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can not launch phenix gui
by lzhlizehou＠outlook.com 29 Mar '25

29 Mar '25

Dears, I am using Ubuntu 24.04 and have successfully installed phenix-1.21.2-5419. However, when I attempt to launch the GUI by running the phenix command, it fails with the following error: Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 961, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 34, in <module> run(sys.argv[1:]) File "/usr/local/phenix-1.21.2-5419/build/../modules/phenix/wxGUI2/command_line/main.py", line 28, in run wxapp = App.PhenixApp(args) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 84, in __init__ wx.App.__init__(self, 0) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 118, in OnInit show_splash_screen(timeout=2000) File "/usr/local/phenix-1.21.2-5419/modules/phenix/wxGUI2/App.py", line 1015, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/usr/local/phenix-1.21.2-5419/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) Could you kindly advise on how to resolve this issue? I would greatly appreciate your assistance. Looking forward to your reply. Best regards Li

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Call for Abstracts - Combining experimental data with predicted models - Session at the ACA Meeting, July 18-23, 2025
by Christopher Williams 24 Mar '25

24 Mar '25

Dear All, Rakhi Rajan and I are co-chairing the session "Combining experimental data with predicted models for structure determination" session at the 75th American Crystallographic Association Meeting in Lombard, IL (near Chicago) from July 18–23, 2025. It's a great meeting, and we encourage both general attendance and submissions for our session. We welcome abstract submissions for both talks and posters. If you're interested, please submit your abstract at https://www.acameeting2025.com/. Deadlines are fast approaching: March 31 – Deadline for oral abstracts & travel grant applications April 30 – Deadline for poster abstracts We invite contributions of novel methods and pipelines for combining prediction and experiment. We also invite stories of working with predictions and data. Have you gotten into the weeds with AlphaFold? Has structure prediction let you better design an experiment? Or has experimental data revealed an important detail missing from prediction? We want to hear about it! If you're interested in sponsoring our session, please reach out as well. -Christopher Williams ---Richardson Lab, Duke University -Rakhi Rajan ---University of Oklahoma

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Issues with zero B-factor and ADP refinement
by sylee00＠snu.ac.kr 23 Mar '25

23 Mar '25

Dear all, I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version. Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement: When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage. Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated. At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer. I would appreciate any insights or suggestions on how to resolve this. Thanks

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phenix low resolution refinement strategies
by a131943017＠163.com 20 Mar '25

20 Mar '25

Hi, how do I set the optimization parameters to make free R lower for 3.2Å x-ray crystallography data, or in other words, how do I go about determining whether the optimization strategy is appropriate or not? Questions from a Phenix Beginner.

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seeking help for phenix - coot model building
by tim smith 20 Mar '25

20 Mar '25

Hi everyone, I’m currently working on building a model and have encountered some difficulties with the map-model process. I would greatly appreciate it if anyone could assist me in either helping to build the model or teaching me how to do it. I’m happy to offer a suitable reward for your time and help. Thank you in advance for considering! Regards, Stim

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CSD changes conformation to planar during phenix.refine
by Andrea Smith 20 Mar '25

20 Mar '25

Hi all, I have a structure where I clearly see that one of the cysteines is oxidised. I have modelled CSD instead of CYS and when I do real space refine in Coot, the CSD sits nicely in the density. When I submit the phenix.refine job, I can see that the geometry changes and now the SOOH is planar. I tried to add the CSD.cif from PDB into phenix.refine as restraints, but it doesn't help and during the automatic refinement the geometry is changed to planar again. Anyone experienced same thing? What do I do? Thank you, Andrea

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Trouble with GTP/GDP refinement.
by DIEGO ORTIZ DE ELGUEA LOPEZ DE DICASTILLO 18 Mar '25

