- phenixbb - phenix-online.org

twinning and translational NCS issues
by Wenhui Xi 06 Jun '26

06 Jun '26

Hi all, i have this crystal which was reported severe issues with twinning and translational NCS, thus when i tried to refine its structure, the Rfree would go up to nearly 60% which making directly solving its structure very hard. i'm writing to ask are there any helpful ways to deal with this issue? Thank you! Joyce [image: image.png]

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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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POSITION AVAILABLE: Visiting Research Specialist Position at the University of Illinois at Chicago
by Yury Polikanov 06 Jun '26

06 Jun '26

*Visiting Research Specialist Position Available in the Polikanov Lab <https://sites.google.com/view/polikanovlab>Department of Biological Sciences, University of Illinois at Chicago* *The Polikanov Laboratory <https://sites.google.com/view/polikanovlab> in the Department of Biological Sciences at the University of Illinois at Chicago is looking for a talented, skillful, and highly motivated researcher to fill the Visiting Research Scientist position to study the structure and function of the bacterial ribosome.* For full consideration, please submit your application along with a Cover Letter, CV, and three references by May 31, 2025. Cover letter should describe previous research accomplishments and scientific interests as well as how these fit within the scope of the research in the Polikanov lab. Questions can be addressed to Yury Polikanov at yuryp(a)uic.edu. Visiting Research Specialist- UIC Department of Biological Sciences, Polikanov Lab Hiring Department: Biological Sciences Location: Chicago, IL USA Requisition ID: 1033622 Posting Close Date: 05/31/2025 Link to Apply: https://uic.csod.com/ux/ats/careersite/1/home/requisition/14681?c=uic *Position Summary:* The Polikanov Lab is seeking a Visiting Research Specialist. Successful candidate will conduct research by using X-ray crystallography and cryo-EM techniques to obtain a structural basis for various functions of the bacterial ribosome and its inhibition by different small-molecule inhibitors. The successful candidate should have a strong theoretical background in standard biochemical, molecular biology, and biophysical methods, as well as practical skills in the most standard methods currently used in molecular biology and biochemistry (such as protein expression, purification, etc.). Knowledge in X-ray crystallography or other structural techniques is desired but not required. The successful candidate would conduct research and assist with training laboratory personnel in various techniques, experiments, and the appropriate use of research equipment. He/She would also perform data analysis and manage, document, and help with the dissemination of research activities for publication and outreach. *Duties & Responsibilities:* - Record keeping: log and track inventory of chemicals, reagents, and lab supplies - Maintain accurate records of experiments, procedures, and results - Keep the laboratory clean, organized, and free of contaminants - Glassware & Equipment Maintenance - Prepare culture media, buffers, and reagents according to protocols - Assist other researchers in the lab in conducting experiments - Purify bacterial ribosomes and all additional components necessary for the experiments, such as recombinant proteins, tRNAs - Train undergraduate and graduate students in research methods, use of equipment, record keeping, and laboratory database entry *Minimum Qualifications :* - Bachelor’s degree in biology, chemistry, biochemistry, biophysics, or related field required. Master’s degree in science preferred. - A minimum of 3 years of related research experience. - Strong background in biochemistry and molecular biology - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification) *Salary:* The budgeted salary range for the position is $48,000 to $60,000. The pay offered to the selected candidate will be determined based on factors including (but not limited to) the experience and qualifications of the selected candidate, including equivalent years in rank, training, and field or discipline; internal equity; and external market pay for comparable jobs. *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 over 300,000 alumni, and is one of the largest employers in the city of Chicago. Benefits eligible positions include a comprehensive benefits package which offers: Health, Dental, Vision, Life, Disability & AD&D insurance; a defined benefit pension plan; paid leaves such as Vacation, Holiday and Sick; tuition waivers for employees and dependents. Click for a complete list of *Employee Benefits <https://www.hr.uillinois.edu/benefits/>*. *Final authorization of the position is subject to availability of funding.* *UIC is an EOE including Disability/Vets.* *The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act* *The University of Illinois System requires candidates selected for hire to disclose any documented finding of sexual misconduct or sexual harassment and to authorize inquiries to current and former employers regarding findings of sexual misconduct or sexual harassment. For more information, visit **https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899 <https://www.hr.uillinois.edu/cms/One.aspx?portalId=4292&pageId=1411899>*

