- phenixbb - phenix-online.org

Instruct-ERIC Workshop on “Sample Preparation for Single Particle Analysis by Cryo-Electron Microscopy”
by Jose Artur Brito 24 Jul '24

24 Jul '24

Dear Colleagues, We hereby announce a 4-day workshop on "Sample Preparation for Single Particle Analysis by Cryo-Electron Microscopy" [1 [1]]. The course is funded by Instruct-ERIC and will be held at the Iberian Nanotechnology Laboratory (Braga, Portugal), between the 7th and 10th of October this year. The Workshop is aimed primarily at Ph.D students and young Post-Doctoral researchers, is set to provide in-depth training on sample preparation for single particle analysis (SPA) by cryo-electron microscopy (cryo-EM), and is hosted by a team of experts from ITQB NOVA [2 [2]], INL [3 [3]], CNB-CSIC [4 [4]], i3S [5 [5]], and SciLifeLab [6 [6]]. Participants will engage in a comprehensive course featuring a blend of lectures and hands-on tutorials. The lectures will delve into the principles of SPA, covering theoretical and practical aspects of preparing biological samples for negative staining, quality assessment and data collection. The workshop will highlight recent advancements in protein production and stabilization, as well as the latest technological innovations in grid preparation and sample manipulation. Attendees are encouraged to bring their samples, providing a unique opportunity to apply newly acquired skills to their specific research needs. Practical sessions will offer hands-on experience with vitrification using a plunge-freezing device and optimizing grids for sample screening with a cryo-transmission electron microscope (TEM). Participants will be limited to 12 to allow a closer interaction between the participants and the tutors. Candidate selection will be based on a short CV, a motivation letter from the Applicant, and a recommendation letter from the Supervisor. Registration deadline is August 19, 2024, and can be done at the following link: https://www.events.inl.int/instruct-eric-workshop Registration fee is 250Eur for Academics and 500Eur for Non-Academic, and includes accommodation, lunches, coffee-breaks and social dinner. Please feel free to contact us if you have any question. On behalf of the organizing team, hoping to see you in Braga, Jose Artur Brito - ITQB NOVA [1] https://instruct-eric.org/events/16th-instruct-eric-hands-on-workshop-sampl… [2] https://www.itqb.unl.pt/ [3] https://www.inl.int/ [4] http://www.cnb.csic.es/index.php/en [5] https://www.i3s.up.pt/ [6] https://www.scilifelab.se/ -- Links: ------ [1] https://instruct-eric.org/events/16th-instruct-eric-hands-on-workshop-sampl… [2] https://www.itqb.unl.pt/ [3] https://www.inl.int/ [4] http://www.cnb.csic.es/index.php/en [5] https://www.i3s.up.pt/ [6] https://www.scilifelab.se/

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AutoBuild trouble
by Atsushi Nakagawa 17 Jul '24

17 Jul '24

Dear all, I cannot run AutoBuild from GUI both on dev-5383 and 1.21.1. The process terminated with the following message during the process of AutoBuild_multiple_models. Job terminated with at new message window shown below, ********************************************************************************* Failed to carry out AutoBuild_multiple_models: ‘module’ object has no attribute ‘run_autobuild’ ********************************************************************************* Is there any problem on my installation or parameters? AutoBuild runs with the older version (1.20). Thank you for your help. Atsushi

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running phenix
by khkim＠korea.ac.kr 16 Jul '24

16 Jul '24

Dear colleagues, Running phenix received an error (below). Status window indicates "You appear to have another session of PHENIX running already (hostname...), which has locked your project database". I had tried to change project directories. Many thanks. Error in sys.excepthook: Traceback (most recent call last): File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 898, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/usr/local/bin/phenix-1.20.1-4487/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/bin/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/usr/local/bin/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 74, in __init__ wx.App.__init__(self, 0) File "/usr/local/bin/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/usr/local/bin/phenix-1.20.1-4487/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/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 120, in OnInit self.start_gui() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 191, in start_gui self.launch_main() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 507, in launch_main frame = PhenixGUI() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 51, in __init__ self.setup_panels() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 171, in setup_panels self.refresh_project_list() File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 360, in refresh_project_list self.add_projects(group_name=current_group) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/wxGUI2/Home/Main.py", line 352, in add_projects group_name=group_name) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/phenix/tracking/project_db.py", line 72, in get_project_summaries group_id = self.get_group_id_by_name(to_unicode(group_name)) File "/usr/local/bin/phenix-1.20.1-4487/modules/phenix/phenix/tracking/project_db.py", line 608, in get_group_id_by_name assert (name in [None, "None", "All", "All groups"]) AssertionError