18 Mar '25

Dear phenixbb: I'm working with a GTP binding protein and have had some problems running phenix_refine. In my unit cell there are two molecules one with GDP and one with GTP, which I added in Coot(0.9.8). When refining the following error message pops-up : "Fatal problems interpreting model file: Number of atoms with unknown nonbonded energy type symbols:4 Please edit the model file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modifications and apply_cif_link parameter definitions if necessary". Checking the log file I found that the problem seems to be hydrogen atoms from these ligands Number of atoms with unknown nonbonded energy type symbols: 4 "HETATM 6499 H5' GTP A 501 .*. H " "HETATM 6502 H5'' GTP A 501 .*. H " "HETATM12939 H5' GDP B 501 .*. H " "HETATM12940 H5'' GDP B 501 .*. H " Including the corresponding .CIF files (dowloaded from PDB) did not solve the problem and the same error popped. Since I'm in the initial stages of the refinement I'm running phenix with bindividuals. Could anybody save my day giving me some light into this issue? Cheers, Diego

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.cif file has 'UNK' auth_asym_id
by Kevin M Jude 14 Mar '25

14 Mar '25

I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors. Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16 ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O TER ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1 ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1 I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419. -- 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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Pdb validation report via phenix
by Stachowski, Tim 12 Mar '25

12 Mar '25

I’ve always found the phenix.get_pdb_validation tool to be super helpful to gauge where my refinements are relative to the PDB, especially since I work mainly through the command line. But sometime around late last year, the R-free metric stopped being calculated (probably related to “EDS: FAILED”). Is there a way to bring this part of the tool back – or does anyone have a work around they can share? I’m running the command like: phenix.get_pdb_validation_report final-coot-3_refine_001.reflections.cif final-coot-3_refine_001.cif with version: phenix-2.0rc1-5599 Thanks Tim -- Tim Stachowski, PhD St. Jude Children’s Research Hospital ________________________________ Email Disclaimer: www.stjude.org/emaildisclaimer Consultation Disclaimer: www.stjude.org/consultationdisclaimer

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Refining the structure of Ribosome and the system crash
by Rajnandani Kashyap 12 Mar '25

12 Mar '25

Hello Everyone I am trying to run jobs in phenix (real space refinement alignment with the other modelling jobs), but the system always crashes, and refinement doesn't complete. This is the structure of ribosome, and I am wondering what to do to get through the refinement. Is there any specific parameters I should be using. I tried to change the processors to 15 for a 20-processor computer. Let me know. Thanks in advance. FYI: There is no error message in the log. Best, Rajnandani ---------------------------------------------------------------------- Rajnandani Kashyap, Ph.D. Postdoctoral Fellow Department of Biochemistry and Molecular Biology Saint Louis University, Antony Lab 1205 Carr Lane, DRC 451 St. Louis, MO 63104 https://orcid.org/0000-0002-9141-1168 -----------------------------------------------------------------------

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Ion placement (anomalous) + occupancy refinement
by miha.pavsic＠fkkt.uni-lj.si 06 Mar '25

06 Mar '25

Hi everyone, I have a dataset from a protein that contains 2 Ca2+ binding sites. The Ca2+ loaded protein was crystallized in the presence of Tb3+ which at one site mostly replaced Ca2+, however at the other site the Tb3+/Ca2+ ratio appears to be much lower (judging from anomalous map; data collected at 1.3 Å wavelength, MR for phasing). The occupancy sum of Tb3+ and Ca2+ at each of the two sites is strongly believed to be 1. While I am aware of the ion placement option in phenix.refine, I am not so sure how to refine the partial occupancies using anomalous data, if possible. Many thanks for any hints, Miha

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AKM in Phenix
by lucas.santosouza＠outlook.com 06 Mar '25

06 Mar '25

Hi everyone, Is there still support for the generation of Average Kick Maps in Phenix? I am using both versions 1.21.2-5419 and the nightly build 2.0rc1-5555. I added kicked=True to the maps.params, but phenix.maps gives me "Unused parameter definitions: maps.map_coefficients.kicked (file "maps.params", line 53)". I also cannot see the "Kicked map" check box in the Create Maps GUI. Cheers, Lucas

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Refine partially occupied ligand in active site containing chloride ions
by Stephen.carr＠rc-harwell.ac.uk 06 Mar '25

