March 2024 - phenixbb - phenix-online.org

Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 06 Jun '26

06 Jun '26

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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Research Specialist Position at the University of Illinois to Study Ribosome Structure | POLIKANOV Lab
by Yury Polikanov 06 Jun '26

06 Jun '26

*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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RapiData at SSRL 2024
by Smith, Clyde 22 Jan '26

22 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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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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iNEXT/3D-Bioinfo AI in structural biology workshop announcement
by Jon Agirre 15 Apr '24

15 Apr '24

Dear all, It is our pleasure to announce the joint iNEXT-Discovery and 3D-Bioinfo workshop on "AI advances in structural biology and drug discovery", to be held in Grenoble on 13-14 May 2024. The rapid advancements in Artificial Intelligence (AI) and Machine Learning (ML) have opened up new horizons in the field of Structural Biology and Drug Discovery. This workshop is addressed to scientists in industry and academia, and aims to bridge the gap between the recent developments in AI technologies and experimental approaches in translational research. From understanding biological structures to accelerating the drug discovery processes, participants will gain insights into the latest AI models, as well as high throughput experimental techniques. Through a series of invited and selected talks (abstract submission will remain open until 25 April 2024), attendees will explore the power of combining AI and experimental approaches in translational research. Abstracts will be considered for oral and poster presentations. Please register and send your abstract before 25 April 2024. Website: https://instruct-eric.org/events/ai-approaches-in-structural-biology-and-dr… Registration fee: £50 (includes catering) Venue: EPN campus, Grenoble, France. Dates: 13-14 May 2024 Best regards, Jon Agirre, on behalf of the organising committee: Jose A. Marquez (Instruct-ERIC), Magalie Matthieu (Sanofi-Aventis), Rebecca Thompson (ThermoFisher), Max Nanao (ESRF), Carlos Oscar Sorzano (Instruct-ERIC), Jon Agirre (Instruct-ERIC/3D-Bioinfo liaison), Sameer Velankar (EMBL-EBI, 3D-Bioinfo), Evangelia Chrysina (ICB-NHRF, Greece). -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) Main editor at Acta Crystallographica Section F: Structural Biology Communications CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK

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Partial occupancy refinement of overlapping inhibitor+water sites
by Matt Jordan McLeod 18 Mar '24

18 Mar '24

Hi all, I am trying to navigate phenix.refine to occupancy refine a partially occupied inhibitor vs. the waters that it displaces. For instance I have molecule resseq 802 in chain A, and waters 1-6 in chain W that are overlapping. When just refining occupancy of the molecule there are clear sites for the waters. How can I refine both of them together so that I can get an occupancy of the molecule vs the group of waters (which should have nearly identical occupancies)? Maybe, a bit more information on the differences in refinement strategy for the occupancy vs fix occupancy vs group occupancy would be more broadly helpful. I tried to make them all a group, but that didn't work as the refinement pushed the waters out and reduced their occupancies to ~0 while leaving the small molecule occupancy about the same as without water. [cid:2b35e3b8-08e5-44ae-9b70-8fdcff613f1a] *Waters are only placed, they are not refined), small molecule is refined to 0.71 occupancy.* -- Matthew Jordan McLeod, PhD Post-Doctoral Fellow | Thorne Lab Cornell University G11 Physical Sciences Building 142 Sciences Drive Ithaca, NY 14853-3501 (607) 279 9382

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uniq segid problem
by jp d 14 Mar '24

