- phenixbb - phenix-online.org

ReadySet and cif
by p.auffinger＠unistra.fr 02 Apr '26

02 Apr '26

Hi, Is it possible to get a cif file as an output when using the ReadySet gui ? What is "Output file base" ? If I precise "output.cif" the program seems not to be happy ! Thanks, Pascal

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Hydrogens on modified residues -- ReadySet
by p.auffinger＠unistra.fr 02 Apr '26

02 Apr '26

Dear all, ReadySet encounters some issues when adding hydrogens to modified residues. I used the 7k00 ribosome structure as a test. I noticed missing hydrogens on G7M, 4OC, UR3, MA6, 6MZ, 2MA, OMU, 2MG. Additionally, hydrogens are missing on IAS and on the NH groups of D2T, MS6 and 4D4. An amino hydrogen is also missing on 4D4. When using Coot on this file, everything looks much better except that some hydrogens are added to amino acid backbones of modified residues that need to be removed by hand. Any ideas ? Thanks a lot, Pascal

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Issues refining a cyclic peptide with non-natural residues
by Dayna Louise Holroyd 31 Mar '26

31 Mar '26

Hi all, I am currently refining a cyclic peptide which I have modelled into my 3A crystal structure. The peptide contains multiple non-natural amino acids, two of which haven't been defined in the PDB before by a three letter code (made cif files with elbow for these). I have been adding custom restraint files each refinement round to connect residues at the ends and maintain cyclisation. I am encountering various issues during refinement: 1. Certain pairs of non-natural residues drift apart after refinement if I do not include restraints between the two residues. 2. Some backbone dihedral angles are much smaller than expected, while other angles appear unusual or physically implausible, even after defining particular angles in the restraint files. I suspect that some of these issues may be related to the compact nature of the cyclic peptide and the presence of undefined residues, but I am unsure how to address them effectively. Has anyone refined similar cyclic peptides with non-natural residues and can offer advice on my problems with restraints, compact backbone angles, non-natural residues, etc? Any guidance or ideas would be greatly appreciated. Many thanks, Dayna Holroyd PhD Candidate Protein Crystallography and Structural Biology Laboratory School of Biological Sciences | College of Science ADELAIDE UNIVERSITY

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Industrial Biostructures America conference 2026
by Xu, Rui [JRDUS] 27 Mar '26

27 Mar '26

The Industrial Biostructures America conference will take place on May 11 & 12, 2026 at the Sanofi Cambridge Crossing site in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Sandra Gabelli - Global Head of Protein and Structural Chemistry at Merck * Dr. Derek Lowe - Director in Chemical Biology at Novartis and author of widely-read science and industry web site "In the Pipeline" Conference information is available at https://industrialbiostructuresamerica.org<https://industrialbiostructuresamerica.org/> along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Membrane Proteins, chaired by Dr. Elena Levin (UCB) * Conformational dynamics (allostery), chaired by Dr. Rui Xu (J&J) * Fragments and Proximity, chaired by Dr. Kerren Swinger (Takeda) * Tools of the Trade and Cryo-EM, chaired by Dr. Eva Cunha (Proteros) * Biologics, chaired by Dr. Joe Batchelor (Sanofi) * AI/ML in Drug Discovery and the Future of Structural Biology, chaired by Dr. Jill Chrencik (Merck) We also plan on a panel discussion on the topic of "Frontiers in Structural Biology for Drug Discovery and Development" The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for additional information

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Re: coot-1 linked to phenix
by Roberto Steiner 25 Mar '26

25 Mar '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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How to do map sharpening?
by Francisco 25 Mar '26

