- phenixbb - phenix-online.org

Industrial Biostructures America (IBA) Conference 2026
by Xu, Rui [JRDUS] 05 Nov '26

05 Nov '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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phenix.reflection_file_converter
by Whitley, Matthew (NIH/NCI) [C] 30 Oct '26

30 Oct '26

Hello all, I am trying to perform a simple task using phenix.reflection_file_converter on the command line, but I am not getting the results I want and would be happy to receive advice as to how to do this properly. I am using Phenix 2.1-6048 on an Apple M3 Pro laptop. The input is a scaled and merged reflection file in MTZ format containing F, SIGF, IMEAN, and SIGIMEAN columns. I want to (i) transfer all four existing columns to the output file and (ii) generate R-free flags. When I try phenix.reflection_file_converter scaled_and_merged_data.mtz --label="F,SIGF,IMEAN,SIGIMEAN" --generate_r_free_flags --r_free_flags_fraction=0.05 --mtz=output.mtz I get the error: Unknown --label=F,SIGF,IMEAN,SIGIMEAN If I use multiple --label flags: phenix.reflection_file_converter scaled_and_merged_data.mtz --label="F,SIGF” --label="IMEAN,SIGIMEAN" --generate_r_free_flags --r_free_flags_fraction=0.05 --mtz=output.mtz the process executes successfully, but only the I columns from the second --label flag are present in the MTZ output. The first --label flag was not transferred to the output. I can create the desired output containing both F's and I's using the Phenix GUI, but I need to do this from the command line for scripting purposes. What is the proper command line syntax for transferring all existing columns to the output? Thanks, Matthew ____________________________ Matthew J. Whitley, Ph.D. [c] Scientist, RAS Structural Biology Group Cancer Research Technology Program (CRTP) Frederick National Laboratory for Cancer Research National Institutes of Health ATRF Room C1024 Matthew.Whitley(a)nih.gov<mailto:[email protected]>

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DEN restraints and ECHT disorder models
by Roberto Battistutta 19 Oct '26

19 Oct '26

Dear all, From which version of Phenix are the DEN restraints and ECHT disorder models implemented in the ensemble refinement (as described in Ploscariu, N., Burnley, T., Gros, P. & Pearce, N. M. (2021). Improving sampling of crystallographic disorder in ensemble refinement. Acta Cryst. D77, 1357-1364)? Thank you very much, 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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B-factors increase for ligands, phenix 2.2.1-6174
by jan.abendroth＠ucb.com 03 Oct '26

03 Oct '26

Hi all, I have seen this odd behavior with a couple of ligands in phenix 2.2.1-6174: B-factors of some well-defined ligands increase significantly during a refinement, in the range of 2-fold compared with surrounding protein residues. The density hints for full occupancy - just about as strong as for the neighboring residues. As a test, I changed the occupancy of the ligand to 0.8. Phenix refines back to 1.0. If I turn off occupancy refinement, B-factors for the ligand increase even more. While the geometry looks fine, I am left with significant positive difference density. I have refined several structures for both targets with different ligands and never ran into this. Has this been seen before and is there anything I could try? I have already tested versions 6190 and 6048 and see the same behavior. Thanks, Jan

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emplace_local error funning from ChimeraX with 2.2-6143
by Kevin M Jude 30 Sep '26

30 Sep '26

Running Tools>Phenix>Local EM Fitting from ChimeraX 1.12, using phenix 2.2-6143, I get the failure pasted below. When I point ChimeraX to phenix 2.1-6048, the search is successful. phenix.voyager.emplace_local exited with error code 1 Command: /programs/i386-mac/phenix/2.2-6143/phenix_bin/phenix.voyager.emplace_local map1=half_map1.mrc map2=half_map2.mrc d_min=3.4 model_file=model.pdb sphere_center=(121.216,117.898,130.99) --json --json-filename emplace_local_result.json stdout: Starting phenix.voyager.emplace_local on Wed Sep 30 11:54:00 2026 by kjude =============================================================================== Processing files: ------------------------------------------------------------------------------- No files found Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- map1=half_map1.mrc map2=half_map2.mrc d_min=3.4 model_file=model.pdb sphere_center=(121.216,117.898,130.99) Final processed PHIL parameters: ------------------------------------------------------------------------------- model_file = model.pdb map1 = half_map1.mrc map2 = half_map2.mrc d_min = 3.4 sphere_center = (121.216,117.898,130.99) Starting job =============================================================================== Traceback (most recent call last): File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/New_Voyager/scripts/em_placement_script.py", line 729, in em_placement_code results = prepare_docking_sphere( ^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/New_Voyager/_prepare_docking_sphere.py", line 55, in prepare_docking_sphere results = prepare_map_for_docking.assess_cryoem_errors( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/opt/sbgrid/i386-mac/phenix/2.2-6143/lib/python3.11/site-packages/cctbx/maptbx/prepare_map_for_docking.py", line 1952, in assess_cryoem_errors total_ordered_volume = flex.mean(ordered_mm.map_data()) * unit_cell.volume() ^^^^^^^^^^^^^^^^^^^ AttributeError: 'NoneType' object has no attribute 'map_data' stderr: AttributeError: 'NoneType' object has no attribute 'map_data' During handling of the above exception, another exception occurred: Sorry: Search failed -- 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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prediction.phenix-online.org maintenance
by Billy Poon 27 Sep '26