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Re: [phenixbb] C-beta outliers - it is 1.20 version issue
by Andrea Smith 13 Jul '24

13 Jul '24

Thank you everyone for suggestions. As it turns out, there is a problem in the 1.20 phenix version that I was using. I updated to 1.21 as suggested by Dorothee, repeated one refinement job and had no more C-beta outliers, so I am guessing I will not have them in other models either. Best, Andrea On Friday, June 14, 2024 21:16 CEST, Nigel Moriarty <nwmoriarty(a)lbl.gov> wrote: Andrea Can you send me files off-line? Cheers Nigel ---Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated BioimagingLawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Email : NWMoriarty(a)LBL.govWeb : CCI.LBL.govORCID : orcid.org/0000-0001-8857-9464 On Thu, Jun 13, 2024 at 9:59 AM Andrea Smith <andrea.smith(a)uochb.cas.cz> wrote: Hi all, I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is). Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement? Thanks, Andrea _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

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refine and Table 1
by Andrea Smith 09 Jul '24

09 Jul '24

Hi everyone, * I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before. * I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message: "a model is referenced in the phil which is not in the data manager". What does this mean? * I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.) Is all of this caused by the changes the ChimeraX's dssp command did to my pdb? Thank you, Andrea Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.

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Re: [phenixbb] refine and Table 1
by Andrea Smith 09 Jul '24

09 Jul '24

Hi Yi Min, my problem number 2 was indeed resolved after I restarted my system. Thank you, Andrea On Tuesday, July 09, 2024 14:47 CEST, Yi Min Ng <yimin_ng(a)outlook.com> wrote: Hi Andrea, I am still new to this field and I have previously came across your #2 problem when trying to generate Table 1 using Phenix. I don't know exactly what was causing the problem but I somehow managed to generate Table 1 after restarting the GUI. You might want to try restarting the software if you haven't tried so? Hope some experts will be able to help you with the problems soon 🤞 Best wishes,Yi Min ______________________________________________________________________________ From: phenixbb-bounces(a)phenix-online.org <phenixbb-bounces(a)phenix-online.org> on behalf of Andrea Smith <andrea.smith(a)uochb.cas.cz> Sent: 09 July 2024 14:25 To: phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> Subject: [phenixbb] refine and Table 1 Hi everyone, * I have an issue with phenix.refine being unable to open generated pdb and mtz files in coot after refinement. It claims “ERROR: refinement output file not found!” This started happening after I opened the model in ChimeraX and used dssp command and then saved model as pdb that I used for further refinements. The files generated from phenix.refine actually exist, but instead of just being named e.g. myprotein_refine20.pdb they are called myprotein_refine19_refine020.pdb (yes there is an extra refine and an extra 0). This has never happened to me before. * I am also trying to generate "Table 1" for journal. I input my pdb into model file and mtz into reflection file. When I click Run, I get an error message: "a model is referenced in the phil which is not in the data manager". What does this mean? * I also tried to validate my model using pdb validate server, but when I upload cif files generated as output from phenix.refine, the server shows “Error processing uploaded files…Click to reload”. (However, when I use the Get PDB validation report task in phenix, I get a validation report pdf with no issues.) Is all of this caused by the changes the ChimeraX's dssp command did to my pdb? Thank you, Andrea Running Phenix 1.21-5207 from GUI on Ubuntu 20.04.3.