14 Mar '24

hi, phenix is crashing with "segid is not unique" problems i have an old job that ran fine in 1.20, in 1.21-5207 i get this (same job script) Sorry: residue.id_str(suppress_segid=false): segid is not unique: pdbres="ALA 65 " segid="PPP " i think the appropriate place in the log is this: Chain: " " Number of atoms: 41993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Duplicate atoms: {' A,C1*': 112, ' A,C2': 112, ' A,C2*': 112, ' A,C3*': 112, ' A,C4': 112, ' A,C4*': 112, ' A, C5': 112, ' A,C5*': 112, ' A,C6': 112, ' A,C8': 112, ' A,N1': 112, ' A,N3': 112, ' A,N6': 112, ' A,N7': 112, ' A,N9': 1 12, ' A,O1P': 112, ' A,O2*': 112, ' A,O2P': 112, ' A,O3*': 112, ' A,O4*': 112, ' A,O5*': 112, ' A,P': 112, ' C,C1*': 71 , ' C,C2': 71, ' C,C2*': 71, ' C,C3*': 71, ' C,C4': 71, ' C,C4*': 71, ' C,C5': 71, ' C,C5*': 71, ' C,C6': 71, ' C,N1': 71, ' C,N3': 71, ' C,N4': 71, ' C,O1P': 71, ' C,O2': 71, ' C,O2*': 71, ' C,O2P': 71, ' C,O3*': 71, ' C,O4*': 71, ' C, O5*': 71, ' C,P': 71, ' G,C1*': 179, ' G,C2': 179, ' G,C2*': 179, ' G,C3*': 179, ' G,C4': 179, ' G,C4*': 179, ' G,C5': 179, ' G,C5*': 179, ' G,C6': 179, ' G,C8': 179, ' G,N1': 179, ' G,N2': 179, ' G,N3': 179, ' G,N7': 179, ' G,N9': 179, ' G,O1P': 179, ' G,O2*': 179, ' G,O2P': 179, ' G,O3*': 179, ' G,O4*': 179, ' G,O5*': 179, ' G,O6': 179, ' G,P': 179, ' U,C1*': 69, ' U,C2': 69, ' U,C2*': 69, ' U,C3*': 69, ' U,C4': 69, ' U,C4*': 69, ' U,C5': 69, ' U,C5*': 69, ' U,C6': 69, ' U,N1': 69, ' U,N3': 69, ' U,O1P': 69, ' U,O2': 69, ' U,O2*': 69, ' U,O2P': 69, ' U,O3*': 69, ' U,O4': 69, ' U,O4*': 69, ' U,O5*': 69, ' U,P': 69} Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 82, 'rna2p_pyr': 63, 'rna3p': 10, 'rna3p_pur': 497, 'rna3p_pyr': 444} Link IDs: {'rna2p': 146, 'rna3p': 1372} the 1.20 log does not have these messages and finished normally. maybe a wildcard problem with those stars ? we are not using the '*' in our files has anyone seen that ? should i go back to 1.20 ? or force it to use the 1.20 chem data lib ? thanks jpd

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red blobs
by Andrea Smith 14 Mar '24

14 Mar '24

Hi, i am working on a structure where I have a few relatively big red blobs (please see attached print screens with maps at 1.2 and 3.5 rmsd). The data were processed at BESSY, mtz was used in Phaser and refined in phenix.refine. Can someone explain why this happens (and whether it is an issue)? Thank you, Andrea

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Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble
by Elke De Zitter 13 Mar '24

13 Mar '24

Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The project focuses on the development and optimization of bio-scavengers targeting toxic organophosphorus compounds. The successful candidate will employ time-resolved crystallography and in silico protein design methodologies. The 2-year postdoctoral position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than three years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate needs to be a good team player as well as being capable of working independently. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates should apply through the University Grenoble Alpes job portal at https://emploi.univ-grenoble-alpes.fr/job-offers/postdoctoral-researcher-in… (application deadline: 02/04/2024 ). For inquiries regarding the position and application process, please contact Elke De Zitter at elke.de-zitter(a)ibs.fr . All the best, 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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EMBO Workshop on Molecular Neurobiology, 13th to 17th May 2024, Crete
by Jonathan Elegheert 11 Mar '24

11 Mar '24

Dear all, I would like to bring to your attention the EMBO Workshop on Molecular Neurobiology (https://meetings.embo.org/event/24-mol-neurobiology), which will be held from 13th to 17th May 2024 on the beautiful Greek island of Crete, at the Fodele Beach resort (https://www.fodelebeach.gr/). This is a workshop covering the latest breakthroughs in structural biology, biophysics, imaging, and biological models in neurobiology. Given its cross-disciplinary nature, this EMBO workshop presents a broad overview of the field and an insight into the latest technologies and results. It provides a space for learning, for forging new collaborations, and for presenting ideas that will contribute to the future of molecular neurobiology. The workshop also presents an excellent opportunity for early-career scientists to present their work, with a large number of talks that will be selected from submitted abstracts. The workshop poster is attached to this mail, and more information, as well as the registration links, can be found on the following web page; https://meetings.embo.org/event/24-mol-neurobiology The abstract submission deadline is 6th of March. Please do not hesitate to contact me directly for any questions, and we hope to see many of you there! Best wishes, on behalf of the organising committee, Jonathan ----------------------------------------------------------------- Jonathan Elegheert, PhD Team Leader CNRS Scientist Interdisciplinary Institute for NeuroScience (IINS) <https://www.iins.u-bordeaux.fr/> UMR5297 CNRS / UB Centre Broca Nouvelle-Aquitaine 146 rue Léo Saignat BP 61292 33076 Bordeaux Cedex <https://goo.gl/maps/CFNm4dUvzrmmHUM1A> France T: +33 (0)5 33 51 48 57 E: jonathan.elegheert(a)u-bordeaux.fr W: https://www.iins.u-bordeaux.fr/ELEGHEERT Twitter: @ElegheertLab <https://twitter.com/ElegheertLab> -----------------------------------------------------------------

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