Deprecation of ligand model coordinates in MOL2/SDF format starting Dec 10

09/17

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.

Programmatic access should be updated to access model coordinates in CIF format

New Features Index

• 09/17 wwPDB News: Deprecation of FTP File Download Protocol on November 1, 2024

• 09/17 Deprecation of ligand model coordinates in MOL2/SDF format starting Dec 10

• 09/15 Celebrating National Postdoc Appreciation Week

• 08/26 Register for the Sept 18 Virtual Office Hour on Molecular Animations

• 08/21 Register for the Sept 12 Virtual Office Hour: Streamlining PDB Deposition

• 08/14 Register for the Sept 9 Mol* Virtual Office Hour

• 08/14 wwPDB News: PDB Archive Serves Structures Determined by Integrative and Hybrid Methods (IHM)

• 08/05 Join our DevOps Team at Rutgers

• 07/03 Meet the RCSB PDB at ISMB

• 06/28 Register for the July 9 Virtual Office Hour on APIs

• 06/25 Register Now for Webinar on Teaching Enzymology

• 06/18 Register Now for Crash Course: Python Scripting for Molecular Docking

• 06/11 Register for the July 9 Virtual Office Hour on APIs

• 06/04 Register for June 13 Virtual Office Hour: Generating DSN6 and MTZ Files

• 05/27 Notice: NGL Viewer Deprecation

• 05/14 Switch from MMTF to BCIF

• 05/09 Announcement: EDMAPS.rcsb.org Shutdown

• 05/01 Register Now for a Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

• 04/30 wwPDB News: Coming soon: Annotation of Protein Modifications in the PDB

• 04/01 Register Now for a Virtual Deep Dive into Computed Structure Model Exploration at RCSB.org

• 03/31 Explore Mechanism and Catalytic Site Annotations

• 03/29 Take the EDMAPS.rcsb.org Survey

• 03/24 Register for the April 1 Mol* Virtual Office Hour

• 03/12 wwPDB News: Paper Published on CryoEM Archiving and Validation Recommendations

• 02/25 Register for the March 28 Office Hour to Ask A Biocurator

• 02/12 Use a Python Package to Access the RCSB PDB Search API

• 01/30 Notice: NGL Viewer Deprecation

• 01/24 Take the CSM User Survey and Win

• 01/18 Undergrads: Spend your summer with RCSB PDB

• 01/15 Switch from MMTF to BCIF

• 01/08 wwPDB News: Resources for Supporting the Extended PDB ID Format (pdb_00001abc)

• 01/07 Applications Open for Director

• 01/03 wwPDB News: Time-stamped Copies of PDB and EMDB Archives