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Phenix 2.1-6048 macOS / REEL (eLBOW) stability issue
by Xavier Brazzolotto 04 Jun '26

04 Jun '26

Hi, Phenix users and developers Using the recent Phenix release (2.1.6048), I am experiencing stability issues when inspecting eLBOW results in the REEL interface. The REEL interface systematically closes after some manipulations, crashing the whole Phenix interface. Are any users also impacted? I am using a Phenix on a MacBook Pro M2 (Apple Silicon) Xavier

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Seeking Advice on Difficult MR Case: TFZ 6–8 for All Search Models, R-free ~0.50
by syedsuhail7654＠gmail.com 03 Jun '26

03 Jun '26

I am working on a protein containing two domains: an N-terminal FHA domain and a C-terminal RING domain. I have collected a native dataset that extends to 2.45 Å resolution in space group P2₁2₁2 with unit-cell parameters approximately a = 46.9 Å, b = 91.9 Å, c = 165.0 Å. I have been struggling to obtain a convincing molecular replacement solution despite trying multiple approaches. What I have tried so far: Full-length AlphaFold model as a search model. Splitting the AlphaFold model into individual FHA and RING domains. Sequential/domain-wise MR searches. Aggressive model trimming. Poly-alanine versions of the models. Various combinations of domain placement strategies. However, the results remain largely the same: TFZ values are consistently in the range of 6–8. LLG values are not particularly convincing. Refinement of the best solutions leads to R-free values around 0.50 or higher. Electron-density maps are not readily interpretable. No solution has shown clear evidence of being correct after refinement and map inspection. At this stage I am trying to determine whether the issue is: Failure of MR due to domain rearrangement between the FHA and RING domains. Incorrect number of molecules in the asymmetric unit. Partial placement of domains that is being missed. Crystal pathologies such as pseudo-symmetry or translational NCS. Some other issue that I may be overlooking. I would appreciate suggestions on: Additional diagnostics to assess whether any of these TFZ 6–8 solutions might actually be correct. Strategies for multi-domain MR in cases where AlphaFold-based models are unsuccessful. Whether further model editing is likely to help. Other MR pipelines that may be worth trying before moving to experimental phasing. Any advice would be greatly appreciated.

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Macromolecular Crystallography - CSHL Course October 2026
by Paul Adams 19 May '26

19 May '26

Dear Colleagues A reminder that the Cold Spring Harbor Macromolecular Crystallography course will take place October 11-27th 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. Many applicants ultimately receive some form of financial support. If anyone has any questions please send me an e-mail, and we will be happy to answer all queries. Paul Adams, Dorothee Liebschner, Janet Newman, James Pflugrath, Tom Peat <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> Macromolecular Crystallography <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> October 11 - 27, 2026 Applications Due: July 17 Instructors Paul Adams, Lawrence Berkeley National Laboratory Dorothee Liebschner, Lawrence Berkeley National Laboratory Janet Newman, UNSW, Australia James Pflugrath, Rigaku Americas Corporation (ret.), Texas Co-Instructor Tom Peat, UNSW, Australia X-ray crystallography has been the cornerstone of structural biology for half a century and remains the technique of choice for atomic resolution understanding of macromolecules and for structure guided drug discovery. This course combines laboratory and computational instruction to train course participants in the major techniques used to determine three-dimensional structures. It is designed for scientists with a working knowledge of protein structure and function, but who are new to macromolecular crystallography or who wish to increase their in-depth knowledge of macromolecular crystallography. The advent of methods for the accurate prediction of protein structures is accelerating crystallography experiments, and the course will train researchers in how to best use these models. Topics Basic Diffraction Theory Structure Presentation Coordinate Deposition Structure Validation Model Building and Refinement Electron Density Maps Improvement Using Predicted Models in Structure Solution and Completion Protein Structure Prediction Structure Solution by Experimental Phasing Methods (SAD, MAD, MIR, and others) and Molecular Replacement Data Collection and Processing Synchrotron X-ray Sources and Optics Crystallization (Proteins, Nucleic Acids, Complexes and Membrane Proteins) Participants have extensive hands-on training in well-equipped labs in how to crystallize proteins and determine crystal structures by several methods, while learning through lectures on theory and methods. Both basic and advanced subjects are covered during lectures, which are given by leaders in the field. Informal discussions behind the techniques are frequent and students are expected to pose questions to be answered in interactive sessions. For further information and to apply please visit the Macromolecular Crystallography course website. <https://6zadfgnab.cc.rs6.net/tn.jsp?f=001vX26f7F6RuZoXG6GBghaPG6Gmt5I2bQPqw…> Cold Spring Harbor Laboratory - Meetings & Courses | 1 Bungtown Road | Cold Spring Harbor, NY 11724 US Unsubscribe <https://visitor.constantcontact.com/do?p=un&m=001S3f9XM7Br7nKhcnZ-APDwA==&c…> | Update Profile <https://visitor.constantcontact.com/do?ch=5f75c3d0-c591-11e3-b735-d4ae52843…> | Constant Contact Data Notice <https://www.constantcontact.com/legal/customer-contact-data-notice> -- 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) 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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hydrogens.refine = individual *riding
by p.auffinger＠unistra.fr 16 May '26

