[3dem] Use Shortlinks to Transition to the PDB Beta Archive

[Justin Flatt]

The PDB Beta Archive [1] will replace the current archive July 21, 2027. 
The PDB Beta Archive organization supports the transition to extended 
PDB IDs. Users are strongly encouraged to start using this new directory 
structure and extended PDB IDs now.

"Shortlinks" [2] are URLs that can be used for downloading data from the 
beta archive today without the need to know or code specific file paths, 
e.g.,

https://urldefense.com/v3/__https://files-beta.wwpdb.org/download/pdb_00001abc.cif.gz__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-_E__POU$ 

When the PDB Beta Archive becomes the main PDB Archive, shortlink users 
will only need to update the domain name for these shortlinks:

https://urldefense.com/v3/__https://files.wwpdb.org/download/pdb_00001abc.cif.gz__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-1Y1dtcd$ 

wwPDB recommends that users with automated workflows adopt shortlinks 
today.

EXAMPLE SHORTLINKS

  	* https://urldefense.com/v3/__https://files-beta.wwpdb.org/download/pdb_00001abc.cif.gz__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-_E__POU$ 
  	* https://urldefense.com/v3/__https://files-beta.wwpdb.org/download/pdb_00001abc-sf.cif.gz__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-1QWBojc$ 
  	* https://urldefense.com/v3/__https://files-beta.wwpdb.org/download/pdb_00001abc_nmr-data.str.gz__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-xFbWvRR$ 
  	* https://urldefense.com/v3/__https://files-beta.wwpdb.org/ligands/download/ATP.cif__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-7xFo6mT$ 
  	* …

TRANSITION RESOURCES

  	* PDB ID Extension FAQ [3]
  	* PDB Beta Archive Overview: includes beta archive access, scripts, 
shortlink URLs, and other resources [4]
  	* PDBx/mmCIF software resources [5]
  	* Understanding PDBx/mmCIF format [6]
  	* PDBx/mmCIF User Guide [7]
  	* PDBx/mmCIF Dictionary [8]
  	* PDB -> PDBx/mmCIF correspondences [9]
  	* An online PDBx/mmCIF Editor [10]



Links:
------
[1] 
https://urldefense.com/v3/__https://www.wwpdb.org/news/news.php?year=2026*69ebcdca1103c56d3f444159__;Iw!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-_gcsnP1$ 
[2] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-beta-ftp-sites*dataStCon__;Iw!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-1IryNCv$ 
[3] https://urldefense.com/v3/__https://www.wwpdb.org/documentation/pdb-id-extension-faq__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-13ovBko$ 
[4] https://urldefense.com/v3/__https://www.wwpdb.org/ftp/pdb-beta-ftp-sites__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-4q7S9km$ 
[5] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/software-resources.html__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-4fzcO0D$ 
[6] 
https://urldefense.com/v3/__https://pdb101.rcsb.org/learn/guide-to-understanding-pdb-data/beginner**Bs-guide-to-pdbx-mmcif__;4oCZ!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-27Uk4FW$ 
[7] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/user-guide/guide.html__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-4i2SiGs$ 
[8] https://urldefense.com/v3/__https://mmcif.wwpdb.org/__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-5TpsbNS$ 
[9] https://urldefense.com/v3/__https://mmcif.wwpdb.org/docs/pdb_to_pdbx_correspondences.html__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-185xr9V$ 
[10] https://urldefense.com/v3/__https://pdbj.org/cif-editor/__;!!Mih3wA!FEYjH4zLEm5rql24FZBGMLgmTKgbFzNKvuJv9as0nTNV0cvb4sb5yxczc8QTMByAuxuXTb_RNBMNTHwl-4qjm_Fk$ 
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