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Computations Crystallography Newsletter (CCN) Submissions
by Nigel Moriarty 01 Jul '24

01 Jul '24

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 22 JAN 2024. Please consider writing an article of general interest to the community. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, 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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real_space_refine is un-glycosylating my protein
by robert＠oeffner.net 01 Jul '24

01 Jul '24

Hi, I am trying to do a refinement with phenix.real_space_refine (RSR) on an EM map with a protein and a known ligand (NAG is the monomer code). In the pdb file supplied the C1 atom in the NAG molecule is positioned nicely in the EM density at a distance of 1.38Å from a ND2 atom in an ASN residue of the protein. The O1 atom in the NAG molecule is not present suggesting there should be a covalent bond here I believe. Both ASN and the NAG molecule have the same chainID. The problem is that RSR moves the sugar away even though I have used command line options such as pdb_interpretation.automatic_linking.link_carbohydrates=True or even pdb_interpretation.automatic_linking.link_all=True. The atoms end up at an un-bonded distance of 2.85Å from each other after refinement to the point that one of them is poking out of the density. Are my phil parameters incorrect? I noticed that I don't get an error message if I misspell say pdb_interpretation.automatic_linking.link_carbohydrates to pdb_interpretation.automatic_linking.link_carbohydrate. RSR still runs to completion so I'm wondering if it actually interprets the PHIL parameter at all. Another peculiarity is that the log file comments that NAG is an unusual residue rather than stating it is a well-known carbohydrate. If anyone on here knows how to compel phenix RSR into creating automatic links to carbohydrates suggestions would be much appreciated. Many thanks, Rob

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Extra map coefficients in 1.21.1-5286
by Dr. Kevin M Jude 29 Jun '24

29 Jun '24

In my latest installed version of phenix, I find that additional, redundant map coefficients are being added to the output mtz file. I compare an identical refinement originally run in 1.21rc1_5058 and then repeated in 1.21.1-5286. *_filled and *_4 appear to be redundant, and the final sets of coefficients (*_no_fill and *_5), appear to include the test set reflections, even though I’ve selected Exclude R-free set from map coefficients in the gui. This is a little bit confusing, but primarily an annoyance because auto-open mtz in coot can’t figure out which coefficients to use. 1.21rc1_5058 Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -42 41 0 100.00 -3.3 16.0 52.38 1.96 H H 2 NONE 0 28 0 100.00 10.3 10.3 52.38 1.96 H K 3 NONE 0 27 0 100.00 10.3 10.3 52.38 1.96 H L 4 NONE -94.4 13012.5 269 98.44 85.01 85.49 45.63 1.96 J I-obs 5 NONE 0.2 337.4 269 98.44 4.44 4.44 45.63 1.96 Q SIGI-obs 6 NONE 0.0 1.0 269 98.44 0.05 0.05 45.63 1.96 I R-free-flags 7 NONE 10.2 2509.6 321 98.14 129.94 129.94 36.90 1.96 F F-obs-filtered 8 NONE 1.3 35.8 321 98.14 10.11 10.11 36.90 1.96 Q SIGF-obs-filtered 9 NONE 0.1 2250.2 321 98.14 125.18 125.18 36.90 1.96 F F-model 10 NONE -180.0 180.0 321 98.14 4.35 89.81 36.90 1.96 P PHIF-model 11 NONE 0.0 2971.8 1165 93.23 117.81 117.81 36.90 1.96 F 2FOFCWT 12 NONE -180.0 180.0 1165 93.23 4.65 89.89 36.90 1.96 P PH2FOFCWT 13 NONE 0.0 2971.8 0 100.00 117.93 117.93 52.38 1.96 F 2FOFCWT_filled 14 NONE -180.0 180.0 0 100.00 4.85 90.05 52.38 1.96 P PH2FOFCWT_filled 15 NONE 0.0 738.9 1165 93.23 46.86 46.86 36.90 1.96 F FOFCWT 16 NONE -180.0 180.0 1165 93.23 4.75 90.35 36.90 1.96 P PHFOFCWT 1.21.1-5286 Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -42 41 0 100.00 -3.3 16.0 52.38 1.96 H H 2 NONE 0 28 0 100.00 10.3 10.3 52.38 1.96 H K 3 NONE 0 27 0 100.00 10.3 10.3 52.38 1.96 H L 4 NONE -94.4 13012.5 269 98.44 85.01 85.49 45.63 1.96 J I-obs 5 NONE 0.2 337.4 269 98.44 4.44 4.44 45.63 1.96 Q SIGI-obs 6 NONE 0.0 1.0 269 98.44 0.05 0.05 45.63 1.96 I R-free-flags 7 NONE 10.3 2535.0 321 98.14 131.25 131.25 36.90 1.96 F F-obs-filtered 8 NONE 1.3 36.1 321 98.14 10.21 10.21 36.90 1.96 Q SIGF-obs-filtered 9 NONE 0.0 2261.4 321 98.14 126.66 126.66 36.90 1.96 F F-model 10 NONE -180.0 180.0 321 98.14 3.96 89.82 36.90 1.96 P PHIF-model 11 NONE 0.0 3119.6 1165 93.23 119.71 119.71 36.90 1.96 F 2FOFCWT_1 12 NONE -180.0 180.0 1165 93.23 4.33 89.89 36.90 1.96 P PH2FOFCWT_1 13 NONE 0.0 3119.6 0 100.00 119.85 119.85 52.38 1.96 F 2FOFCWT_filled 14 NONE -180.0 180.0 0 100.00 4.44 90.05 52.38 1.96 P PH2FOFCWT_filled 15 NONE 0.0 780.4 1165 93.23 45.28 45.28 36.90 1.96 F FOFCWT_2 16 NONE -180.0 180.0 1165 93.23 4.21 90.36 36.90 1.96 P PHFOFCWT_2 17 NONE 0.0 3119.6 0 100.00 119.74 119.74 52.38 1.96 F 2FOFCWT_4 18 NONE -180.0 180.0 0 100.00 4.60 90.01 52.38 1.96 P PH2FOFCWT_4 19 NONE 0.0 3119.6 321 98.14 119.56 119.56 36.90 1.96 F 2FOFCWT_no_fill 20 NONE -180.0 180.0 321 98.14 4.40 89.94 36.90 1.96 P PH2FOFCWT_no_fill 21 NONE 0.0 780.4 321 98.14 45.68 45.68 36.90 1.96 F FOFCWT_5 22 NONE -180.0 180.0 321 98.14 4.12 90.23 36.90 1.96 P PHFOFCWT_5 Best wishes Kevin -- 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 Phone: (650) 723-6431<tel:%28650%29%20723-6431>

