July 2024 - phenixbb - phenix-online.org

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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Research Specialist Position at the University of Illinois to Study Ribosome Structure | POLIKANOV Lab
by Yury Polikanov 21 Apr '25

21 Apr '25

*Research Specialist Position Available, Department of Biological Sciences, University of Illinois at Chicago - Polikanov Lab* *The Polikanov Laboratory in the Department of Biological Sciences at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the Research Specialist position to study the structure and function of the bacterial ribosome.* For fullest consideration, please submit an application and cover letter describing your scientific interests and how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group at https://uic.csod.com/ux/ats/careersite/1/home/requisition/7573?c=uic *Position Summary:* The research in the Polikanov Laboratory at UIC is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. This position is involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. Expected contributes to the design and delivery of research projects and collaborates with researchers to develop, execute, and interpret research projects. Performs complex laboratory and data collection techniques. *Duties & Responsibilities:* - Perform research relevant to the assigned projects; - Isolate, purify, and crystallize bacterial ribosomes; - Purify all additional components necessary for the crystallization experiments, such as recombinant proteins, tRNAs; - Collect X-ray diffraction data from the ribosome crystals at the APS and NSLS-II Synchrotrons; - Perform structural data analysis; - Coordinate, analyze, and document results for publication; - Directly participate in writing papers and grants based on the experimental data; - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry; - Attend weekly group meetings and journal club seminars. - Perform other related duties and participate in special projects as assigned. *Minimum Qualifications:* - A bachelor’s degree in chemistry, biochemistry, biophysics, or a related field is required. - A master’s degree in chemistry, biochemistry, biophysics, or a related field is preferred. - A minimum of 3 years related research experience. - Possesses and applies comprehensive knowledge of research principles, concepts, practices, and methods. - Proficient in standard molecular biology and biochemistry lab techniques, such as protein expression, and purification *Preferred Qualifications:* - Experience in structural biology (cryo-EM or X-ray crystallography); - Experience in RNA biology, ribosome, and/or protein synthesis fields. *About the University of Illinois Chicago:* UIC is among the nation’s preeminent urban public research universities, a Carnegie RU/VH research institution, and the largest university in Chicago. UIC serves over 34,000 students, comprising one of the most diverse student bodies in the nation and is designated as a Minority Serving Institution (MSI), an Asian American and Native American Pacific Islander Serving Institution (AANAPSI) and a Hispanic Serving Institution (HSI). Through its 16 colleges, UIC produces nationally and internationally recognized multidisciplinary academic programs in concert with civic, corporate and community partners worldwide, including a full complement of health sciences colleges. By emphasizing cutting-edge and transformational research along with a commitment to the success of all students, UIC embodies the dynamic, vibrant and engaged urban university. Recent “Best Colleges” rankings published by U.S. News & World Report, found UIC climbed up in its rankings among top public schools in the nation and among all national universities. UIC has nearly 260,000 alumni, and is one of the largest employers in the city of Chicago. *The University of Illinois System is an equal opportunity employer, including but not limited to disability and/or veteran status, and complies with all applicable state and federal employment mandates. Please visit Required Employment Notices and Posters <https://www.hr.uillinois.edu/cms/one.aspx?portalId=4292&pageId=5705> to view our non-discrimination statement and find additional information about required background checks, sexual harassment/misconduct disclosures, COVID-19 vaccination requirement, and employment eligibility review through E-Verify. **The university provides accommodations to applicants and employees. Request an Accommodation <https://jobs.uic.edu/request-and-accomodation/>*

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Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 31 Oct '24

31 Oct '24

Hi Andrea, in your case, phenix.refine seems to fill bulk solvent into volumes that are not actually filled by solvent. It might help to optimize the mask, see https://phenix-online.org/documentation/reference/refinement.html#bulk-solv… "6. Mask parameters". Best, Kay -- Kay Diederichs http://strucbio.biologie.uni-konstanz.de email: Kay.Diederichs(a)uni-konstanz.de Tel +49 7531 88 4049 Fachbereich Biologie, Universität Konstanz, Box M647, D-78457 Konstanz This e-mail is digitally signed. If your e-mail client does not have the necessary capabilities, just ignore the attached signature "smime.p7s".

