcXKhIVF4fp3_y-5Y-PEsc3jUuB4YlthalO4I$ 
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