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Postdoctoral Job Position in Infectious disease and Small Angle X-ray Scattering
by Susan Tsutakawa 26 Jun '24

26 Jun '24

Dear fellow structural biologists, I would appreciate it if you could forward this message to any graduate students that might be interested. We have an opening for a Postdoctoral Fellow to use small angle X-ray scattering (SAXS) on global health problems and biopreparedness in response to infectious disease work at the SIBYLS <http://bl1231.als.lbl.gov/> Beamline in the Advanced Light Source Synchrotron (ALS) at Lawrence Berkeley National Laboratory (LBNL) In this exciting role, you will work with a multi-disciplinary team of scientists as part of the ArpaH program <https://arpa-h.gov/>, structurally characterizing purified proteins from pandemic-potential organisms and relevant antibodies. The primary technique used will be Small Angle X-ray Scattering, which provides distance information that can reflect protein conformations and complexes in solution. You will work with a team to develop portable instrumentation to enable high throughput SAXS sample handling that can work at other synchrotrons. Through this work, you will develop ties to other national laboratories and within Berkeley Lab, specifically within the National Energy Research Scientific Computing Center (NERSC <https://www.nersc.gov/>), a division within the Computing Sciences Area’s <https://cs.lbl.gov/>. Prior experience in structural biology, protein biochemistry, and basic programming would be advantageous. Experience in SAXS is not a requirement. For more details. please see https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=102111 This position has an anticipated start date of September 1, 2024. LBNL is located in the San Francisco Area in Berkeley, CA. Sincerely, Susan Tsutakawa Head of Structural Biology Molecular Biophysics and Integrated Bioimaging Biosciences Area Lawrence Berkeley National Laboratory.

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Multiple postdoctoral and Ph.D. positions at IBS (Grenoble)
by Elke De Zitter 26 Jun '24

