October 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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Re: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 05 Dec '24

05 Dec '24

Just a reminder that registration is open for the CCP4 Study Weekend taking place in January 2025. Early bird deadline is 11 November so if you want to save some money or are a student wanting a standard bursary register ASAP. Applications for Travel bursaries are now open but close at the end of the month so get your applications in now! Hope to see you there!! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK) From: McIntyre, Karen (STFC,RAL,SC) Sent: 26 September 2024 13:15 To: CCP4 WG2 <ccp4wg2(a)listserv.stfc.ac.uk>; CCP4 WG1 <ccp4wg1(a)listserv.stfc.ac.uk>; ccp4bb(a)jiscmail.ac.uk Subject: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models Importance: High Dear all, Registration is now open for the 2025 CCP4 study weekend entitled " Using software, AI and other methods to advance macromolecular models". This year the CCP4 Study Weekend will be held as a hybrid event from the 7th to 9th January 2025, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2025 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. There is no better way to start 2025 than to put participation in that exciting meeting at the top of your "New Year's Resolutions" list! Key Dates: * Early bird registration final date: 11 November 2024; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 11 November which cover the cost of registration plus one night accommodation in halls (1 night in hotel will be subsidised for those students choosing to stay in the hotel); * Travel bursaries are available for students and young postdocs studying at overseas labs to help cover cost of travel to UK. The deadline for applications is 31 October 2024; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). * Registration for virtual delegates will close 9 January 2025. Key Timings Diamond MX user meeting will start at 11:00 on 7TH January 2025 CCP4 study weekend 2025 will start at ~17:30 on 7th January 2025 the event will finish at ~16:30 on 9th January 2025 We hope to see you there! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK)

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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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Tool to calculate Q-scores?
by Guillaume Gaullier 29 Oct '24

29 Oct '24

Hello phenixbb, It would be convenient to have a tool to calculate Q-scores [1], with suggested command-line name phenix.qscore or phenix.model_map_qscore. It would work just like phenix.model_map_cc but report Q-scores instead (average per chain by default, but if requested also per-residue backbone / side chain / whole residue averages, or per ligand). And phenix.validation_cryoem could report these scores as well, in addition to the CCs that it already reports. There is already a tool to do this in ChimeraX [2], which is very helpful for interactive work. But for automated calculation of these scores from many models and maps, it would be more convenient to have a phenix tool for it. If it already exists, sorry I overlooked it (but I looked up both the latest documentation and phenix command completion and couldn't find anything like it), and I'll be happy if somebody can point me to it! Cheers, Guillaume [1]: https://doi.org/10.1038/s41592-020-0731-1 [2]: https://github.com/tristanic/chimerax-qscore När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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MASSIF-1 10 year celebration symposium
by Matthew BOWLER 25 Oct '24

25 Oct '24

Dear CCP4 community, I would like to draw your attention to a one day symposium we are holding here in Grenoble to celebrate 10 years of fully automatic data collection at the ESRF/EMBL beamline MASSIF-1 - from starting with basic characterisation and data collection we now measure crystal volumes, dynamically adapt beam diameters, automatically collect and merge kappa sweeps, helical and multi-crystal data sets and even automatically mount crystals from trays using the EMBL CrystalDirect robot. With a great line-up of speakers we will highlight some of the research enabled by MASSIF-1, how it has inspired other beamlines around the world, as well as some history of the project. You can find more details in the attached flyer and register in the link below. We look forward to seeing you in Grenoble! Matthew Bowler and Didier Nurizzo. https://www.esrf.fr/home/events/conferences/2024/massif-1-symposium.html -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France =================================================== Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ http://www.esrf.eu/MASSIF1 https://twitter.com/id30_massif1 https://www.embl.org/people/person/mbowler/ ===================================================

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Bursaries available for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 25 Oct '24

25 Oct '24

Standard Student Bursaries As in year’s past, CCP4 has made funding available for students, to help with the costs of attending Study Weekend, in the form of a bursary. All students are eligible for a standard bursary which covers the registration fee plus one night’s accommodation in halls. Bursaries will be given out to all students registering during the early bird registration period – 26th September to 11th November 2024. Students obtaining a standard bursary will only need to pay for any additional night’s accommodation. Students wishing to stay in the hotel rather than Rutland halls, will have 1 nights accommodation subsidised at the halls rate and will therefore pay a reduced rate for this night. Additional nights accommodation will need to be paid at the standard cost. Please also note that should you obtain a bursary and cancel after the latest cancellation date of 6 December 2024 you WILL be liable to pay.  This is because we have had a number of students obtaining bursaries and then cancelling last minute.  Places can be transferred to other people at no charge.  Travel bursaries Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be e-mailed to ccp4sw(a)stfc.ac.uk<mailto:[email protected]> : Lauren Giles CCP4 Study Weekend Travel Bursary Applications for travel bursaries need to be in by Thursday 31st October 2024. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:[email protected]] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time – hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30**********

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working with composite models
by Dmitry Semchonok 24 Oct '24

24 Oct '24

Dear Colleagues, We're encountering an issue with composite model refinement and would appreciate your advice. Our scenario: 1. We built two separate models based on two subtracted maps of a single complex. 2. We have a lower-resolution map of the full complex. 3. We merged the two models into the full complex and refined it against the full map. The problem: When refining the merged model against the full map using real-space refinement in Phenix, the clashscore progressively worsens. Has anyone experienced similar issues, or can you offer suggestions on addressing this problem? Thank you for your insights. Best regards, Dmitry

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About cryo-EM map sharpening in Phenix
by Shanti Pal Gangwar 17 Oct '24

17 Oct '24

Hello everyone, I'm working on anisotropic map sharpening in Phenix version 1.21-5207-00 with a cryo-EM map of a multiprotein complex. Should I provide the sequence files for each component individually, or would it be better to compile all the sequences into a single file? In addition, shall I provide the full sequence even if a segment of the protein is not resolved in the map? I would appreciate any advice! Shanti Pal

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AQuaRef - issues with torch-cluster installation
by Martin Malý 16 Oct '24

16 Oct '24

Dear colleagues, I'm trying to install AQuaRef. However, I'm struggling with running `bash config/update_phenix.sh aimnet2` which is part of `bash build_into_phenix.sh aimnet2`. This script wants to install the python package torch-cluster. However, I'm getting the error: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] I'm getting the same error when I tried to install only this package using the command `qrefine.python -m pip install torch-cluster`. I have a laptop with Ubuntu 22.04. I have all the usual development packages installed (build-essential, linux-headers, gcc, g++, ...). According Python, I have libpython3-dev, libpython3.10-dev, python3-dev, python3.10-dev. I can see that qrefine.python has a version of 3.9, so I also installed libpython3.9-dev, python3.9-dev and python3.9-distutils from ppa:deadsnakes/ppa but it did not help. I am also attaching a full log from the torch-cluster installation. It seems that the package torch has been installed successfully in prior. Do you have please an idea what is wrong and how to fix it? Thank you. Martin

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