Deprecation of ligand model coordinates in MOL2/SDF format

[Jose Duarte]

Starting December 10, 2024, RCSB PDB will no longer serve ligand model coordinates in MOL2 or SDF format. These files are currently served under https://files.rcsb.org/ligands/download/< ccd_id >_model.mol2 and https://files.rcsb.org/ligands/download/< ccd_id >_model.sdf.

Model and ideal coordinates for chemical components in CIF format will continue to be available from https://files.rcsb.org/ligands/download/< ccd_id >.cif.

Programmatic access should be updated as needed.

Ligand data files for ideal coordinates will continue to be served in MOL2 and SDF formats under

https://files.rcsb.org/ligands/download/< ccd_id >_ideal.mol2
https://files.rcsb.org/ligands/download/< ccd_id >_ideal.sdf

Information about all files available for download from RCSB PDB is available at: https://www.rcsb.org/docs/programmatic-access/file-download-services 

Best regards

Jose

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Jose Duarte

RCSB Protein Data Bank

San Diego Supercomputer Center

UC San Diego

La Jolla CA, USA