26 Jun '24

Dear all, We have four immediate openings for postdoctoral researchers and one opening for a Ph.D. student in the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The first postdoctoral project focuses on the development and optimization of bio-scavengers targeting toxic compounds. The researcher with use time-resolved crystallography and in silico design methodologies. Interested candidates can find more information at [ https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for… | https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for… ] (application deadline: 12/07/2024 ). In the second postdoctoral project, the researcher will study the binding of toxic compounds to their physiological target and subsequent chemical reactivation via time-resolved crystallography. The third postdoctoral project is focused on the development of an experimental approach for the determination of the photoinduced structural dynamics of photosensitive biomolecules both in vitro and in cell using time-resolved X-ray scattering techniques. More information and the application procedure can be found on [ https://emploi.cnrs.fr/Offres/CDD/UMR5075-VALLAN-024/Default.aspx?lang=EN | https://www.ibs.fr/en/careers/job-offers/two-year-postdoctoral-position-for… ] (application deadline 30/06/2024). In the fourth postdoctoral project, the researcher will apply serial diffraction techniques (SSX, SFX, SED) to structurally study natural and recombinant protein nanocrystals Last, a 3-year funded PhD fellowship is available to explore the structural dynamics of the orange carotenoid protein by means of time-resolved serial crystallography. Applicants for the postdoctoral positions must have obtained a Ph.D. in structural biology, biophysics, biochemistry, physics, chemistry, or a related field. The candidates must show a track-record of publications in peer-reviewed journals. Applicants for the Ph.D. position are expected to have a master's degree in one of the above mentioned fields. All candidates are expected to be proficient in English and highly motivated to learn new skills. The candidates need to be a good team player as well as being capable of working independently. For inquiries regarding the positions and application processes, please contact Elke De Zitter ( [ mailto:[email protected] | elke.de-zitter(a)ibs.fr ] ), Martin Weik ( [ mailto:[email protected] | martin.weik(a)ibs.fr ] ), Giorgio Schiro ( [ mailto:[email protected] | giorgio.schiro(a)ibs.fr ] ) or Jacques-Philippe Colletier ( [ mailto:[email protected] | jacques-philippe.colletier(a)ibs.fr ] ) Best regards, Martin, Giorgio, Jacques-Philippe and Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zitter(a)ibs.fr

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Hardware migration
by Billy Poon 18 Jun '24

18 Jun '24

Hi everyone, We are in the process of migrating these bulletin boards to new hardware over the next few weeks. I will make another post once the migration is completed. Nothing will be changed until then. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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Test post
by Billy Poon 18 Jun '24

18 Jun '24

This is a test message using the new hardware. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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C-beta outliers
by Andrea Smith 14 Jun '24

14 Jun '24

Hi all, I am running Phenix v. 1.20.1-4487 on Windows and I keep on getting C-beta outliers of methionine residues after phenix.refine (happened in different data from two different proteins). Even if I correct the methionines in Coot (and they fit perfectly in the density), I get the outliers at the end of refinement again (while these outliers don't fit the density and I can see a green difference map where the C-beta is). Why is this? Is there a way to tell phenix.refine not to move a specific amino acid during refinement? Thanks, Andrea

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Help with Phenix/Rosetta Interface Installation
by Lucas Souza 14 Jun '24

14 Jun '24

Dear all, I have been trying to install rosetta (both release 371 and 20221.16.61629)/phenix (1.21.1-5286) interface in Ubuntu 24.04, but with no success at all. Both Rosetta installation and "rosetta.build_phenix_interface" ends up with no erros. But, when I run "rosetta.run_tests" or try to "phenix.rosetta_refine" I always get the error below: ------- /Generating 2 models on 1 processors... / /DEBUG dumping error message ERROR: Rosetta exited with status 139 stderr output: AN INTERNAL ERROR HAS OCCURED. PLEASE SEE THE CONTENTS OF ROSETTA_CRASH.log FOR DETAILS. Segmentation fault (core dumped) Traceback (most recent call last): File "/home/lucas/pckg/phenix-1.21.1-5286/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 315, in <module> run(sys.argv[1:], create_dir=True) File "/home/lucas/pckg/phenix-1.21.1-5286/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 198, in run debug=params.output.debug) File "/home/lucas/pckg/phenix-1.21.1-5286/modules/phenix/phenix/rosetta/refine.py", line 329, in __init__ self.run_jobs() File "/home/lucas/pckg/phenix-1.21.1-5286/modules/phenix/phenix/rosetta/refine.py", line 403, in run_jobs check_result(result) File "/home/lucas/pckg/phenix-1.21.1-5286/modules/phenix/phenix/rosetta/refine.py", line 394, in check_result raise RuntimeError("Aborted due to error in job %d." % result.job_id) RuntimeError: Aborted due to error in job 1./ /Something tells me this is related to the drop of support to Python2 in the new Ubuntu release, but I could not figure out what exactly is the issue. I uploaded both stdout and ROSETTA_CRASH.log in this email./ ------- If anyone can help me with this issue, I would be very happy. Thank you all! Lucas