25 Mar '26

Hi... I am trying to sharpen a map (x-ray) with the new phenix.auto_sharpen -> phenix.map_sharpening program. Got a script that basically runs phenix.xtriage to get the fraction of solvent content and some things and then I do ... ``` phenix.map_sharpening \ sharpening_method=b-factor \ mtz_in="$MTZ_IN" \ map_coeff_labels="2FOFCWT,PH2FOFCWT" \ map_model.model="$PDB_IN" \ crystal_info.resolution="$RESOL" \ b_factor_sharpening.b_factor_sharpening_crystal_info.solvent_content="$SOLVENT" \ b_factor_sharpening.b_factor_sharpening_crystal_info.is_crystal=True \ > sharpen.log 2>&1 ``` The problem is that I cannot open the mtz file in coot (mtz dump is attached) ... BUT ... I can open the sharpened map (ccp4 format) ... BUT ... the map is not covering the protein completely.. How do I do that? (1.png 2.png just showing the limits of the map) In gui mode I do get the map over the protein...BUT I cannot select the "FOFCWT,PHFOFCWT" labels (3.png ... That's the second part of the plan...) I am using phenix-dev 5989 Thanks a lot for your help

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Re: Monomer of dimer?
by Andrea Smith 25 Mar '26

25 Mar '26

Hi Liu, we had a case in our lab where we had one molecule in the ASU even for a swapped dimer, so it is possible to have one molecule in the asymmetric unit even if your protein is a dimer. I would think that your problem might be somewhere else. Did you check with Xtriage if it can flag some issues with the data? Andrea On Wednesday, March 25, 2026 07:31 CET, "princeadam(a)163.com" <princeadam(a)163.com> wrote: Dear PhenixBB community, I am currently working on solving the structure of protein X (110 amino acids). The protein forms a dimer in solution, and dimerization is functionally relevant. Based on initial analysis, the asymmetric unit (ASU) was estimated to contain one copy [unit cell: 82.699, 82.699, 36.435, 90 , 90, 120]. The data extend to 1.2 Å resolution, but the final R factors are around 0.23/0.25, which seem higher than expected at this resolution, and we have not been able to improve them further. When I examined the structure using symmetry mates in PyMOL, I observed a clear dimer that appears biologically meaningful. This makes me suspect that the ASU estimation might be incorrect—especially for a small protein like this, the ASU could potentially contain a dimer rather than a monomer. However, every time I use a dimer model as the search model for molecular replacement, Phaser consistently returns a monomer solution. I would greatly appreciate any suggestions on how to successfully obtain the dimeric model that matches the crystallographic symmetry. Thank you in advance for your help! Best regards, Liu _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org To unsubscribe send an email to phenixbb-leave(a)phenix-online.org Unsubscribe: phenixbb-leave@%(host_name)s

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How to start the Phenix Coot Implementation manually
by Biertuempfel, Christian (NIH/NHLBI) [E] 20 Mar '26

20 Mar '26

Dear all, Is there a clever way how to start the coot implementation from phenix manually? Basically, I am running phenix on one machine and I would like to open coot on another. I tried to copy/import my phenix database and project files on the “coot machine" but the paths are not properly imported. Which files are read when clicking “Open in Coot” in the GUI? Can I somehow run “Open in Coot” from the command line? Thanks, christian

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Test message sorry for the noise
by Nigel Moriarty 20 Mar '26

20 Mar '26

Cheers Nigel --- Nigel W. Moriarty Building 91, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.gov Web : CCI.LBL.gov ORCID : orcid.org/0000-0001-8857-9464

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unrealistic low clashscore in phenix.refine
by Kevin M Jude 18 Mar '26

18 Mar '26

I’m using phenix 2.0-5936 on my M1 Mac. I notice in phenix.refine that the run status reports a realistic clashscore (7.5) for my structure, but in the Molprobity tab of phenix.refine the reported clashscore is 0.77, with only 4 clashes identified with a maximum overlap of 0.472 Å. Running Comprehensive Validation (X-rayNeutron) gives a full list of 76 overlapping pairs, maximum overlap 0.705 Å, and a clashscore of 7.65. -- 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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CBMS - Lecture Series - Serganov
by Stojanoff, Vivian 18 Mar '26

