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

News Index

• 11/21 PDB-101 Focus: Peak Performance

• 11/19 Paper Published: Using Augmented Reality

• 11/17 Nov 18-24: World Antimicrobial Awareness Week

• 11/14 Nov 17: WHO's Cervical Cancer Elimination Day of Action

• 11/13 November 14 is World Diabetes Day

• 11/11 Developers: Switch to Sequence Coordinates Service by May 31, 2025

• 11/10 Meet RCSB PDB at ABRCMS

• 11/05 Paper Published: IHMCIF

• 11/04 Take the Visualization User Survey and Win

• 10/31 wwPDB News: Deprecation of FTP File Download Protocol on November 1, 2024

• 10/29 wwPDB News: Poster Prize Awarded at The Protein Society

• 10/27 Meet RCSB PDB at SACNAS

• 10/25 Register for Upcoming Training Events

• 10/22 wwPDB News: Poster Prize Awarded at LACA

• 10/20 Interview with Director Emerita Helen Berman

• 10/18 Happy Birthday, PDB!

• 10/17 Happy Birthday, Irving Geis

• 10/16 wwPDB News: The Nobel Prize in Chemistry 2024

• 10/16 Register for the November 4 Mol* Virtual Office Hour

• 10/15 PDB-101 Focus: Peak Performance

• 10/15 wwPDB News: wwPDB Data Release Policy on Public Preprint Archives

• 10/10 Paper Published: MolViewSpec Toolkit

• 10/09 Register for the November 7 Virtual Office Hour on Supporting Extended PDB IDs

• 10/09 Explore Structural Biology with CSMs

• 10/08 wwPDB News: Annotation of Protein Modifications in the PDB

• 10/07 Fall Newsletter Published

• 10/02 wwPDB News: Access IHM structures at wwPDB DOI Landing Pages

• 09/30 Explore Inktober SciArt images

• 09/29 Register Now for Webinar: Unlock Rapid Analyses Across the Whole PDB Using BinaryCIF

• 09/25 Structural Biology and Nobel Prizes

• 09/25 Register for the October 8 Advanced Search Office Hour

• 09/24 Announcement and FAQ: EDMAPS.rcsb.org Shutdown October 16

• 09/23 Applications Open for Director

• 09/21 Watch the Webinar: Teaching Enzymology

• 09/20 Education Corner: Building Machines in the Classroom

• 09/17 Poster Prize Awarded at ACA 2024

• 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

• 09/12 Molecular Landscapes

• 09/08 PDB-101 Focus: Peak Performance

• 09/03 Poster Prize Awarded at ISMB 2024

• 08/28 wwPDB News: Biocurator Milestone: >10,000 Depositions Processed

• 08/27 Paper Published: Exploring protein 3D similarities via comprehensive structural alignments

• 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

• 08/20 PDB-101 Focus: Peak Performance

• 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)

• 08/13 August is National Immunization Awareness Month

• 08/05 Join our DevOps Team at Rutgers

• 07/30 August 2 is National Coloring Book Day

• 07/25 July 28 is World Hepatitis Day

• 07/23 PDB-101 Focus: Peak Performance

• 07/16 Paper Published: RCSB PDB supporting research and education worldwide

• 07/08 Summer Newsletter Published

• 07/03 Meet the RCSB PDB at ISMB

• 07/01 Meet the RCSB PDB at ACA

• 06/30 Postdocs: Join our Development Team in San Diego

• 06/30 Switch from MMTF to BCIF

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

• 06/27 Notice: NGL Viewer Deprecation

• 06/25 Paper Published: Cryo-EM Ligand Modeling Challenge

• 06/25 Register Now for Webinar on Teaching Enzymology

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

• 06/18 wwPDB News: Announcing the New PDBx/mmCIF User Guide

• 06/16 Paper Published on NextGen Archive

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

• 06/11 PDB-101 Focus: Peak Performance

• 06/06 wwPDB News: Biocurator Milestone: >10,000 Depositions Processed

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

• 06/04 Molecular Origami: Build 3D Paper Models of Protein Domains

• 05/31 Register for the June 4th Webinar

• 05/27 Notice: NGL Viewer Deprecation

• 05/26 Explore the Structural Biology of Evolution

• 05/20 Education Corner: Creating 3D Protein Models and Videos

• 05/16 PDB-101 Focus: Peak Performance

• 05/14 Switch from MMTF to BCIF

• 05/13 Register for the June 3 Mol* Virtual Office Hour

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

• 05/08 wwPDB News: Poster Prize Awarded at DiscoverBMB

• 05/07 wwPDB News: Celia Schiffer Elected to National Academy of Sciences

• 05/05 Video: How Neurons Communicate

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

• 04/30 Annual Report Published

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

• 04/23 April 24 to 30 is World Immunization Week

• 04/21 Celebrate DNA Day on April 25

• 04/18 April 22 is Earth Day

• 04/16 Spring Newsletter Published

• 04/14 Paper Published: Folding paper models of biostructures for outreach and education

• 04/09 Register Now for a Webinar on Understanding PDB Validation: Which experimental structures should I rely on?

• 04/08 wwPDB News: CASP16 Call for Targets

• 04/02 Video: Immunology and Cancer

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

• 04/01 Paper Published on NMR Restraint Validation

• 03/31 Explore Mechanism and Catalytic Site Annotations

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

• 03/26 Education Corner: Bringing Proteins to Life

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

• 03/21 March 24 is World TB Day

• 03/20 Meet RCSB PDB at the #DiscoverBMB Meeting

• 03/17 Paper Published: Visualizing groups of PDB structures and CSMs

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

• 03/11 March 11-17: Brain Awareness Week

• 03/06 wwPDB News: Poster Prize Awarded at The Biophysical Society Meeting

• 02/29 March 4 is International HPV Awareness Day

• 02/27 February 29 is Rare Disease Day

• 02/27 wwPDB News: Latest Developments on the EMDB Published

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

• 02/23 wwPDB Preprint Published on NMR Restraint Validation

• 02/20 wwPDB Preprint Published on CryoEM Archiving and Validation Recommendations

• 02/16 PDB-101 Focus: Peak Performance

• 02/14 wwPDB Preprint Published on NextGen Archive

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

• 02/11 Molecular Valentines

• 02/06 Meet RCSB PDB at The Biophysical Society Meeting

• 02/01 February 4 is World Cancer Day

• 01/30 Register for VIZBI 2024 (March 13–15)

• 01/30 Notice: NGL Viewer Deprecation

• 01/24 Take the CSM User Survey and Win

• 01/19 Register for the February 13 Mol* Webinar

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

• 01/16 Register for the February 5 RCSB.org Office Hour

• 01/15 Switch from MMTF to BCIF

• 01/10 Celebrate #NationalMilkDay

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

• 01/08 Winter Newsletter Published

• 01/07 Applications Open for Director

• 01/04 Top Molecules of the Month in 2023

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