27 Sep '26

Hi all, The AlphaFold prediction server is currently undergoing some maintenance so predictions may fail intermittently. The server should be back to normal by Monday, September 28 around 9 am Pacific time. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 92R0129 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Some about the phenix.real_space_refine with Cryo-EM refinement
by liulj＠ku.edu 08 Sep '26

08 Sep '26

Hello: I have a few questions/comments with phenix.real_space_refine on Cryo-EM structures that may need your clarification. I am running version 2.2-6143, but the previous 2.1-???? gave similar experience. Thanks! 1) ADP refinement seems to be seeded randomly among runs? With exactly same inputs, while the output coordinates (x,y,z) showed always to be exactly same, there are difference in B-factors. While most of those BFs showed marginal difference, some are actually not too small. For example: ATOM 19872 CG ASP D 609 160.261 175.386 111.504 1.00 94.06 C ATOM 19873 OD1 ASP D 609 159.374 176.102 110.995 1.00 98.69 O ATOM 19874 OD2 ASP D 609 161.312 175.850 111.994 1.00 97.73 O ---------------------------- ~30 A2 difference out of 60-90 A2 ---------- ATOM 19872 CG ASP D 609 160.261 175.386 111.504 1.00 66.78 C ATOM 19873 OD1 ASP D 609 159.374 176.102 110.995 1.00 71.45 O ATOM 19874 OD2 ASP D 609 161.312 175.850 111.994 1.00 64.91 O 2) I found also the default "rotamers.restraints.enabled=true" could really shift the rotamer's refinement adversely. It easily drops the favored rotamer percentage of a good model (refined or manually built) from above 90%s down to 70%s, and likely could never be refined back even with hard endeavors until it was turned off. This is very different experience from that in phenix.refine -- mostly it helped (at least do not set back largely if maps looked good) in the latter. 3) The "rotamers.fit=outliers_or_poormap", upon my tests, is another interesting default? The "outliers_and_poormap" option mostly worked much better for me, while the former one can shift large regional chains a lot (like push long chain out of map; sounds like much over weighted for their contribution?). This even drove me think if there exists a confusion between Boolean and natural languages for this default? 4) Does the default "weight=None" mean this was turned off/NA currently, and all weights were set automatically.... I tested with different values but did not make changes (but BFs as mentioned in 1) above). The instruction says it could be invoked... Best regards, Lijun

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Mac installation problem
by Engin Özkan 06 Sep '26

06 Sep '26

Hi, When I try to install the latest release (2.2.1) on an M1 MacBook Pro using the GUI installer, I get the error "The operation couldn’t be completed. (com.apple.installer.pagecontroller error -1.) Couldn't open "Phenix-2.2.1-6174-MacOSX-arm64.pkg" I have already removed extended attributes, so that's not the problem. Checking xattr gives this % xattr ~/Downloads/Phenix-2.2.1-6174-MacOSX-arm64.pkg com.apple.macl This is also not a time-out issue; the installer just never launches. Best, Engin -- Engin Özkan, Ph.D. Associate Professor Dept of Biochemistry and Molecular Biology University of Chicago http://ozkan.uchicago.edu

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Please submit a comment on proposed NIH review changes if you are US-based
by Tom Terwilliger 16 Aug '26

16 Aug '26

Hi everyone, It is time to let your views be known if you are a US-based researcher. The NIH proposes to replace overall impact scores with just 3 categories, “most competitive,” “competitive,” and “not discussed.” Further they propose to not tell the grant proposers what their scores are or what the basis of funding or not funding was. It is not hard to see how this would allow the NIH to judge proposals on political rather than scientific bases. You can read the proposed changes and submit comments at *https://rfi.grants.nih.gov/?s=6a2b1c22c3fcfda46e0badd2 <https://rfi.grants.nih.gov/?s=6a2b1c22c3fcfda46e0badd2>* I just did it and it took a couple minutes. You can submit anonymously if you want to. A most informative and easy-to-read Forbes article on this was published today. I highly recommend reading it: *https://www.forbes.com/sites/brucelee/2026/08/15/nih-proposes-big-change-in-how-grants-applications-evaluated/ <https://www.forbes.com/sites/brucelee/2026/08/15/nih-proposes-big-change-in…>* The changes are quite short and sort of sound sensible until you read the article in Forbes or until you think about the changes carefully. All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Phenix version 2.2 released
by Paul Adams 05 Aug '26

05 Aug '26

Dear Colleagues, The Phenix developers are excited to announce that version 2.2 of Phenix is now available (build 2.2-6143). Binary installers for Linux, Mac OSX, and Windows, and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this new version of Phenix include: - phenix.agent: (NEW!) run Phenix and Coot tools via an agent using natural language - Added MCP server and skills for running Phenix with an agent - phenix.validate_ligands: (NEW!) per-ligand validation of real-space fit (RSCC for the ligand and its surroundings), difference density, clashes and H-bonds, ADPs and occupancies (ligand vs. environment), geometry outliers, missing atoms and alternative conformations, available in the GUI, with a results table, per-ligand details and CSV export and replaces mmtbx.development.validate_ligands - phenix.pdb_deposition: (NEW!) start PDB deposition and upload model and data files from Phenix - phenix.find_reference: now with GUI - Phenix now uses the new fast xcif parser - Updated Nucleic Acid restraints (ideal and e.s.d.) - Coot 1.3.1 included in Mac and Linux installers 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 previously 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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