- phenixbb - phenix-online.org

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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