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Ordered solvent in phenix.refine
by Oliver H. Weiergräber 11 Sep '24

11 Sep '24

Hello, after switching from version 1.20 to 1.21, I noticed that the updated list of waters generated by the ordered_solvent option in phenix.refine is no longer numbered sequentially; it seems a final re-numbering step is now skipped. Is this intentional? Of course it can be advantageous to keep waters from changing their numbers, e.g. if they are part of occupancy groups. On a related note, is there a mechanism to protect certain "important" waters from being deleted while all the rest is updated as usual? One obvious option would be a dedicated chain ID, but afaik phenix.refine accepts a chain ID for output but not for input waters ... Best regards, Oliver ================================================== Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ==================================================

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Presence of negative density in Sim Omit map
by Renuka Kadirvelraj 12 Aug '24

12 Aug '24

Presence of negative density in Sim Omit map Hi Phenixbb, We would appreciate your advice regarding an odd problem that has cropped up with one of our crystal structures. We have a protein structure in space group P6(3)22 at 2.1 A resolution and in the final refinement stages with Rwork of 0.20 and Rfree of 0.22. When we ran simulated annealing to rebuild an outlier Lysine residue in a loop, the Sim Omit map showed the positive density expected from the omission of the loop (contour level 3 sigma, colored green in attached pics). However, flanking the positive density, there is a complimentary negative density (in red). We are puzzled as to the cause of the appearance of the negative density. Can you help us? Many thanks, Renu --------------------------------------------- Renu Kadirvelraj, Ph.D. Research Scientist A428, Biochemistry and Molecular Biology 120, East Green Street University of Georgia Athens, GA 30602 Tel: (706) 583 0303

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phenix.refine command line: what to change on the subsequent def file to point to the desired input pdb
by Alejandro Buschiazzo 02 Aug '24

02 Aug '24

Dear phenix users/developers Some time ago there were several modifications on the names/specifications of important parameters/options (such as miller_array for structure factor files, etc) Running phenix.refine by command lines (no gui) is my favorite, and I am now running into several difficulties: 1- what’s the difference between miller_array and default_miller_array; or model and default_model? 2- what’s the precise definition of phil_files and default_phil? What to change if I manually edit my .eff? 3- how should I use the new automatically created .def file for subsequent refinement cycles after I’ve manually rebuilt (I need to point to the new pdb input file: I usually screw this up, can’t seem to use the newly created .def as my starting instructions file anymore, it complains that I have problems in the right definition of the input pdb, or too many models...) 4- I often fall into a loop where by default newly created .eff files include a dry_run=true option (e.g. when I deliberately tell phenix.refine to overwrite previous .eff files) Thanks a lot for clarifying on these issues: and sorry, for I couldn’t find obvious answers to them in the documentation (probably my fault!!) Also, I am using phenix v 1.21.1-5286 (on a Sonoma MacOS laptop) With best wishes Alejandro

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Reminder: Macromolecular Crystallography - CSHL Course October 2024
by Paul Adams 30 Jul '24

30 Jul '24

Dear Colleagues, We have extended the deadline for the course applications to August 9th. A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 13-29th this year (pleased see below for more details). This comprehensive course is an outstanding place to learn both the theoretical and practical aspects of macromolecular crystallography. There are extensive lectures and practical sessions from world recognized experts in crystallization, data collection, data processing, structure solution, refinement, and validation. The goal of the course is for researchers who have had some exposure to structural biology to become experts in crystallography. This is an experience in macromolecular crystallography learning that cannot be found anywhere else, and the student/teacher ratio is often 1:1. Please follow the link below to the course web site. In particular, please note the information about the various fellowships, scholarships, and stipends that are available. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road, Cold Spring Harbor, NY 11724 -- 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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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 17 Jul '24

17 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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