- 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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replacement for mmtbx.water_screen
by Kay Diederichs 15 Jan '26

15 Jan '26

Dear developers, CCP4wiki (https://wiki.uni-konstanz.de/ccp4/index.php/Properties_of_proteins) mentions mmtbx.water_screen as a program that can tell ions from water, given a PDB file. Tried that with a recent Phenix installation but the program no longer exists. Is there any similar functionality available? Thanks, Kay

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Phenix version 2.0 released
by Paul Adams 12 Jan '26

12 Jan '26

Dear Colleagues, The Phenix developers are pleased to announce that the long awaited version 2.0 of Phenix is now available (build 2.0-5936). Binary installers for Linux, Mac OSX, and Windows, and the source installer, are available at the download site: http://phenix-online.org/download This is the first official release of Phenix that is based on Python 3. Moving forward, Python 2 will no longer be supported. Other highlights for this new version of Phenix include: - Phenix help chatbot available at https://phenix-online.org/chatbot - AI analysis of result files available in GUI (non-commercial only, requires free Google and Cohere API keys) - phenix.aquaref: Full-model AI-accelerated quantum refinement for crystallography & cryo-EM - phenix.refine: - occupancy refinement for water is now the default - use longer X-H distances if scattering table is 'electron' (for electron diffraction, cryoEM) - rotamer fitting for aa side chains with alternative conformations (use fit_altlocs_method, not the default) - alternative conformation aware water picking (use include_altlocs, not the default) - phenix.real_space_refine: option to refine two group ADP per residue (main and side chain) - phenix.fit_h: optimize position of H atoms with rotational degrees of freedom against density map - phenix.magref: new tool for pixel size (magnification) refinement for cryoEM - phenix.renumber_fab: (NEW!) renumber FAB chains using Kabat, Chothia or Martin conventions - phenix.find_reference: (NEW!) automatically find and prepare reference model - phenix.holton_geometry_validation: Composite geometry validation score - phenix.create_alt_conf: Create model with alternative conformations using high-resolution data - phenix.process_predicted_model: Allow alternative defaults to work better using pae matrix - phenix.combine_focused_maps: allow applying both normalization and scale factors - phenix.ligandfit: Trim model outside of map area for cryo-EM maps - phenix.fetch_pdb: added ability to download Cryo-EM data - phenix.map_correlations (calculates map-map and map-model correlations, with optional translational offsets) replaces phenix.get_cc_mtz_mtz, phenix.get_cc_mtz_pdb, phenix.map_model_cc, phenix.model_map_cc, and phenix.get_cc_map_map This publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix has been funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is currently funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Adjunct Professor, Department of Bioengineering, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 91, Room 410 Building 978, Room 4126 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 91R0183 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ][ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Industrial Biostructures America (IBA) Conference 2026
by Xu, Rui [JRDUS] 08 Jan '26

08 Jan '26

We are pleased to share that the Industrial Biostructures America<https://www.industrialbiostructuresamerica.org/> (IBA) Conference will return to the Boston/Cambridge area on May 11-12, 2026, hosted at Sanofi's Cambridge Crossing R&D campus. IBA is a forum for the structural biology community across North America, bringing together leading voices to share insights on the application of structural biology technologies to drug discovery challenges across the industry. This event also fosters valuable networking opportunities and collaborative discussions that drive our field forward. Registration is now open, with early-bird rates before March 1, 2026. Note that the last meeting sold out, so please ensure you reserve your spot. Conference information is available at Industrial Biostructures America<https://www.industrialbiostructuresamerica.org/> along with registration and abstract submission forms. Scientific sessions will cover the following topics: * Proximity & fragments * Membrane protein structure * Conformational dynamics & allostery * Cryo-EM & practical applications of state-of-the-art techniques * Biologics and protein engineering * AI/ML in drug discovery and the future of structural biology For exhibitor/sponsorship opportunities or any other questions, please contact us at iba(a)proteros.com. Looking forward to seeing you in May! Rui Xu Sr. Principal Scientist Johnson and Johnson

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transform C2 to P1 and the R-free set
by Jorge Iulek 27 Dec '25

