February 2025 - phenixbb - phenix-online.org

Cryo_fit installation
by omar.debei＠unipr.it 06 Jun '26

06 Jun '26

Hi everyone, I was wondering if you could help me with installing cryo_fit on an Ubuntu machine. I followed the instructions here for the cryo_fit installation. Then, I tried to follow this guide to install gromacs_cryo_fit. However, I got stuck at the "Install using a provided script" step. Do I need to install GROMACS separately before proceeding? Any tips would be greatly appreciated! Many thanks, Omar

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AKM in Phenix
by lucas.santosouza＠outlook.com 06 Jun '26

06 Jun '26

Hi everyone, Is there still support for the generation of Average Kick Maps in Phenix? I am using both versions 1.21.2-5419 and the nightly build 2.0rc1-5555. I added kicked=True to the maps.params, but phenix.maps gives me "Unused parameter definitions: maps.map_coefficients.kicked (file "maps.params", line 53)". I also cannot see the "Kicked map" check box in the Create Maps GUI. Cheers, Lucas

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.cif file has 'UNK' auth_asym_id
by Kevin M Jude 06 Jun '26

06 Jun '26

I’ve finished refining a structure with three protein chains A, B, C. The pdb file looks ‘normal’ to me, but when I inspect the .cif file written by phenix, the auth_asym_id for chains B and C is ‘UNK’. label_asym_id is correct for all chains. I’m not really sure what the difference is between the auth_ and label_ fields. When I try to perform actions on the .cif file, I get duplicate atom label errors. Here’s a few example lines from the .pdb and .cif files, where auth_asym_id is field 6 and label_asym_id is field 16 ATOM 460 OXT PRO A 59 5.272 55.689 31.481 1.00 52.63 O ANISOU 460 OXT PRO A 59 6541 6212 7244 1448 1260 96 O TER ATOM 461 N ALA B 2 39.292 61.974 39.403 1.00 67.81 N ANISOU 461 N ALA B 2 7118 8729 9916 -1711 -388 2066 N ATOM 460 OXT . PRO A 59 ? 5.27169 55.68852 31.48123 1.000 52.63052 O ? A ? 58 1 ATOM 461 N . ALA UNK 2 ? 39.29207 61.97430 39.40271 1.000 67.80544 N ? B ? 1 1 I’m able to convert the pdb file to a usable cif file using gemmi but wanted to report this weird behavior with phenix 1.21.2_5419. -- 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

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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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IBA2025 - May 5&6 2025 - Cambridge MA
by Chip Lesburg 30 Mar '25

30 Mar '25

The Industrial Biostructures America conference will take place on May 5 & 6, 2025 at the MassBioHub in Cambridge MA. The conference was launched in 2018 to bring the industry-based structural biology community together for two days of presentations and networking. This is a great place for industrial structural biologists, as well as those who are industry-curious. The conference will feature keynote presentations by: * Dr. Stephen K. Burley, Director RCSB Protein Data Bank and Rutgers University Professor * Dr. James Fraser, Professor and Chair Department of Bioengineering and Therapeutics Sciences at UCSF * Dr. Stephen Harrison, Professor Harvard Medical School/Investigator Howard Hughes Medical Institute * Dr. Mark Murcko, Founding CSO/Board Member at Dewpoint Therapeutics and Relay Therapeutics Conference information is available at https://industrialbiostructuresamerica.org along with guidelines for submitting abstracts for scientific presentations during the conference. Scientific sessions will cover the following topics: * Structural Biology of Targeted Protein Degradation: Glues, TCs & DUBs * Developing Fragments to Drugs: Challenges & Victories * Molecular Dynamics and Allostery - Bridging Experimental and Computational Drug Discovery * Membrane Protein Structure Guided Design * CryoEM Synergies with Molecular Modeling and Computational Models * Biologics (Antibody Design & ADCs) * AI/ML in Structural Biology and Drug Discovery * Hot Topics (SBDD, Kinases, RNA) The abstract deadline is April 1. Space is limited so if you're interested, please register soon. Contact us at iba(a)proteros.com<mailto:[email protected]> for information regarding Exhibitor and Sponsor opportunities [cid:logo_c70edd4a-e7f0-4d54-be6f-d03f53f0c961.png] Charles Lesburg Vice President, Structural Biology odysseytx.com<https://protect.checkpoint.com/v2/___https:/odysseytx.com/___.YzJ1Om9keXNzZ…> This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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Register by Feb. 28th for the West Coast Structural Biology Workshop
by Michael Thompson 21 Feb '25