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(IUCr) The evolution of raw data archiving and the growth of its importance in crystallography
by John R Helliwell 12 Jun '24

12 Jun '24

Dear Colleagues, Our article on this topic, which I imagine will be of keen interest, published this afternoon, is available open access from this weblink:- https://journals.iucr.org/m/issues/2024/04/00/lt5067/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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ADP-BEF-link.cif
by Heidi Schubert 10 Jun '24

10 Jun '24

Hi AAA ATPase modelers Could anyone send me the .cif file to define the link between ADP and a BeFx ion? I’m hoping this has not only the revised angle/bond info between O3B and Be but also the new angle between the Be and Fs different from the planar simple ion. AND, for my hexamer I assume the apply_link.def file then just reads with repetitive 5-line groups: refinement.pdb_interpretation.apply_cif_link { data_link = ADP-BEF residue_selection_1 = chain A and resname ADP and resseq 901 residue_selection_2 = chain A and resname BEF and resseq 902 } Where I change out the chain name but keep calling them residues_selection1 and 2? Many thanks Heidi Heidi Schubert Research Professor Department of Biochemistry University of Utah Rm 116 BPRB 20 S 2030 E Salt Lake City, UT 84112 heidi(a)biochem.utah.edu<mailto:[email protected]> 801-585-9776

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high and low resolution in Phenix 1.21.1-5286-000
by Dominik Oberthuer 30 May '24

30 May '24

Hi, because of an update to Sonoma, I also had to update to Phenix 1.21.1-5286-000. When I'm running phenix.refine from the GUI, use an MTZ with resolution e.g. from 1.65 - 51A, use "High resolution" and "Low resolution" to refine against a specific range of data, phenix.refine does not cut off the data beyond the limits set there, but instead takes all of the data. For sure, I cut the MTZ before, but many times it is about trying out which data to include and not include and this is not really how it should be... Is this known? Is there any way to solve this issue? Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

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NIGMS Mature Synchrotron Program Evaluation
by Paul Adams 20 May '24

20 May '24

Dear Colleagues, Apologies for the US-centric posting, but I think this is of interest to many of the bulletin board subscribers who make use of synchrotron facilities in the US. NIH is seeking feedback on the Mature Synchrotron Program: https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html This program supports synchrotron-based user resources where the technologies are at an advanced level, including Macromolecular Crystallography, Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based techniques that generate important data, with an emphasis on structural biology. Responses to the RFI will be accepted through 6/17/2024. All comments will be anonymous and should be submitted electronically via a web form at: https://www.research.net/r/P30_RFI As the Director of one of the resources it has been suggested that I help make the community aware of the RFI, so there is the opportunity to provide feedback in a timely manner. Feel free to pass this on to any of your colleagues who may be interested. Cheers, Paul -- 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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"<" symbol in reflection mmcif status column
by Kreitler, Dale 17 May '24

17 May '24

Looking at some output reflection cif files from phenix.refine I'm wondering what does "<" mean in the status column and why would F_calc_with_sovlent structure factors also be missing for these reflections? In some cases I can see it coincides with unobserved reflections, but this doesn't seem consistent. Any insight or links to documentation that describe these values would be much appreciated. Thank you, Dale loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent ... 30 0 48 65.2227 18.9183 72.4766 0 5.77152 -2.25565e-14 3 o 77.6435 1.95165e-15 30 0 49 206.068 7.45891 200.645 120 ? ? 19 < ? ? 30 0 50 33.324 17.5773 1.10423 -120 0.328059 -120 10 o 0.916822 -120 30 0 51 23.7705 14.8724 10.7438 180 2.40893 1.88332e-14 6 o 16.3173 180 ... 32 7 2 ? ? 11.4163 118.276 ? ? 5 < ? ? 32 7 3 ? ? 52.373 -121.74 ? ? 10 < ? ? 32 7 4 ? ? 33.1269 -26.1149 ? ? 3 < ? ? 32 7 5 ? ? 106.054 -86.2146 ? ? 19 < ? ? ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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ADP refinement in phenix.real _space_refine
by Luca Pellegrini 16 May '24

