- phenixbb - phenix-online.org

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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Re: coot-1 linked to phenix
by Roberto Steiner 28 Jan '26

28 Jan '26

Hi Chiara I have installed coot-1 using homebrew and using /opt/homebrew/Cellar/coot/1.1.20/bin/coot works for me. Ciao Roberto Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours. On 28/01/2026, 13:27, "Rapisarda, Chiara /FR via phenixbb" <phenixbb(a)phenix-online.org <mailto:[email protected]>> wrote: 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 _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org <mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org <mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s

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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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real space refinement of 3Fe4S cluster
by Amy Fernandez 19 Jan '26

19 Jan '26

Hello Phenix BB, I'm attempting to refine a model with a 3Fe4S cluster into a medium resolution cryoEM map. Every time I run a refinement job, the cluster comes out all wonky, as in the attached image. I found one previous thread on this topic and when I played with the "superpose_ideal_ligand" setting, I got an error stating that the F3S residue is missing atoms. Should I just generate a restraint file? Any advice on how others have handled this welcome. Best, Amy __________________________________________________ Amy Fernandez Berger Lab<https://berger.med.jhmi.edu/> - The Johns Hopkins University School of Medicine PhD Candidate - Program for Molecular Biophysics<https://pmb.jhu.edu/>

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Obtaining standard cif restrain file for ligand in PDB
by Lei Chen 17 Jan '26

17 Jan '26

Dear all, I am building a model of a digitonin molecule into the density map. Several released PDB entries contain digitonin (ligand code: AJP). However, I could not find the corresponding mmCIF restraint file (AJP.cif) for refinement. I generated one using phenix.elbow, but it failed PDB validation, likely because the generated parameters differ from the standard reference. Could you please advise on where I can obtain the standard restraint file for AJP? I have checked the RCSB PDB website, but it appears to provide coordinate files rather than refinement restraints. Thank you for your help. Best regards, Lei

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