06 Mar '25

Dear phenix bb, I am trying to refine a ligand in the active site of my protein where the ligand occupancy is ~50%. The empty active site contains two chloride ions and the residual density from these ions is very prominent when the model is refined with the ligand alone. I would like to refine the model with both the ligand and chloride ions present and have been trying to do this with altLoc flags but so far with no luck. I'm assuming that since the Cl ions more-or-less directly overlay atoms from the ligand positional refinement keeps pushing them out of the density. I'm sure there is a simple way to get around this and I would be grateful for any suggestions. Best wishes, Steve Dr Stephen Carr Research Complex at Harwell (RCaH) Rutherford Appleton Laboratory Harwell Oxford Didcot Oxon OX11 0FA United Kingdom Email stephen.carr(a)rc-harwell.ac.uk tel 01235 567717 This email and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorized recipient of the addressee, please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to this email. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Research Complex at Harwell. There is no guarantee that this email or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. We use an electronic filing system. Please send electronic versions of documents, unless paper is specifically requested. This email may have a protective marking, for an explanation, please see: http://www.mrc.ac.uk/About/informationandstandards/documentmarking/index.htm.

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Program crash
by F.Xavier Gomis-Rüth 05 Mar '25

05 Mar '25

Dear all, I recently upgraded my MacOS to Sequoia 15.3.1 and found that previous phenix jobs that ran without problem suddenly crashed with the installation (phenix-1-21.2-5419) I had since August 2024. So I installed the latest on-built (phenix-2.0rc-5617) but it nonetheless crashed with the message below. Any help would be greatly appreciated. Best, Xavier XGRMAC:cyc3 > Could not import the compiled Python-sander interface.Traceback (most recent call last): File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 8, in <module> run_program(real_space_refine.Program) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/iotbx/cli_parser.py", line 980, in run_program task.run() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 704, in refine_xyz self.minimization_ncs() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 794, in minimization_ncs weight = real_space_weight.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 394, in refine real_space_result = refinery( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 126, in refine minimized = mmtbx.refinement.minimization_ncs_constraints.lbfgs( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 424, in __init__ minimizer = scitbx.lbfgs.run( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 456, in compute_functional_and_gradients t,g = self.target_and_grads_object.target_and_gradients( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 242, in target_and_gradients t_restraints, g_restraints = restraints_target_and_grads( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/mmtbx/refinement/minimization_ncs_constraints.py", line 110, in restraints_target_and_grads ef = restraints_manager.energies_sites( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1524, in energies_sites pair_proxies = self.pair_proxies( File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/Applications/phenix-2.0rc1-5617/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 59.7151 > 50: distance: 0 - 1: 15.382 distance: 1 - 2: 14.133 distance: 1 - 3: 15.077 distance: 4 - 5: 11.010 distance: 5 - 6: 5.064 distance: 5 - 8: 12.166 distance: 6 - 7: 9.252 distance: 6 - 15: 4.656 distance: 8 - 9: 6.568 distance: 9 - 10: 41.112 distance: 9 - 11: 19.959 distance: 10 - 12: 4.365 distance: 11 - 13: 12.611 distance: 12 - 14: 28.654 distance: 13 - 14: 25.314 distance: 15 - 16: 7.291 distance: 16 - 17: 12.341 distance: 16 - 19: 4.354 distance: 17 - 18: 11.820 distance: 17 - 26: 9.661 distance: 19 - 20: 7.438 distance: 20 - 21: 17.074 distance: 20 - 22: 19.126 distance: 21 - 23: 7.637 distance: 22 - 24: 3.434 distance: 23 - 25: 24.169 distance: 24 - 25: 8.875 distance: 26 - 27: 10.037 distance: 27 - 28: 9.377 distance: 27 - 30: 12.844 distance: 28 - 29: 12.437 distance: 28 - 34: 22.926 distance: 30 - 31: 46.409 distance: 31 - 32: 6.849 distance: 31 - 33: 21.459 distance: 34 - 35: 12.375 distance: 34 - 40: 15.635 distance: 35 - 36: 10.511 distance: 35 - 38: 12.461 distance: 36 - 37: 11.525 distance: 36 - 41: 15.668 distance: 38 - 39: 9.083 distance: 39 - 40: 10.922 distance: 41 - 42: 15.925 distance: 42 - 43: 26.537 distance: 42 - 45: 20.600 distance: 43 - 44: 14.038 distance: 43 - 48: 40.043 distance: 45 - 46: 18.721 distance: 45 - 47: 12.152 distance: 48 - 49: 19.936 distance: 49 - 50: 9.210 distance: 49 - 52: 4.170 distance: 50 - 51: 6.051 distance: 50 - 56: 10.707 distance: 52 - 53: 13.486 distance: 53 - 54: 25.122 distance: 53 - 55: 30.977 distance: 56 - 57: 24.676 distance: 57 - 58: 6.469 distance: 57 - 60: 24.810 distance: 58 - 59: 19.649 distance: 58 - 65: 16.713 distance: 60 - 61: 19.749 distance: 61 - 62: 27.563 distance: 62 - 63: 31.258 distance: 63 - 64: 39.081 distance: 65 - 66: 17.034 distance: 66 - 67: 13.877 distance: 66 - 69: 30.087 distance: 67 - 68: 30.739 distance: 67 - 70: 22.852 distance: 70 - 71: 17.537 distance: 71 - 72: 19.009 distance: 71 - 74: 23.249 distance: 72 - 73: 32.627 distance: 72 - 81: 23.614 distance: 74 - 75: 30.150 distance: 75 - 76: 11.440 distance: 75 - 77: 13.841 distance: 76 - 78: 23.906 distance: 77 - 79: 27.669 distance: 78 - 80: 29.196 distance: 79 - 80: 27.009 --

