id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 6067 Update RCSB biounit fetch to new URLs if needed Tom Goddard Tom Goddard "The RCSB is updating their mmCIF assembly files and changing the ftp site for fetching them in May 2022. The assembly files will also contain multiple chains instead of multiple models. We need to verify that the ChimeraX (and Chimera) will still work with the URL changes. We need to make sure the NIAID scripts that use fetched biounit files still work. Begin forwarded message: From: Jasmine Young Subject: pdb-l: Distributing PDBx/mmCIF Formatted Assembly Files Date: February 2, 2022 at 6:59:30 AM PST To: pdb-l@lists.wwpdb.org Dear PDB users, Starting May 3, 2022, the PDB archive will distribute assembly files in PDBx/mmCIF format, allowing direct access and visualization of the curated assemblies for all PDB entries. Currently, PDBx/mmCIF formatted assembly files are provided for structures that are non-PDB compliant, however the coordinates use model numbers to differentiate alternate symmetry copies of PDB chain IDs. This method is not ideal, nor necessary, for the current archive PDBx/mmCIF format and has lead to limited use of these files in community software tools. In response to this issue and recommendations by the wwPDB advisory committee, we are implementing updated, standardized practices for generation of assembly files for all PDB entries. These updated PDBx/mmCIF format assembly files will have improved organization of assembly data to support usage by the community. These files will include all symmetry generated copies of each chain within a single model, with distinct chain IDs (_atom_site.auth_asym_id and _atom_site.label_asym_id) assigned to each. Generation of distinct chain IDs in assembly files are based upon the following rules: # Chain IDs of the original chains from the atomic coordinate file will be retained (e.g., A) # Assign unique chain ID (atom_site.label_asym_id and atom_site.auth_asym_id) for each symmetry copy within a single model. Rules of chain ID assignments: * The applied index of the symmetry operator (pdbx_struct_oper_list.id) will be appended to the original chain ID separated by a dash (e.g., A-2, A-3, etc.) * If there are more than one type of symmetry operators applied to generate symmetry copy, a dash sign will be used between two operators (e.g., A-12-60, A-60-88, etc.) In addition, entity ID and chain ID mapping categories will be provided: _pdbx_entity_remapping and _pdbx_chain_remapping. A new directory (ftp.wwpdb.org/pub/pdb/data/assemblies/mmCIF/) will be created for the distribution of these updated assembly files. The directory containing the existing assembly mmCIF files for large entries will be removed (ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/ ). wwPDB asks all PDB users and software developers to review code and address any limitations related to PDB assemblies. Sample files are made available for testing purposes and to support community adoption at GitHub.com/wwpdb/assembly-mmcif-examples (https://github.com/wwpdb/assembly-mmcif-examples). If you plan to use these assembly files for graphical viewing, check if your visualization software (e.g., PyMol, ChimeraX, etc.) supports instantiation of assemblies directly from atomic coordinate files (_struct_assembly related categories), you do so for improved efficiency. For any further information please email info@wwpdb.org. -- Regards, Jasmine =========================================================== Jasmine Young, Ph.D. Biocuration Team Lead RCSB Protein Data Bank Research Professor Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Rd Piscataway, NJ 08854-8087 Email:jasmine@rcsb.rutgers.edu Phone: (848)445-0103 ext 4920 Fax: (732)445-4320 =========================================================== The archive of messages, sent to pdb-l@lists.wwpdb.org, can be found at: https://lists.wwpdb.org/empathy/list/pdb-l.lists.wwpdb.org To subscribe via email, send a message with subject or body 'subscribe' to: pdb-l-request@lists.wwpdb.org and follow the instructions in the newly received email. To unsubscribe via email, send a message with subject or body 'unsubscribe' to: pdb-l-request@lists.wwpdb.org and follow the instructions in the newly received email." defect closed moderate 1.4 Core fixed Eric Pettersen all ChimeraX