27 Dec '25

Dear all, I got a set of images (very recently) . Dials gives me: +------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+-----------+ | Solution | Metric fit | rmsd | min/max cc | #spots | lattice | unit_cell | volume | cb_op | |------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+-----------| | * 2 | 0.3001 | 0.066 | 0.272/0.272 | 10685 | mC | 212.43 81.92 133.04 90.00 113.12 90.00 | 2129290 | a-2*b,a,c | | * 1 | 0 | 0.052 | -/- | 10559 | aP | 81.95 113.64 133.10 68.50 89.98 69.13 | 1065523 | a,b,c | +------------+--------------+--------+--------------+----------+-----------+-------------------------------------------+----------+-----------+ Many indications are that the 2-fold axis is not really crystallographic, but a pseudo one. My point in this case is that reflections related by this "almost" 2-fold axis should go into the same set, free and work, this in the (new) P1 setting. I could not devise clearly how to get a program to do this automatically (say, flag reflections with this pseudo 2 related for free -set ) . Is there? I understand cb_op is the real space operation, possibly out of a crystallography package I can get that, but easier if there is a crystallographic tool. Any thoughts? Thanks, Jorge (Season's Greetings)

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amberprep problem
by George Phillips 25 Dec '25

25 Dec '25

I am trying to run phenix.AmberPrep in phenix-2.0-5885 and get the flollowing but cannot find a leap.log file to check. Any clues? pdb file attached. Thanks, George georgep@Y56NQ4XRRC 7W26 % phenix.AmberPrep noH.pdb minimise=amber_all ================================================================================ Running pdb4amber on noH.pdb ================================================================================ ================================================== Summary of pdb4amber for: noH.pdb =================================================== ----------Chains The following (original) chains have been found: A B S ---------- Alternate Locations (Original Residues!)) The following residues had alternate locations: None -----------Non-standard-resnames ---------- Missing heavy atom(s) None ================================================================================ Setting up library files for non-standard residues ================================================================================ ================================================================================ Preparing asu files and 4phenix_noH.pdb ================================================================================ Checking output filenames file : noH_asu.prmtop Sorry: Output file not present : noH_asu.prmtop Check contents of “leap.log"

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Phenix real space refine use for Cryo-EM model refinement
by dishajawadekar295＠gmail.com 22 Dec '25

22 Dec '25

Hi, I am using Phenix real space refine to refine my cryo-EM model. My model is looking good (based on molprobity statistics) but I would like to run an additional round of Phenix refinement without allowing the program to move the side chains. From what I see, Phenix moves the side chains by default. What settings can I use to avoid this? Thank you.

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phenix.polder issue
by robert＠oeffner.net 19 Dec '25

19 Dec '25

Hi, I think there's a slight glitch in Polder which I am currently testing. The program works fine. However, the log file shows the full phil parameter for the selection string solvent_exclusion_mask_selection whereas the json file does not. As an example I have a log file: ------------------------------------------------------------------------------- data_manager { miller_array { file = "../74343_262277_1_1.mtz" } default_miller_array = "../74343_262277_1_1.mtz" model { file = "../74343_262277_4_1+ligands.pdb" } default_model = "../74343_262277_4_1+ligands.pdb" } polder { box_buffer = 5 } solvent_exclusion_mask_selection = ( chain Y and ( ( resseq 1 and name C1 \ ) or ( resseq 1 and name C2 ) or ( \ resseq 1 and name C3 ) or ( resseq 1 and \ name C4 ) or ( resseq 1 and name C5 ) or \ ( resseq 1 and name N6 ) or ( resseq 1 \ and name C7 ) or ( resseq 1 and name H8 \ ) or ( resseq 1 and name H9 ) or ( \ resseq 1 and name H10 ) or ( resseq 1 \ and name H11 ) )) mask_output = True output { overwrite = True } But in the polder_modified.eff.json file it reads: ------------------------------------------------------------------------------- { "data-manager-miller-array-file": "../74343_262277_1_1.mtz", "data-manager-default-miller-array": "../74343_262277_1_1.mtz", "data-manager-model-file": "../74343_262277_4_1+ligands.pdb", "data-manager-default-model": "../74343_262277_4_1+ligands.pdb", "polder-box-buffer": 5, "solvent-exclusion-mask-selection": "(", "mask-output": true, "output-overwrite": true } Regards, Rob

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new XDS package (BUILT=20251103) for academic users
by Kay Diederichs 16 Dec '25