21 Feb '25

The registration and abstract submission deadlines for the 26th West Coast Structural Biology Workshop are just one week away... Register today, and be a part of this iconic meeting with over 50 years of tradition!! See below for a message about the conference: Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 28, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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Postdoc and PhD positions in quantum/protein/electron crystallography. Application deadline March 2nd
by Paulina Dominiak 03 Feb '25

03 Feb '25

Dear Colleagues, We currently have several positions available in my group at the University of Warsaw - both postdoc and PhD. The research project combines quantum crystallography with protein crystallography, focusing on 3DED/microED techniques. We're interested in hearing from researchers with different backgrounds: * Software developers who want to learn crystallography * Protein crystallographers looking to expand their skills * Small-molecule crystallographers experienced with X-ray charge density studies * Researchers familiar with electron crystallography Detailed information about the positions, project description, and application links can be found at: http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/ <http://4xeden.uw.edu.pl/2025/01/18/bio-qcr/> Application deadline: March 2nd, 2025 Please share this opportunity with qualified candidates who might be interested. For additional information, feel free to contact me directly. Best regards, Paulina -- Prof. dr hab. Paulina M. Dominiak Group Leader Electron Density Modelling Group Laboratory for Structural and Biochemical Research (LBSBio) Biological and Chemical Research Centre Department of Chemistry University of Warsaw ul. Zwirki i Wigury 101 02-089 Warszawa, Poland Room: 3.125 E-mail:[email protected] Phone: (48) 22 55 26 714 WWW:http://4xeden.uw.edu.pl

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DEADLINE EXTENDED: 26th West Coast Structural Biology Workshop
by Michael Thompson 03 Feb '25

03 Feb '25

Dear Colleagues, The registration and abstract submission deadlines for the upcoming West Coast Structural Biology Workshop have been extended! The UPDATED deadlines for registration and abstract submission are Feb. 28, 2025 and Feb. 21, 2025 respectively. The meeting is scheduled for March 23-26, 2025 at its traditional location, the Asilomar Conference Center in Pacific Grove, CA. The conference website can be found at: https://wcsbw2025.macromolecules.xyz/. The WCSBW is a bi-annual meeting that showcases the latest methods, developments, and discoveries in structural biology, including X-ray Crystallography, Cryo-EM, NMR, and other methods. We strongly encourage anyone interested in method development and solutions to technical challenges in structural analysis to attend, even if you're not from the west coast. Importantly, the WCSBW aims to highlight the work of trainees, so all oral presentations (except keynotes) will be given by students and postdocs. The 26th edition of this meeting will include: * Opportunities to connect with leaders in the field, exchange practical advice, and stay at the forefront of structural biology advancements. * Exciting oral research presentations and engaging poster sessions. * Inspiring keynote presentations, featuring Prof. Bil Clemons from Caltech, and Dr. Junko Yano from Lawrence Berkeley National Lab. * A 2-hour workshop hosted by the Phenix developers, detailing the use of new tools for structure determination and analysis. * A networking session with scientists from west coast biotech companies for students and postdocs who are entering the job market. * Good company and beautiful views of the pacific ocean! Some details about the conference are included below, and more information is available at our website (see link above). We hope to see you at Asilomar in March! -Mike Thompson (UC Merced) and Alec Follmer (UC Davis) P.S. We ask for your help in sharing this announcement with any students, postdocs, staff, colleagues, collaborators, or friends that might be interested. Thanks! Conference Details: March 23-26, 2025 at Asilomar Conference Center in Pacific Grove, CA Visit the conference website at: https://wcsbw2025.macromolecules.xyz/ Registration: https://book.passkey.com/event/50870517/owner/10793795/home Registration fee is $200, plus lodging fees (meals included). Attendees need to book their lodging accommodations at Asilomar when registering for the conference. Both single and double occupancy rooms are available. If you do not have a roommate and would like us to pair you with one to lower costs, or if you would like to register for the conference and arrange your own accommodations offsite, please contact us at wcsbw2025(a)gmail.com<mailto:[email protected]>. Abstract Submission: https://wcsbw2025.macromolecules.xyz/registration/ All oral presentations at the WCSBW, except for the keynotes, will be given by trainees. Students (undergraduate or graduate) and Postdocs are welcome to submit abstracts for oral presentations. We welcome abstracts for poster presentations from attendees at any career stage. The deadline for submitting abstracts is February 21, 2025, and attendees must be registered for the meeting in order for their abstracts to be considered. Abstracts that are submitted for oral presentations and not selected will be automatically considered as poster abstracts. --- Michael C. Thompson, Ph.D. (he/him) Assistant Professor Dept. of Chemistry and Biochemistry University of California, Merced https://thompsonlab.science<https://urldefense.com/v3/__https://thompsonlab.science__;!!LQC6Cpwp!-fv-nQ…>

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