16 May '24

While refining a protein-DNA complex in a cryoEM map (~2.5-7A), I have noticed the following behaviour of ADP refinement: - If NCS is on for the protein chains, no ADP refinement of the DNA takes place. - If NCS is off, ADP refinement behaves oddly: one strand of dsDNA is refined with atomic ADPs, the other strand with group ADPs (one per nucleotide). The group ADPs take up unphysical values (lower ADPs in poor map regions), whereas the atomic ADPs look sensible. - To get the ADP refinement of DNA to behave normally, I need to both leave NCS out and set nproc=1 explicitly (haven’t tried other values). I wonder if any of this has been seen before or am I not doing this correctly? Phenix-dev-5330 iMac, Catalina 10.15.7, 8-core Intel i9 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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ligand links
by Heidi Schubert 14 May '24

14 May '24

Hi, Do you think you can link one ligand to two other molecules. (one NON-POLYMER and one peptide). I guess my other option is to create a new ligand. I assumed you pre-deleted the atoms that are supposed to be deleted in the link? I did delete them and it complained and I put them back in and it’s complaining. Pretty similar errors, but I’m wondering if it’s just the second link that’s causing problems. I’ve got files PNS.cif ACE.cif PNS-SER.cif ACE-PNS.cif apply_link_ACE-PNS.def apply_link_PNS-SER.def Heidi [A screenshot of a computer error Description automatically generated]

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Error upon Phenix installation - Manjaro WSL2
by Nicolas Caramello 03 May '24

03 May '24

Dear PhenixBBers, I call upon your wisdom because I recently tried to install Phenix 1.20 on a windows subsystem for linux distribution of Manjaro (Archlinux based) and have failed with the following error : ========================================================================== Phenix Installation version: 1.20.1-4487 machine type: intel-linux-2.6-x86_64 OS version: 5.15.146.1-microsoft-standard-WSL2 destination: /home/my_machine/phenix-1.20.1-4487 # of processors: 20 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 268, in <module> installer(sys.argv[1:]).install() File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary self.reconfigure(log=log) File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/home/my_machine/phenix-installer-1.20.1-4487-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/home/my_machine/phenix-1.20.1-4487/conda_base/bin/python /home/my_machine/phenix-1.20.1-4487/modules/cctbx_project/libtbx/configure.py --current_working_directory /home/my_machine/phenix-1.20.1-4487/build --command_version_suffix 1.20.1-4487 phenix phaser phasertng solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda' failed with exit code 127 Trying to install Phenix 1.21 has produced the same error. I have not managed to solve this, regardless of whether I was running the installation command with sudo privileges or as root. For context, I successfully installed Phenix 1.20 on the same machine and same distribution 6 months ago, but had to reinstall everything since and it does not work anymore now. Have you heard of such an error? Do you have a hint on how to fix it? Best regards, Nicolas Caramello PhD student Structural Biology Group - ESRF /Institut für Nanostruktur/- /und/ Festkörperphysik- Universität Hamburg

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ccp4 thread: "what happened to Molprobity"
by Pavel Afonine 01 May '24

01 May '24

Hi All, I hope someone from Molprobity end reads CCP4 mailing list where people report issues with Molprobity (server and from within Phenix). Just in case this needs someone's attention. Pavel

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on the criteria for outliers, phenix.molprobity and wwPDB validation
by Jorge Iulek 29 Apr '24

29 Apr '24

Hi all, I had already noticed that outliers spotted by phenix with its validation tool, with the nice feature to carry one straight to the "suspicious" residue in a coot session for visual inspection, differs a bit from what comes spotted from wwPDB validation, generally the latter spotting some few more residues. To one current structure, which at low resolution, I notice there is a bit larger difference between the number of spotted residues. I see from wwPDB validation, molprobity is also used to spot outliers for many of the analyses. I see the current molprobity version used is 4.02b-467, but I could not yet devise the molprobity version used by phenix. Of course, there would also be the "library" used in each case to spot the outliers. Maybe someone ever listed what is considered in each case, and their differences, or a link to that is welcome for me. What would be the best criteria for spotting is of course a good discussion. But a superficial question I would make is if there is a way to make phenix.molprobity output to resemble the one from wwPDB validation, at least the ones accounted by molprobity? Jorge

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