March 2026 - phenixbb - phenix-online.org

How to do map sharpening?
by Francisco 22 Mar '26

22 Mar '26

Hi... I am trying to sharpen a map (x-ray) with the new phenix.auto_sharpen -> phenix.map_sharpening program. Got a script that basically runs phenix.xtriage to get the fraction of solvent content and some things and then I do ... ``` phenix.map_sharpening \ sharpening_method=b-factor \ mtz_in="$MTZ_IN" \ map_coeff_labels="2FOFCWT,PH2FOFCWT" \ map_model.model="$PDB_IN" \ crystal_info.resolution="$RESOL" \ b_factor_sharpening.b_factor_sharpening_crystal_info.solvent_content="$SOLVENT" \ b_factor_sharpening.b_factor_sharpening_crystal_info.is_crystal=True \ > sharpen.log 2>&1 ``` The problem is that I cannot open the mtz file in coot (mtz dump is attached) ... BUT ... I can open the sharpened map (ccp4 format) ... BUT ... the map is not covering the protein completely.. How do I do that? (1.png 2.png just showing the limits of the map) In gui mode I do get the map over the protein...BUT I cannot select the "FOFCWT,PHFOFCWT" labels (3.png ... That's the second part of the plan...) I am using phenix-dev 5989 Thanks a lot for your help

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How to start the Phenix Coot Implementation manually
by Biertuempfel, Christian (NIH/NHLBI) [E] 20 Mar '26

20 Mar '26

Dear all, Is there a clever way how to start the coot implementation from phenix manually? Basically, I am running phenix on one machine and I would like to open coot on another. I tried to copy/import my phenix database and project files on the “coot machine" but the paths are not properly imported. Which files are read when clicking “Open in Coot” in the GUI? Can I somehow run “Open in Coot” from the command line? Thanks, christian

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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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Industrial Biostructures America conference 2026
by Xu, Rui [JRDUS] 09 Mar '26

09 Mar '26

The Industrial Biostructures America conference will take place on May 11 & 12, 2026 at the Sanofi Cambridge Crossing site in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Sandra Gabelli - Global Head of Protein and Structural Chemistry at Merck * Dr. Derek Lowe - Director in Chemical Biology at Novartis and author of widely-read science and industry web site "In the Pipeline" Conference information is available at https://industrialbiostructuresamerica.org<https://industrialbiostructuresamerica.org/> along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Membrane Proteins, chaired by Dr. Elena Levin (UCB) * Conformational dynamics (allostery), chaired by Dr. Rui Xu (J&J) * Fragments and Proximity, chaired by Dr. Kerren Swinger (Takeda) * Tools of the Trade and Cryo-EM, chaired by Dr. Eva Cunha (Proteros) * Biologics, chaired by Dr. Joe Batchelor (Sanofi) * AI/ML in Drug Discovery and the Future of Structural Biology, chaired by Dr. Jill Chrencik (Merck) We also plan on a panel discussion on the topic of "Frontiers in Structural Biology for Drug Discovery and Development" The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for additional information

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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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