16 Dec '25

Dear XDS users, the latest binaries of the XDS package are available for academic users from the “downloading” link at https://xds.mr.mpg.de/ . As the linked “Release Notes” indicate, a few changes were made to output formats, and the requirement for a dynamic library (libquadmath.so), which is not installed by default in most Linux distributions, was eliminated. If you are already running BUILT=20250714, there is no reason to upgrade. In addition to the routine testing against specific datasets performed by Wolfgang Kabsch and me for new XDS packages, this one was tested against a larger database of datasets put together by Clemens Vonrhein and Gerard Bricogne (Global Phasing), who also devised a range of analysis and display tools. A procedure for comparing this and future XDS packages against earlier ones, using a further expanded database, is being implemented in the “XDS reproducibility project” that was convened by Max Burian (Dectris) and is hosted in the Dectris Cloud. Besides the five people mentioned, Camilla Larsen (Dectris), Gleb Bourenkov (EMBL Hamburg) and Ashwin Chari (Max Planck Institute for Multidisciplinary Sciences, Göttingen) are contributing to this project. We expect this effort will ensure the reliability of the XDS package, improve its usage, and enhance the resulting data quality. Best wishes, Kay

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REMINDER – Abstract Submission - 2026 ISMSM || DEADLINE - December 15
by Jose Artur Brito 11 Dec '25

11 Dec '25

Dear Colleagues, This is a reminder that abstract submission for the 7th International Symposium on Microbial Sulfur Metabolism (7th ISMSM), will CLOSE in December 15th. The meeting will take place in Lisbon, Portugal, from 17–20 March, 2026, and will bring together researchers from across the globe to explore the latest advances in microbial sulfur cycling, from molecular mechanisms to ecological, environmental and health perspectives. A number of talks will be selected from the abstracts, so please register and submit your abstract! https://wmsm.itqb.unl.pt/registration/ 👉 For more information visit: https://wmsm.itqb.unl.pt/ Please share this announcement with colleagues and collaborators who may be interested. We look forward to welcoming you in Lisbon next March! The Organising Committee Inês Cardoso Pereira, Filipa Sousa, José Artur Brito, Andreia Pimenta and Américo Duarte ismsm(a)itqb.unl.pt --

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Phenix density modification - EMDB deposition
by Dmitry Semchonok 20 Nov '25

20 Nov '25

Dear Colleagues, I am preparing to deposit a cryo-EM structure to EMDB/PDB and have encountered an important question regarding resolution reporting and half-map deposition after Phenix density modification. My Situation: 1. I performed 3D refinement in CryoSPARC, generating two independent half-maps 2. I calculated FSC between these original half-maps at the 0.143 threshold: X Å resolution. 3. I processed these half-maps through Phenix resolve_cryo_em for density modification 4. Phenix reports improved resolution of Y Å (based on corrected FSC as documented in your resolve_cryo_em guide) 5. I generated the corresponding FSC XML file from Phenix showing Y Å Questions: When I deposit to EMDB, I understand the policy requires depositing the original, unmodified half-maps (unfiltered, unmasked, unsharpened). However, when EMDB validates the deposition by independently recalculating FSC from these half-maps, they will obtain X Å, not Y Å. This creates an apparent contradiction: • Deposited FSC XML file: Y Å (from Phenix) • EMDB independent FSC calculation from deposited half-maps: X Å (from originals) * When you apply corrections for correlations introduced by density modification in resolve_cryo_em, does this mean the Y Å resolution should be reported as the official resolution, even though the original half-maps show X Å? * What is the recommended workflow when depositing density-modified maps to ensure consistency and avoid validation conflicts? Additionally: • No atomic model was used; only sequence information • The density modification improved map quality and interpretability as intended Thank you. Kind regards, Dmitry

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path errors phenix 1.21.2-5419 MacOS
by Guenter Fritz 18 Nov '25

18 Nov '25

Dear Phenix developers, I spotted two little errors in the path when phenix_ready_set or phenix.elbow calling files (I fixed it myself by copying the files/folder to the right place) Just for the notes: phenix.ready_set ....... Reduce warnings ERROR CTab(/opt/phenix-1.21.2-5419/lib/python3.9/site-packages/*elbow*/resources/monomer_het_dict.txt): could not open The path should be /opt/phenix-1.21.2-5419/lib/python3.9/site-packages/resources ------------------------------------------ phenix.elbow ....... AssertionError: Missing the file /opt/phenix-1.21.2-5419/lib/python3.9/site-packages/elbow/*elbow*/smiles Path should be /opt/phenix-1.21.2-5419/lib/python3.9/site-packages/elbow/smiles Best regards, Guenter