18 Mar '26

Dear Colleagues, you are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Alexander A. Serganov Associate Professor, Department of Biochemistry and Molecular Pharmacology NYU Grossman School of Medicine NYU Langone Health WEDNESDAY, March 25, 13:30 (EST) "Redefining dogmas in bacterial physiology: the case of mRNA” Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/QkF6wZmvRJCTtT9RG0djuw Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: The degradation of mRNA plays a crucial role in determining the number of mRNA molecules and, consequently, influences the yield of protein biosynthesis across all organisms. While the regulation of mRNA lifetime is well-recognized as vital for gene expression in eukaryotes, it has long been assumed that bacteria lack sophisticated mechanisms for regulating mRNA stability and degradation. Our findings challenge this assumption, revealing that bacterial mRNAs possess unexpected properties and employ molecular mechanisms that rival in complexity those in eukaryotic systems. ================= Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973

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Matplotlib error for 2.0-5936
by matthew.belousoff＠monash.edu 16 Mar '26

16 Mar '26

Hey guys, Few details first: OS: Linux Mint 22.1 Kernel: 6.8.0-71 Phenix Build: Phenix-2.0-5936-CUDA12-Linux-x86_64 Generally everything works fine, but when I run a RealSpace refinement job, afterwards going through the diagnostic details is quite slow and the console keeps printing out: findfont: Font family 'Courier' not found. findfont: Font family 'Monaco' not found. findfont: Font family 'Helvetica' not found. This seems like a matplotlib error to me. I will note that I didn't get these errors with any older versions of phenix on the same system. cheers, matt B

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PDB Deposition Problems – Sequence Not Detected in mmCIF
by caleb.gaine＠gmail.com 13 Mar '26

13 Mar '26

I am currently trying to validate my structure using the wwPDB Validation Server before deposition. I am submitting the following files: - Full map - Both half maps - Map-to-structure factors - Coordinate file (.mmCIF) However, when I attempt to submit the entry I receive the following errors: - Coordinate Issues: Not Known - Sequence: The sample sequence has not been provided I have already added the sequence data to the mmCIF file using the Phenix tool: mmtbx.prepare_pdb_deposition After running the tool, I verified that the mmCIF file contains the expected sequence-related records. For example: _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id _entity_poly_seq.hetero 1 1 MET no 1 2 ALA no 1 3 LYS no 1 4 LEU no 1 5 THR no 1 6 LYS no ... (continued) and: loop_ _entity_poly.entity_id _entity_poly.nstd_linkage _entity_poly.nstd_monomer _entity_poly.pdbx_seq_one_letter_code _entity_poly.pdbx_seq_one_letter_code_can _entity_poly.pdbx_strand_id _entity_poly.pdbx_target_identifier _entity_poly.type 1 no no ;MAKLTK ... (continued) For reference the .fasta file looks like this. >Chain A MAKLTK ... (continued) Despite these sequence records being present in the mmCIF file, the validation server still reports that the sequence has not been provided and flags coordinate-related issues. Has anyone encountered a similar problem or knows what might be causing the validation server to not recognize the sequence information? Any suggestions would be greatly appreciated.

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phenix.ready_set with cif file for ligand,
by Guenter Fritz 12 Mar '26

12 Mar '26

Hi phenix team, hi Nigel, (it is macOS 15.7.3, phenix version 2.0-5936) I want to run phenix.ready_set on a protein with ligand. The run fails with some error in phenix elbow (I paste it below). When I run phenix.elbow on the ligand, like phenix.elbow vchfs_0210_phenix_001.pdb --residue UNL it works perfectly fine. I tried to provide phenix.ready_set with the cif file from the separate phenix.elbow file, but it fails again with the same error. Maybe I overlook something? Best regards, Guenter ------------------- error message below -------------------------- (base) guenter@Guenters-MacBook-Pro phenixqr % phenix.ready_set vchfs_0210_phenix_001.pdb INPUT Reading model from vchfs_0210_phenix_001.pdb Writing effective parameters to vchfs_0210_phenix_001.eff - to ligands using eLBOW, phenix.elbow Traceback (most recent call last): File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/ready_set.py", line 1118, in <module> run(args) File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/ready_set.py", line 861, in run rc = run_though_all_the_options( File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/ready_set.py", line 221, in run_though_all_the_options rc = add_hydrogens.run( File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/add_hydrogens.py", line 909, in run rc = add_hydrogens( File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/add_hydrogens.py", line 710, in add_hydrogens hierarchy = remove_incorrect_hydrogens(hierarchy, File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/elbow/command_line/add_hydrogens.py", line 435, in remove_incorrect_hydrogens tmp = get_atom_names(atom_group.resname) File "/Users/guenter/software/PHENIX/2.0-5936/phenix-2.0-5936/lib/python3.9/site-packages/mmtbx/chemical_components/__init__.py", line 201, in get_atom_names for item in cif["_chem_comp_atom"]: KeyError: '_chem_comp_atom'

