January 2024 - phenixbb - phenix-online.org

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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RapiData at SSRL 2024
by Smith, Clyde 09 Jan '25

09 Jan '25

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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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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RealSpaceRefine Nucleic acid SS restraints ?
by CUNIASSE Philippe 01 Feb '24

01 Feb '24

Dear all, I am currently refining a protein-nucleic acid structure obtained by MDFF (NAMD) with a 2.9 Å cryo-EM map. Dues to the poor density of the map at the end of the DNA duplex (likely due to breathing at the ends of the duplex), the structure of the DNA tends to be distorted. I tried to set up a set of nucleic acid restraints (Base pairing and base stacking for the full sequence), however, despite the fact that the syntax was checked and no error message is present in the log file, it seems that the restraints are not taken into account as if the constant restraints were two weak. And indeed when examining the refined structure, the pairing and stacking restraints for the base pairs at the extremities of the DNA duplex are not fulfilled. Have you a suggestion to solve this problem ? Thanks in advance for your help. Best regards. Philippe. ----------------------------------------------- Philippe Cuniasse, PhD/HDR. Institute for Integrative Biology of the Cell (I2BC) UMR 9198 CNRS-CEA-Univ Paris Sud Bat 144 CE-Saclay 91191 Gif-sur-Yvette Cedex, France Tel: (33) 1 69 08 56 35 Fax: (33) 1 69 08 47 12 Email: philippe.cuniasse(a)cea.fr<mailto:[email protected]> Web: http://biodev.cea.fr/rasmot3d/ Web: https://www.i2bc.paris-saclay.fr [signature_2602492259]

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leave residue inside its electron density when neighbor is too close
by Murpholino Peligro 29 Jan '24

29 Jan '24

What is the recommended approach to tell phenix.refine to leave the residue inside its electron density? (crystal neighbors) The green model is the input to phenix.refine, the maps and the yellow model are the output of phenix.refine. As you can see, phenix.refine will move the residue outside the density (to avoid clashes I guess?) I have tried setting the occupancy of OXT to 0.5, but it is not good. (you can see there is a water in a special position, just above the bad residue) Any more ideas?

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phenix.mtriage output model-map
by joe.wilson2023 23 Jan '24

23 Jan '24

Dear Phenix team, I am new to Phenix and using the phenix.mtriage to get the map-model FSC results. It gives the correct results at the same time I also want to produce the mode-map used for the FSC calculation. Is there an option for this? If not how can I reproduce the same model-map with another phenix command? Many thanks, Joe

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ResolveCryoEM problem
by Luca Pellegrini 22 Jan '24

22 Jan '24

Hi, I am trying to run Resolve with two half maps and a sequence file with ncs copies of the sequence. Resolve stops with the message: “Need a symmetry file if ncs_copies > 1 and using models”. But I am not using models. Please advise. Regards, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Joint X-ray / neutron refinement
by Derek Logan 22 Jan '24

22 Jan '24

Hi phenixbb, I'm trying to understand the current status of joint X-ray/neutron refinement in phenix.refine. The announcement of the latest release mentions a change in the algorithm as described in the recent publication. In the documentation: <https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> Structure refinement in PHENIX<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> phenix-online.org<https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> [X] <https://phenix-online.org/documentation/reference/refinement.html#neutron-a…> it's described how you can run joint refinement using a parameter file. Does this mean that it is *only* possible in this way and not through the GUI? The GUI was very useful in the past as it automatically opened Coot with the maps for both X-rays and neutrons, and the refinement statistics for both were displayed in the GUI. As far as I can see joint refinement via the GUI last worked in version 1.19.2-4148 from 2021. Best regards Derek

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treating the water molecules in the model
by Dmitry Semchonok 20 Jan '24

20 Jan '24

Dear colleagues, Please share your experience with how you handle the water molecules. So, we have a refined model and added the water molecules using the Douse protocol. So, should we refine the model again afterwards? Or is the model considered ready? We tried to refine our model with water, but then the water molecules flew away from the places. Please let me know what is the correct way to proceed. Many thanks for considering my request. Sincerely, Dmitry

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General interest: Interoperability of crystallographic data and databases
by John R Helliwell 19 Jan '24

19 Jan '24

Dear Colleagues, I imagine you will be interested in this Feature Article on the "Interoperability of crystallographic data and databases" in the current issue of IUCrJ:- https://journals.iucr.org/m/issues/2024/01/00/lt5064/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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