PDB Deposition Problems – Sequence Not Detected in mmCIF
I am currently trying to validate my structure using the wwPDB Validation Server before deposition. I am submitting the following files: - Full map - Both half maps - Map-to-structure factors - Coordinate file (.mmCIF) However, when I attempt to submit the entry I receive the following errors: - Coordinate Issues: Not Known - Sequence: The sample sequence has not been provided I have already added the sequence data to the mmCIF file using the Phenix tool: mmtbx.prepare_pdb_deposition After running the tool, I verified that the mmCIF file contains the expected sequence-related records. For example: _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET no 1 2 ALA no 1 3 LYS no 1 4 LEU no 1 5 THR no 1 6 LYS no ... (continued) and: loop_ _entity_poly.entity_id _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier _entity_poly.type 1 no no ;MAKLTK ... (continued) For reference the .fasta file looks like this.
Chain A MAKLTK ... (continued)
Despite these sequence records being present in the mmCIF file, the validation server still reports that the sequence has not been provided and flags coordinate-related issues. Has anyone encountered a similar problem or knows what might be causing the validation server to not recognize the sequence information? Any suggestions would be greatly appreciated.
Update for anyone who might be having similar issues: I think there was something wrong with the session. Creating a new session seemed to fix it, and it worked using only a coordinate (.mmCIF) file and a map.
participants (2)
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Caleb Gaine -
caleb.gaine@gmail.com