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ADP refinement in a CryoEM map of heterogeneous quality
by carlos.kikuti＠curie.fr 09 Mar '26

09 Mar '26

Hello there, It's been a while we haven't chatted with anybody from the Phenix crew, I hope you are all doing fine! I'm writing because of an issue with this CryoEM structure at 2.5 angstroms I'm about to deposit. It is a myosin motor domain + part of the lever arm including one light chain. I've used RealSpaceRefine from Phenix 2.0 with very good results: very nice geometry and agreement with the map. The thing is, the lever arm and the light chain move a lot, so the contour in that part is much lower, ~50% the one of the motor domain, of course the map is also more poorly defined. And RealSpaceRefine attributes very low ADPs for the light chain (chain B), but the ones for the lever arm helix (chain A, same as the motor domain) are high, coherent with the difference in map quality. I'm considering "cheating" by putting them two as chain A to try to get this fixed (I'll need to undo this before deposition), but is there a more elegant way to sort this out? The PDB does not complain about the current model, but I'm thinking of readers looking at these ADPs and finding the ensemble really weird (basically a hot arm surrounded by a cold calmodulin-like domain, which is physically impossible). (To me it looks like a different normalization is being applied to the two chains because of the map quality difference, if this makes any sense.) I'm looking forward to your opinions, Carlos

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RCSB PDB is recruiting a Biocurator!
by Yuhe Liang 03 Mar '26

03 Mar '26

*RCSB PDB is recruiting a Biocurator! * The job description and the online application URL can be found at https://www.rcsb.org/pages/jobs#bioStructAnnotRutgers Biological Structure Annotation Specialist (Rutgers) Become a Biocurator and analyze, curate, and validate macromolecular structures from the PDB community. Participate in exciting projects with significant impact on the scientific community. RCSB PDB, the US data center for the global PDB archive, serves thousands of Data Depositors in the Americas and makes 3D macromolecular structure data available at no charge and without usage restrictions to many millions of RCSB.org <https://www.rcsb.org/> users worldwide. Deposition/Biocuration Services provide expert deposition, validation, biocuration, and remediation services to Data Depositors worldwide, ensure PDB data are Findable, Accessible, Interoperable, and Reusable (FAIR) by providing expert data curation which is critical for biological data resources, and develop and promote community-endorsed data standards for archiving and exchange of global structural biology data. Roles: - Analyze, curate, and validate macromolecular structures from the PDB community - Participate in exciting projects with significant impact on the scientific community - Communicate daily with members of the research community - Participate in fun scientific outreach and training activities Knowledge and skills: - Experience in structural biology with a PhD in a relevant field is required - Strong knowledge of cryo-electron microscopy (3DEM) is required to curate and validate macromolecular structures - Experience with small molecule chemistry is a plus - Experience with bioinformatics, cheminformatics, and computer scripting would be an advantage - The successful candidate should be self-motivated, pay close attention to details, possess strong interpersonal communication and writing skills, and have the ability to handle multiple projects *Why Join Us* <https://www.rcsb.org/pages/jobs#whyJoinUs> Apply online at Rutgers <https://go.rutgers.edu/eaurbzrz>. -- YUHE LIANG, Ph.D. Biocuration Lead Deputy, RCSB Protein Data Bank Research Associate, Institute for Quantitative Biomedicine Rutgers, The State University of New Jersey 174 Frelinghuysen Road, Piscataway NJ 08554 P: 848.445.4938 | E: yuhe.liang(a)rcsb.org