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Coot 1 - "Open in Coot" within Phenix - auto loading PDB/mtz/extensions
by kelvin.lau＠epfl.ch 07 Nov '25

07 Nov '25

Hi all As the stability of Coot1 increases I am looking to start the transition there from old Coot I can get Phenix to open Coot 1 via the Open in Coot buttons. However, it does not autoload the PDB/mtz/Phenix extensions. I know there are many differences between Coot 0.9X and Coot1 under the hood so just want to see if this was currently possible or if it’s something due to my parameter setups somewhere. Would be very useful to implement if not. Best Kelvin

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phenix 1.22 based on python 3.9 for Mac ARM
by Roberto Battistutta 06 Nov '25

06 Nov '25

Dear All, does an official versione of phenix 1.22 based on python 3.9 for Mac ARM (M2/M3) exist? I can’t find it in the download page. Or will it come out soon? Thank you. Regards, Roberto. Roberto Battistutta Associate Professor Department of Chemical Sciences University of Padua via Marzolo 1, 35131 Padova - ITALY tel. +39.049.827.5262 fax. +39.049.827.5829 roberto.battistutta(a)unipd.it

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CAHRA 2025: Announcing the 2025 Community-wide Assessment of cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA)
by Tom Burnley - STFC UKRI 05 Nov '25

05 Nov '25

Dear all, We are pleased to announce the 2025 Community-Wide Assessment of Cryo-EM Heterogeneous Reconstruction Algorithms (CAHRA). Cryo-electron microscopy (cryo-EM) has revolutionized structural biology by enabling high-resolution visualization of dynamic biomolecular assemblies. However, a central challenge remains: developing robust computational methods to model different forms of structural heterogeneity—including continuous motions, discrete states, and compositional variations and to accurately estimate population distributions. To encourage the development and benchmarking of heterogeneous reconstruction algorithms and workflows, we invite the cryo-EM community to analyze three new curated experimental and synthetic datasets: 1. Compositional Heterogeneity 2. Conformational Heterogeneity 3. Pose Entanglement Please join us for a webinar where we will introduce this year's challenge: Friday, November 14 12:00 PM Eastern (US, Canada) / 5:00 PM GMT (UK) Registration: ukri.zoom.us/webinar/register/WN_-G-7jbX_Q26o7Q8DiVCcQg<http://ukri.zoom.us/webinar/register/WN_-G-7jbX_Q26o7Q8DiVCcQg> For all challenge information, datasets, and submission timeline, please visit: heterogeneity.notion.site/challenge<http://heterogeneity.notion.site/challenge> Submissions close on June 1, 2026. Please share this with others who may be interested. We hope you’ll join us for this year’s challenge! The CAHRA Team from the Flatiron Institute, CCP-EM/STFC, and Princeton University

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.cif file from phenix for AF3 as template
by Georg Mlynek 04 Nov '25

04 Nov '25

Dear Phenix community, I have solved the structure of protein complex consisting of 6 chains. We have the structure with 5 chains now and still see positive electron density and mass spec analysis gave us some possible candidates which we would like to model with AF3. However just using MSA's AF3 is not placing two chains correctly, therefore I want to give the structure templates for the 5 chains. However using the proposed way to create the files *https://github.com/google-deepmind/alphafold3/issues/462 * I get an error: ValueError: INVALID_ARGUMENT: The number of values (1958407) in a loop is not a multiple of the number of the loop's columns (19) However it works if I use 5Y2E.cif from PDB. Comparing the cif files I see a difference. from phenix: loop_ _atom_site.group_PDB _atom_site.id _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.type_symbol _atom_site.pdbx_formal_charge _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num from 5Y2E loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num After processing 5Y2E loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num Did anybody encountered the same problem and has a workaround? Additionally I would like to ask if anybody knows which entries of the cif file header are really needed for AF3 to run? I would like to make a google colab which does the processing, without relying on the structure module from AF3 code (from alphafold3 import structure). There is a Python Package with the same name "alphafold3" on PyPi but this does not have a structure subpackage. Many thanks, br Georg.

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