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Cryo_fit installation
by omar.debei＠unipr.it 28 Feb '25

28 Feb '25

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

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Register by Feb. 28th for the West Coast Structural Biology Workshop
by Michael Thompson 21 Feb '25

21 Feb '25

The registration and abstract submission deadlines for the 26th West Coast Structural Biology Workshop are just one week away... Register today, and be a part of this iconic meeting with over 50 years of tradition!! See below for a message about the conference: Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 28, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Postdoc and PhD positions in quantum/protein/electron crystallography. Application deadline March 2nd
by Paulina Dominiak 03 Feb '25

03 Feb '25

Dear Colleagues, We currently have several positions available in my group at the University of Warsaw - both postdoc and PhD. The research project combines quantum crystallography with protein crystallography, focusing on 3DED/microED techniques. We're interested in hearing from researchers with different backgrounds: * Software developers who want to learn crystallography * Protein crystallographers looking to expand their skills * Small-molecule crystallographers experienced with X-ray charge density studies * Researchers familiar with electron crystallography Detailed information about the positions, project description, and application links can be found at: http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/ <http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/> Application deadline: March 2nd, 2025 Please share this opportunity with qualified candidates who might be interested. For additional information, feel free to contact me directly. Best regards, Paulina -- Prof. dr hab. Paulina M. Dominiak Group Leader Electron Density Modelling Group Laboratory for Structural and Biochemical Research (LBSBio) Biological and Chemical Research Centre Department of Chemistry University of Warsaw ul. Zwirki i Wigury 101 02-089 Warszawa, Poland Room: 3.125 E-mail:[email protected] Phone: (48) 22 55 26 714 WWW:http://4xeden.uw.edu.pl

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DEADLINE EXTENDED: 26th West Coast Structural Biology Workshop
by Michael Thompson 03 Feb '25

03 Feb '25

Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025 and Feb. 21, 2025 respectively. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 21, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Re: Uknown non bonded
by Yann Lefrançois.C 30 Jan '25

30 Jan '25

Hi thank you for your reply, I'm not working with ligand, but a complexe. I do not have hydrogen in my model, so it seems I have a bigger problem. [image: image.png] I tried to use PDB_REDO, however i'm using mrc format for my ED map Le jeu. 30 janv. 2025 à 16:39, Georg Mlynek <georg.mlynek(a)univie.ac.at> a écrit : > Hi Yann, can you post a screenshot of the error message? It should be > stated there which are causing problems. > > Very often the problems are hydrogens. So just delete those. One easy > way is to do is to open in coot and when saving there is a tick box > without hydrogens. There are also tools in phenix doing this. > > Also you can submit the pdb to PDB_REDO to check if there are more sever > problems. If PDB_REDO runs then there are no big errors. Then just use > the output for phenix refine. > > And as Xavier wrote ligands also can cause problems. But also there most > times the hydrogens. > > Br, Georg. > > > Am 2025-01-30 um 4:26 PM schrieb yannlefrancoiscopy(a)gmail.com: > > Hello, > > I'm a newbie phenix user, and i was trying to refine a model. > > > > and when i tried to refine it, I got an error message saying that some > atoms had unknown nonbonded interaction. > > > > However, there are no indication to which one are problematic, Any tips > on how to find the problematic one and how to correct them ? > > > > best wishes, > > Yann > > _______________________________________________ > > 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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Uknown non bonded
by yannlefrancoiscopy＠gmail.com 30 Jan '25