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Metal distance parameters used by phenix.metal_coordination
by p.auffinger＠unistra.fr 23 Feb '26

23 Feb '26

Hi, We used phenix.metal_coordination to generate metal restraints and it works well. My question is in which file can I find the distances (ideal) used by this program. refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name O and chain Y and resname HOH and resseq A1A8 distance_ideal = 2.140000 sigma = 0.190 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name N7 and chain a and resname G and resseq 1190 distance_ideal = 1.895092 sigma = 0.050 } } refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = name MG and chain V and resname MG and resseq 258 atom_selection_2 = name O and chain Y and resname HOH and resseq 2831 distance_ideal = 2.140000 sigma = 0.190 In this example, the Mg...O ideal distance is 2.14 and we would prefer to use 2.07 Same for Mg...N distances of 1.895092 that should be changed to 2.19 Thanks for letting us know if there is a parameter file for this or even better, an option to use distance values extracted from the input cif file. Pascal

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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 03 Feb '26

03 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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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 23 Jan '26

23 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/>

4 3

Obtaining standard cif restrain file for ligand in PDB
by Lei Chen 18 Jan '26

18 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

2 2

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] 09 Jan '26

09 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 26 Dec '25

26 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 23 Dec '25

23 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.

3 2

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

2 1

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

2 1

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

1 0

.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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Problem when trying to install last nighlty build on Ubuntu 22.04
by emmanuel.bettler＠univ-lyon1.fr 04 Nov '25

04 Nov '25

Hi, on a linux ubuntu 22.04 distribution, when i'm trying to install latest Phenix nightly version 2.0-5824, i have the following error message: [...] PREFIX=/home/ebettler/Soft/phenix-2.0-5824 Unpacking bootstrapper... Unpacking payload... entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. entry_point.py:256: DeprecationWarning: Python 3.14 will, by default, filter extracted tar archives and reject files or modify their metadata. Use the filter argument to control this behavior. concurrent.futures.process._RemoteTraceback: ''' Traceback (most recent call last): File "concurrent/futures/process.py", line 432, in wait_result_broken_or_wakeup File "multiprocessing/connection.py", line 251, in recv TypeError: InvalidArchiveError.__init__() missing 1 required positional argument: 'msg' ''' The above exception was the direct cause of the following exception: Traceback (most recent call last): File "entry_point.py", line 244, in _constructor_extract_conda_pkgs File "concurrent/futures/_base.py", line 449, in result File "concurrent/futures/_base.py", line 401, in __get_result concurrent.futures.process.BrokenProcessPool: A process in the process pool was terminated abruptly while the future was running or pending. The above exception was the direct cause of the following exception: Traceback (most recent call last): File "entry_point.py", line 691, in <module> File "entry_point.py", line 681, in main File "entry_point.py", line 582, in _constructor_subcommand File "entry_point.py", line 246, in _constructor_extract_conda_pkgs RuntimeError: Failed to extract /home/ebettler/Soft/phenix-2.0-5824/pkgs/chem_data-2.0.5824-pyhe0d8492_0.conda: A process in the process pool was terminated abruptly while the future was running or pending. [PYI-197168:ERROR] Failed to execute script 'entry_point' due to unhandled exception! What's wrong ? Any advice are welcome !

