- phenixbb - phenix-online.org

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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Concentric, alternating difference density blob
by Dan Richman 09 Feb '26

09 Feb '26

Hi Phenix folks, Have any crystallographers seen the phenomenon I've captured in these screenshots (linked below to save space), of concentric, semi-spherical, alternating layers of difference density? It seems to be localized at a valine side chain at the edge of the model and reflected across some two-fold symmetry. There's no heavy metal in the crystallization. Overall, the quality of the map and the model refinements are very good; everything has behaved as expected. We're just trying to diagnose this phenomenon and our searches for related descriptions have not yielded anything. https://livejohnshopkins-my.sharepoint.com/:f:/g/personal/drichma6_jh_edu/IgBkH0K7T1_0SL32jIPvr41DAYbp0ZSjTv_VH3TMb8bwd3s?e=CQgBnl Thanks! -- Dan Richman, PhD (he/him/his) Research Associate, James Berger Lab Dept of Biophysics and Biophysical Chemistry Johns Hopkins University School of Medicine mobile: 201-669-0967

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[Wmsm] LAST CALL for registration at the 7th ISMSM, Lisbon, 17-20 March 2026
by Jose Artur Brito 03 Feb '26

03 Feb '26

Dear colleagues, This is the final call for registration for the 7th International Symposium on Microbial Sulfur Metabolism (ISMSM), which will take place in Lisbon, Portugal, from 17–20 March, 2026. This meeting will bring together researchers from across the globe to explore the latest advances in microbial sulfur cycling - from molecular mechanisms to ecological and environmental perspectives. The meeting will include keynote talks, selected oral presentations, poster sessions, and opportunities for informal discussion and networking. We encourage you to register and submit your abstract until 13rd February 2026. https://wmsm.itqb.unl.pt/registration/ For more information visit: https://wmsm.itqb.unl.pt/ We look forward to welcoming you in Lisbon next March! The 7th ISMSM Organizing Committee Inês Cardoso Pereira, Filipa Sousa, José Artur Brito, Andreia Pimenta and Américo Duarte ismsm(a)itqb.unl.pt --

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Submit your IUCr 2026 abstract to microsymposium MS012
by dominika＠work.swmed.edu 02 Feb '26

02 Feb '26

Dear colleagues, We invite you to submit an abstract to Microsymposium MS012, "Next-generation validation metrics for macromolecular structures" at the 27th IUCr Congress (Calgary, Canada; August 11–18, 2026). Session time: Wednesday, August 12, 2026, 2:30–5:00 pm Invited speakers: Mariusz Jaskolski, Daisuke Kihara, Brinda Vallat This microsymposium will focus on emerging concepts, methods, and best practices for validating macromolecular structures across crystallography, cryo-EM, NMR, and integrative/hybrid modeling. We particularly welcome contributed talks that address challenges posed by increasing model complexity, heterogeneous data, and AI/ML-driven structure prediction. Topics of interest include (but are not limited to): ML- and AI-assisted validation and assessment Atomic-level precision, accuracy, and uncertainty metrics Cross-validation against experimental and orthogonal data Validation of ensembles, flexible models, and integrative structures Validation and QA pipelines used in community resources (e.g., PDB, CCDC) We look forward to receiving your abstracts! As part of our commitment to equity, diversity, and inclusion, we particularly encourage abstract submissions from women, early-career researchers, and members of groups historically underrepresented, in order to work together toward building a strong, inclusive, and well-balanced Congress. Please share widely with potentially interested colleagues. Abstract submission: https://event.fourwaves.com/iucr-2026/submission Deadline: February 15, 2026 (please check the submission site for updates) We would be delighted to receive your contributions and to see you in Calgary. With best wishes, Deborah Harrus & Dominika Borek

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You appear to have another session of Phenix running already
by Niklaus guan 30 Jan '26

30 Jan '26

Hi all, I have been experiencing this issue when I start phenix *"You appear to have another session of Phenix running already (hostname=.....), which has locked your project database to prevent corruption. If this is the result of crashing or killing the GUI, you can continue, but only one session should be run at a time. Do you want to override the lock?"* It gives me two options, either No or Yes, neither one starts the Phenix. I wonder if anyone else knows how to fix it. Thank you! Best Kaoling Guan

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coot-1 linked to phenix
by Rapisarda, Chiara /FR 28 Jan '26

28 Jan '26

Hello, I have a Mac that I upgraded to Tahoe, and now coot 0.9 isn’t working any more. I would like to link phenix to coot-1. I can do that by adding: /Applications/ccp4-9/coot_py3/bin/coot To the coot path in preferences, but after a refinement when I open coot , it is open but it is not connected to the phenix refine job and no PDB nor map is open. I am aware that I can manually open the map and pdf, I would like to know if coot-1 can be opened in a way that will allow me to navigate the structure using phenix. When I ask gemini it tells me that I should point it to: /Applications/ccp4-9/bin/coot-py3 But it doesn’t exist in my ccp4 installation. Has anyone successfully managed to link coot-1 to phenix using a good bridge? Any help will be greatly appreciated. Best, Chiara

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RapiData at SSRL 2024
by Smith, Clyde 22 Jan '26

22 Jan '26

Hi everyone, Applications are now open for the 2024 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from April 29 to May 4, 2024. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering) Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2024/ and use the links on the "Application and Registration" page to apply for the course. The application deadline is January 31, 2024. Successful applicants will be notified early in February 2024 and invited to register and book accommodation at SLAC Stanford Guesthouse at that time. A limited amount of support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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