30 Jan '25

Hello, I'm a newbie phenix user, and i was trying to refine a model. and when i tried to refine it, I got an error message saying that some atoms had unknown nonbonded interaction. However, there are no indication to which one are problematic, Any tips on how to find the problematic one and how to correct them ? best wishes, Yann

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open position for a 2(+2) year postdoc working on plant sugar and hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 29 Jan '25

29 Jan '25

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of sugar and hormone transport, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 28. Feb. 2025 using the online application system (link above).

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Reminder: Phenix Postdoc Position - Berkeley, California
by Paul Adams 27 Jan '25

27 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.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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About d99
by Roberto Battistutta 24 Jan '25

24 Jan '25

Dear Phenix people, In "New tools for the analysis and validation of cryo-EM maps and atomic models” (ActaD 2018), it is reported that "map sharpening can affect d99 (Fig. 9g) but it is rather insensitive to masking (Fig. 9h).” I have a case where d99 increases a lot with masking, as shown in the screenshot below (from Mtriage). On the other hand, FSC decreases. What does this mean? Can it be attributed to the fact that there is a strong scatterer in the molecule (a heavy atom) that strongly influences the intensity of the map? Are there other possible explanations (preferential orientation for example)? What is the best way to handle such maps? Thank you for the attention. Best, 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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André Mitschler, former crystallography engineer in the BSI department, Strasbourg
by Alexandre OURJOUMTSEV 24 Jan '25

24 Jan '25

Sorry, my previous e-mail left with a wrong subject… Sacha = = = = Dear all, for those (I expect, many of you) who knew André Mitschler, I resubmit the message below. Sad news. It was a great and non-trivial person. With best wishes, Sacha Urzhumtsev = = = = From: Valerie LAMOUR <lamourv(a)igbmc.fr<mailto:[email protected]>> Sent: Friday, January 24, 2025 4:23 PM Subject: André Mitschler, former crystallography engineer in the BSI department André Mitschler est décédé le 5 Décembre, à l’âge de 83 ans. André était un cristallographe expérimental hors pair. Il a débuté en recherche dans le laboratoire du Prof Weiss où il a eu la charge du premier diffractomètre à RX de l’époque. En 1967, a entamé une fructueuse collaboration avec Dino Moras qui a pu bénéficier de son expertise et son adresse expérimentale pour sa thèse de 3e cycle. Leurs liens ne se sont jamais rompus. En 1981 Il a rejoint le laboratoire de cristallographie de Dino, nouvellement créé à l’IBMC. Il y a effectué le reste d’une fructueuse carrière d’ingénieur CNRS qui, en 1994, s’est poursuivie à l’IGBMC, un nouvel institut créé à Illkirch avec un important soutien de l’industrie pharmaceutique. En 1996, il a rejoint le groupe d’Alberto Podjarny, pour travailler dans la détermination de la structure de l’Aldose Reductase humaine. Les cristaux diffractaient à une résolution extrêmement haute (0.6 Angstroms). La mesure des données a demandé des nouveaux développements et l’utilisation des meilleures lignes synchrotron du monde. André était à la hauteur du défi, avec la capacité de passer de longues heures à monter et tester expérimentalement des cristaux. Il pouvait travailler 72 heures d’affilée dans le synchrotron d'Argonne National Lab. Le travail a culminé en 2008, avec la publication d’un mécanisme enzymatique inattendu. En 1999, il a obtenu la médaille de Cristal du CNRS, en reconnaissance de ses travaux en cristallographie expérimentale. André était aussi un passionné de l’histoire militaire, et a fait une carrière dans l’armée jusqu’à rang de colonel dans la cavalerie. Sa passion par la recherche, sa force de travail et son dévouement pour l’excellence expérimentale sont un exemple à suivre par tous les jeunes chercheurs. //// André Mitschler passed away on December 5th at the age of 83. André was an outstanding experimental crystallographer. He began his research career in Professor Weiss's laboratory, where he was responsible for the first X-ray diffractometer at the time. In 1967, he started a fruitful collaboration with Dino Moras, whose doctoral work benefited greatly from André's expertise and experimental skill. Their professional ties endured throughout their lives. In 1981, André joined Dino’s newly established crystallography laboratory at IBMC, where he spent the remainder of a productive career as a CNRS engineer. In 1994, he continued his work at IGBMC, a new institute in Illkirch supported by the pharmaceutical industry. In 1996, André joined Alberto Podjarny’s group to work on determining the structure of human aldose reductase. The crystals diffracted at an exceptionally high resolution (0.6 Å), which required innovative developments and access to the world's most advanced synchrotron beamlines. André rose to the challenge, demonstrating his ability to spend long hours preparing and experimentally testing crystals. He worked tirelessly, including 72-hour shifts at the Argonne National Laboratory synchrotron. This effort culminated in 2008 with the publication of an unexpected enzymatic mechanism. In 1999, André was awarded the CNRS Crystal Medal in recognition of his contributions to experimental crystallography. André was also a military history enthusiast and pursued a parallel career in the army, rising to the rank of colonel in the cavalry. His passion for research, tireless work ethic, and dedication to experimental excellence remain an inspiration for young researchers.