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Announcement: The American Union of Crystallography
by Joseph Ferrara 01 Nov '25

01 Nov '25

What is the American Union of Crystallography (AUC)? The American Union of Crystallography (AUC) is a nonprofit scientific and educational organization established in 2025 to represent and support the U.S. crystallographic community at both national and international levels. It was formed in response to the USA National Science Foundation's (NSF) decision not to fund the U.S. National Committee for Crystallography (USNC/Cr). As a result, the National Academy of Sciences (NAS) will cease serving as the U.S. adhering body to the International Union of Crystallography (IUCr), effective January 1, 2026. While NSF will continue to support other national scientific committees directly, it has ended centralized funding through the NAS, necessitating the creation of the AUC as an independent successor. The AUC was officially incorporated in the state of Delaware on April 22, 2024, and received Internal Revenue Service 501(c)(3) nonprofit status on August 21, 2025. On September 4, 2025, the IUCr Executive Committee granted the AUC ad interim adhering body status, effective January 1, 2026, enabling it to represent the USA to the IUCr until the General Assembly in Calgary in 2026. Mission and Core Objectives The AUC serves as the national voice for U.S. crystallographers and is committed to advancing crystallographic science through the following objectives: * Represent U.S. crystallographers to the IUCr. * Advocate strong, sustained support of crystallographic research. * Promote interdisciplinary collaboration to accelerate scientific discovery. * Support education and training for the next generation of crystallographers. * Expand outreach to showcase real-world applications of crystallography. * Steward the USNC/Cr's financial resources responsibly. * Operate as a volunteer-led organization responsive to community needs. * Recognize and celebrate distinguished members of the community. Current Priorities With nonprofit status and international recognition in place, the AUC is focused on the following immediate priorities: * Supporting U.S.-based education and training initiatives, including student travel to the IUCr Congress. * Managing the newly established George M. Sheldrick Award for Contributions to Structural Science. * Contributing to the success of the 2026 IUCr Congress and General Assembly in Canada. * Establishing key committees on Workforce & Education, Finance, Ethics, and other areas as needed. * Managing and growing the legacy funds originally held by NAS to support U.S. crystallography. Governance and Community Engagement To ensure transparency and continuity, all current USNC/Cr members will serve on the AUC Board through 2025. Beginning in 2026, Board members will be selected through an open and inclusive nomination process, with active involvement from the U.S. National Division of the American Crystallographic Association (USND, ACA). The AUC's bylaws are modelled on those of the USNC/Cr, and the organization is committed to continued community input as it grows. Why Not the ACA or USND? The ACA is a regional affiliate representing both U.S. and Canadian crystallographers and is not structured to take on U.S.-specific international responsibilities. The USND, while created as a possible successor to the USNC/Cr, is not a standalone legal entity and therefore cannot function as an independent 501(c)(3) organization. A Call to Action The AUC invites all members of the U.S. crystallographic community to support its leadership, mission, and transition by: * Participating in AUC initiatives through service, collaboration, and advocacy. * Supporting the transfer of NAS-held legacy funds to the AUC for continued stewardship. We ask the worldwide crystallographic community to support the AUC by voting to make it the permanent adhering body representing the US at the General Assembly in Calgary in August 2026. Together, we can ensure a strong, sustainable, and globally connected future for U.S. crystallography. Joseph D. Ferrara, Chair USNC/Cr; President and Chair, AUC Lisa J. Keefe, Vice-Chair USNC/Cr; Vice President and Secretary, AUC Ilia A. Guzei, Secretary-Treasurer USNC/Cr; Treasurer, AUC

1 0

Importing a project
by jiyeol3＠uci.edu 29 Oct '25

29 Oct '25

Hi, I am trying to import a project, but every time I do it, it does not load the job history. How do I fix this? The original folder contains all the files.

