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Test message sorry for the noise
by Nigel Moriarty 20 Mar '26

20 Mar '26

Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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unrealistic low clashscore in phenix.refine
by Kevin M Jude 18 Mar '26

18 Mar '26

I’m using phenix 2.0-5936 on my M1 Mac. I notice in phenix.refine that the run status reports a realistic clashscore (7.5) for my structure, but in the Molprobity tab of phenix.refine the reported clashscore is 0.77, with only 4 clashes identified with a maximum overlap of 0.472 Å. Running Comprehensive Validation (X-rayNeutron) gives a full list of 76 overlapping pairs, maximum overlap 0.705 Å, and a clashscore of 7.65. -- Kevin Jude, PhD Structural Biology Research Specialist, Garcia Lab Howard Hughes Medical Institute Stanford University School of Medicine Beckman B177, 279 Campus Drive, Stanford CA 94305

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CBMS - Lecture Series - Serganov
by Stojanoff, Vivian 18 Mar '26

18 Mar '26

Dear Colleagues, you are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Alexander A. Serganov Associate Professor, Department of Biochemistry and Molecular Pharmacology NYU Grossman School of Medicine NYU Langone Health WEDNESDAY, March 25, 13:30 (EST) "Redefining dogmas in bacterial physiology: the case of mRNA” Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/QkF6wZmvRJCTtT9RG0djuw Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: The degradation of mRNA plays a crucial role in determining the number of mRNA molecules and, consequently, influences the yield of protein biosynthesis across all organisms. While the regulation of mRNA lifetime is well-recognized as vital for gene expression in eukaryotes, it has long been assumed that bacteria lack sophisticated mechanisms for regulating mRNA stability and degradation. Our findings challenge this assumption, revealing that bacterial mRNAs possess unexpected properties and employ molecular mechanisms that rival in complexity those in eukaryotic systems. ================= Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973

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Matplotlib error for 2.0-5936
by matthew.belousoff＠monash.edu 15 Mar '26

15 Mar '26

Hey guys, Few details first: OS: Linux Mint 22.1 Kernel: 6.8.0-71 Phenix Build: Phenix-2.0-5936-CUDA12-Linux-x86_64 Generally everything works fine, but when I run a RealSpace refinement job, afterwards going through the diagnostic details is quite slow and the console keeps printing out: findfont: Font family 'Courier' not found. findfont: Font family 'Monaco' not found. findfont: Font family 'Helvetica' not found. This seems like a matplotlib error to me. I will note that I didn't get these errors with any older versions of phenix on the same system. cheers, matt B

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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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Metal distance parameters used by phenix.metal_coordination
by p.auffinger＠unistra.fr 23 Feb '26

23 Feb '26

Hi, We used phenix.metal_coordination to generate metal restraints and it works well. My question is in which file can I find the distances (ideal) used by this program. refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name O and chain Y and resname HOH and resseq A1A8 distance_ideal = 2.140000 sigma = 0.190 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name N7 and chain a and resname G and resseq 1190 distance_ideal = 1.895092 sigma = 0.050 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name O and chain Y and resname HOH and resseq 2831 distance_ideal = 2.140000 sigma = 0.190 In this example, the Mg...O ideal distance is 2.14 and we would prefer to use 2.07 Same for Mg...N distances of 1.895092 that should be changed to 2.19 Thanks for letting us know if there is a parameter file for this or even better, an option to use distance values extracted from the input cif file. Pascal

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modeling mixed metal sites in ligand
by Arthur Glasfeld 10 Feb '26

10 Feb '26

I’m using Phenix to refine an EM-derived model that is a protein complex with a polyoxometallate (POM). The POM has the formula CoTiW11O40(8-), where the Ti and W (as bridged 6-coordinate oxometallates) form an cage around the Co(II) ion with overall Td symmetry. You can google “Keggin” and “POM" to get an idea of the shape. The published structure of the isolated POM modeled 11/12 occupancy of W at each oxometallate center, and 1/12 Ti. At 2.2 Å, our map shows no obvious placement for the Ti relative to the W centers. So far, for simplicity’s sake, we have used a ligand cif file that has 12 W centers in refinement (this was derived from the published crystal structure using Elbow). But to finalize the model, it seems important to acknowledge the presence of the Ti center. A few thoughts have come to us on how to proceed. We could simply annotate our model to indicate the presence of an unmodeled Ti center and continue with the current 12 W model or we could arbitrarily place a Ti ion in each POM (there are 4 in the complex). More realistically (?) we could place two POMs at each site - one containing nothing but W centers at 11/12 occupancy and one with nothing but Ti centers at 1/12 occupancy. But that generates two unrealistic ligands instead of one. The best thing to do would be to have a ligand cif file that has the atom occupancy built into it, but so far as I can tell, Phenix won’t accept that. I’ve also contacted the RCSB for advice, but would welcome any thoughts you all might have, especially if there’s a way to create an accurate ligand description. Thanks in advance, Arthur Glasfeld Mansoor Lab Oregon Health and Science University

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