March 2026 - phenixbb - phenix-online.org

PDB Deposition Problems – Sequence Not Detected in mmCIF
by caleb.gaine＠gmail.com 13 Mar '26

13 Mar '26

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.

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phenix.ready_set with cif file for ligand,
by Guenter Fritz 12 Mar '26

12 Mar '26

Hi phenix team, hi Nigel, (it is macOS 15.7.3, phenix version 2.0-5936) I want to run phenix.ready_set on a protein with ligand. The run fails with some error in phenix elbow (I paste it below). When I run phenix.elbow on the ligand, like phenix.elbow vchfs_0210_phenix_001.pdb --residue UNL it works perfectly fine. I tried to provide phenix.ready_set with the cif file from the separate phenix.elbow file, but it fails again with the same error. Maybe I overlook something? Best regards, Guenter ------------------- error message below -------------------------- (base) guenter@Guenters-MacBook-Pro phenixqr % phenix.ready_set vchfs_0210_phenix_001.pdb INPUT Reading model from vchfs_0210_phenix_001.pdb Writing effective parameters to vchfs_0210_phenix_001.eff - to ligands using eLBOW, phenix.elbow Traceback (most recent call last): File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/ready_set.py", line 1118, in <module> run(args) File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/ready_set.py", line 861, in run rc = run_though_all_the_options( File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/ready_set.py", line 221, in run_though_all_the_options rc = add_hydrogens.run( File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/add_hydrogens.py", line 909, in run rc = add_hydrogens( File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/add_hydrogens.py", line 710, in add_hydrogens hierarchy = remove_incorrect_hydrogens(hierarchy, File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/add_hydrogens.py", line 435, in remove_incorrect_hydrogens tmp = get_atom_names(atom_group.resname) File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/mmtbx/chemical_components/__init__.py", line 201, in get_atom_names for item in cif["_chem_comp_atom"]: KeyError: '_chem_comp_atom'

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ADP refinement in a CryoEM map of heterogeneous quality
by carlos.kikuti＠curie.fr 09 Mar '26

09 Mar '26

Hello there, It's been a while we haven't chatted with anybody from the Phenix crew, I hope you are all doing fine! I'm writing because of an issue with this CryoEM structure at 2.5 angstroms I'm about to deposit. It is a myosin motor domain + part of the lever arm including one light chain. I've used RealSpaceRefine from Phenix 2.0 with very good results: very nice geometry and agreement with the map. The thing is, the lever arm and the light chain move a lot, so the contour in that part is much lower, ~50% the one of the motor domain, of course the map is also more poorly defined. And RealSpaceRefine attributes very low ADPs for the light chain (chain B), but the ones for the lever arm helix (chain A, same as the motor domain) are high, coherent with the difference in map quality. I'm considering "cheating" by putting them two as chain A to try to get this fixed (I'll need to undo this before deposition), but is there a more elegant way to sort this out? The PDB does not complain about the current model, but I'm thinking of readers looking at these ADPs and finding the ensemble really weird (basically a hot arm surrounded by a cold calmodulin-like domain, which is physically impossible). (To me it looks like a different normalization is being applied to the two chains because of the map quality difference, if this makes any sense.) I'm looking forward to your opinions, Carlos

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RCSB PDB is recruiting a Biocurator!
by Yuhe Liang 03 Mar '26

03 Mar '26

*RCSB PDB is recruiting a Biocurator! * The job description and the online application URL can be found at https://www.rcsb.org/pages/jobs#bioStructAnnotRutgers Biological Structure Annotation Specialist (Rutgers) Become a Biocurator and analyze, curate, and validate macromolecular structures from the PDB community. Participate in exciting projects with significant impact on the scientific community. RCSB PDB, the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and makes 3D macromolecular structure data available at no charge and without usage restrictions to many millions of RCSB.org <https://www.rcsb.org/> users worldwide. Deposition/Biocuration Services provide expert deposition, validation, biocuration, and remediation services to Data Depositors worldwide, ensure PDB data are Findable, Accessible, Interoperable, and Reusable (FAIR) by providing expert data curation which is critical for biological data resources, and develop and promote community-endorsed data standards for archiving and exchange of global structural biology data. Roles: - Analyze, curate, and validate macromolecular structures from the PDB community - Participate in exciting projects with significant impact on the scientific community - Communicate daily with members of the research community - Participate in fun scientific outreach and training activities Knowledge and skills: - Experience in structural biology with a PhD in a relevant field is required - Strong knowledge of cryo-electron microscopy (3DEM) is required to curate and validate macromolecular structures - Experience with small molecule chemistry is a plus - Experience with bioinformatics, cheminformatics, and computer scripting would be an advantage - The successful candidate should be self-motivated, pay close attention to details, possess strong interpersonal communication and writing skills, and have the ability to handle multiple projects *Why Join Us* <https://www.rcsb.org/pages/jobs#whyJoinUs> Apply online at Rutgers <https://go.rutgers.edu/eaurbzrz>. -- YUHE LIANG, Ph.D. Biocuration Lead Deputy, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08554 P: 848.445.4938 | E: yuhe.liang(a)rcsb.org

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