October 2026 - 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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