1 0

CBMS Lecture Series - Vanden Zanden
by Stojanoff, Vivian 23 Oct '25

23 Oct '25

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Crystal Vander Zanden University of Colorado www.vanderzanden-lab.com<https://urldefense.com/v3/__http://www.vanderzanden-lab.com/__;!!P4SdNyxKAP…> WEDNESDAY, November 19, 13:30 (EST) "Assessing Membrane Protein Structures Using Liquid Surface X-ray Scattering” Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/2R2GbeNJTa-QtcoJRA7Vjw<https://urldefense.com/v3/__https://bnl.zoomgov.com/meeting/register/2R2Gbe…> Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: In the Vander Zanden lab, we use complementary liquid surface X-ray scattering and molecular dynamics methods to study the structure of protein/membrane interactions, particularly focusing on protein families that have dynamic behavior at membrane surfaces. Specifically, X-ray reflectivity and grazing incidence diffraction will be showcased as powerful tools for determining structural information about peripheral membrane proteins. We will discuss application of these techniques to study three protein/membrane systems: glycolipid recognition proteins, amyloidogenic proteins, and lipoxygenase enzymes. For each of these systems, a lipid monolayer is deposited at the air/water interface in a Langmuir trough, and proteins are injected into the liquid subphase below, where they can bind the membrane. These thin-film measurements are used to deduce an electron density profile describing the membrane and bound proteins. Diffraction data are used to detect semi-ordered species present at the membrane, such as protein assemblies and lipids organized into condensed domains. Overall, we feel these methods are a valuable addition to the classic suite of structural biology techniques, and their strength is the ability to capture a population of membrane proteins exhibiting dynamic behavior. ================= Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973 ________________________________ To unsubscribe from the CCPEM list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCPEM&A=1<https://urldefense.com/v3/__https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?…>

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Off-topic: Postdoc opportunity – Protein–protein interactions / Quantitative Interactomics
by Gergő Gógl 20 Oct '25

20 Oct '25

Dear colleagues, Sorry for the off-topic post, but I would like to share a *postdoctoral position* open in my team at the *Institut de Biologie Valrose (iBV)* in Nice, France. Our group investigates *motif-mediated protein–protein interactions* underlying key biological processes such as *cell signaling* and *cancer*, using *quantitative interactomics* and *biophysical approaches* (e.g. the *native holdup assay*). We are looking for a motivated researcher who has *recently defended their PhD*, with experience in *recombinant protein production and purification*. Expertise in *biochemistry*, *biophysics*, or *structural biology* would be highly relevant, and the position offers opportunities to apply these skills to proteome-wide interaction mapping. *Start date:* as early as December *Contract:* 6 months, with possible extension *Location:* iBV, Nice, France Full details of the call: https://euraxess.ec.europa.eu/jobs/381589 Best regards, *Gergo Gogl* Team *Quantitative Interactomics and Disease-Related Networks* *Institut de Biologie Valrose (iBV), Nice*

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Zero B-factors
by p.auffinger＠unistra.fr 20 Oct '25

20 Oct '25

Hi, I have a large structure for which I just want to update B-factors. Unfortunately, I get zero values for some B-factors. Basically, I modified coordinates of a PDB deposited file and used the deposited cry-EM map. Is there something in the header (present or missing) that could influence the outcome of such a calculation ? Thanks, Pascal

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Structural Biology Full Professorship, University of Innsbruck, Austria
by Bernhard Rupp 18 Oct '25

18 Oct '25

Hi Fellows, a Full Professor position in Structural Biology is open at the Leopold-Franzens University in Innsbruck, Austria. Feel free to contact me about position details and questions, including the origins of the euphemistic title 'Structural Analysis for Pharmacy and Chemistry' in the attached posting. Best regards, BR ------------------------------------------------------ Bernhard Rupp k.k. Hofkristallamt San Diego, CA 92084 https://www.hofkristallamt.org/ https://psilosophy.org/ br(a)hofkristallamt.org +1 925 209 7429 ------------------------------------------------------ Institute of Theoretical Chemistry University Innsbruck Am Innrain 82 A 6020 Innsbruck bernhard.rupp(a)uibk.ac.at +43 676 571 0536 ------------------------------------------------------ Many plausible ideas vanish at the presence of thought ------------------------------------------------------

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Multiple Linux users access same project directory
by André Graça 10 Oct '25

10 Oct '25

Hi everyone, Is there any possibility to set up Phenix so multiple Linux users of the same Linux machine can access the same project directory? Thank you, André

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Generating BIOMT record for icosahedral symmetry
by Lei Chen 06 Oct '25

06 Oct '25

Dear All, I am currently working on depositing a PDB file for an icosahedral virus and have built the pdb for one asymmetric unit (ASU). I am wondering how I can compile or obtain the BIOMT record. I haven't found a detailed protocol online. Thank you, Lei

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