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Phenix Postdoc Position - Berkeley, California
by Paul Adams 24 Jan '25

24 Jan '25

Dear Colleagues, The Phenix team is hiring! We are looking for talented postdoctoral candidates to join the group in Berkeley. Please see the details below, and feel free to pass on to anyone you think might be interested. To access the job posting directly: https://jobs.lbl.gov/jobs/computational-postdoctoral-fellow-6893 Cheers, Paul Berkeley Lab’s (LBNL) Molecular Biophysics and Integrated Bioimaging Division (MBIB) has an opening for a Postdoctoral Fellow to develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. In this exciting role, you will work under the direction of the Deputy Director for this project with primary responsibilities including the development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The goals of the role include the development of automated pipelines for data analysis, structure completion and model validation. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. This will require the organization of results for presentation and viewing by project team members, the wider scientific community, and preparing results for publication in scientific journals. This position has an earliest start date of February 3, 2025. What You Will Do: Develop and implement computational algorithms for structure determination using crystallography and cryo-electron microscopy including: Improved methods for the optimization and completion of models Automated pipelines for data analysis, structure completion, and model validation Apply machine learning methods to problems in crystallography and cryo-electron microscopy. Develop and test new components of the PHENIX software system in collaboration with others. Document software developments. Collaborate with other researchers in the PHENIX program. Summarize research results, publish them in peer-reviewed journals, and contribute to scientific research papers and reports. Contribute to discussions on the determination of future directions. Attend group meetings or conferences/workshops, present status reports, and scientific findings as appropriate. Keep accurate and detailed research notes. What is Required: A recent Ph.D. (within the last 1-2 years) in Computational Crystallography, Computational Cryo-Electron Microscopy, Computational Biology, Bioinformatics, Computational Chemistry or a closely related field. Demonstrated experience in developing computational algorithms for solving problems. Demonstrated experience with computational methods development. Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields. Good programming and mathematical skills, including familiarity with Python and other software development tools. Strong organizational skills including experience maintaining detailed and accurate records of experiment results and analyzed data. Excellent oral and written communication skills including experience organizing/presenting technical reports. Demonstrated interpersonal skills including experience conducting experiments independently and collaborating with a diverse interdisciplinary research team. Desired Qualifications: Experience with machine learning methods, programming with C++, or equivalent object-oriented programming languages. Experience with the practical aspects of crystallography and/or cryo-electron microscopy. Familiarity with macromolecular structure or computational chemistry. -- 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) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.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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