16 May '26

Hi, Can these options be used with real_space refinement - hydrogens.refine = individual *riding - hydrogens.refine_occupancie Thanks, Pascal

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Phenix version 2.1 released
by Paul Adams 06 May '26

06 May '26

Dear Colleagues, The Phenix developers are excited to announce that version 2.1 of Phenix is now available (build 2.1-6048). Binary installers for Linux, Mac OSX, and Windows, and the source installer, are available at the download site: http://phenix-online.org/download Highlights for this new version of Phenix include: - Phenix AI agent available in GUI - Add integration with Coot 1 - Fix integration with PyMOL - Fix bug with reading 16-bit float MRC maps (mode 12) This publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. https://doi.org/10.1107/S2059798319011471 Full documentation is available here: http://www.phenix-online.org/documentation There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix has previously been funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. The maintenance and distribution of Phenix is currently funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- 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) 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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CBMS Lecture Series - Callero - May 6, 2026; 13:30 (EDT)
by Stojanoff, Vivian 01 May '26

01 May '26

You are cordially invited to join the Center for Biomolecular Structure Lecture Series ……….. Guillermo Calero, MD PhD University of Pittsburgh School of Medicine WEDNESDAY, May 6, 13:30 (EDT) "Fine-tuning Time Resolved Experiments to Capture Crystal Biochemistry" Register in advance for this meeting: https://bnl.zoomgov.com/meeting/register/TztZw5fpSr-kBHygBEuzwA Time conversion Link: https://www.worldtimebuddy.com/<https://urldefense.com/v3/__https:/gcc02.safelinks.protection.outlook.com/?…> Abstract: Typically, interactions between enzymes and substrates (or inhibitors), are viewed in terms of small molecules binding to relatively rigid proteins. However, computational and experimental studies demonstrate that proteins undergo a variety of molecular motions over a wide range of timescales. Such conformational flexibility is integral to enzyme activity, drug action and drug resistance. Contemporary structural biology approaches resolve only the structures of thermodynamically stable species. By contrast, time resolved (TR) structural studies using crystallography or single particle cryoEM are innovative tools that reveals details of both the ligand binding process and the stepwise chemistry of the reaction, with important biomedical applications. Through a combination of TR techniques, including UV photolysis of caged substrates, we have used TR techniques to create the first molecular movies of: 1) b-lactam antibiotics binding to b-lactamases; 2) deoxynucleotide addition by HIV-1 Reverse Transcriptase (RT); 3) nucleotide addition by RNA polymerase II (Pol II); and 4) GTP hydrolysis by N-RAS. =================================== Vivian Stojanoff, PhD Education, Training, Outreach User Program p 1(631) 344 8375 e lifescience(a)bnl.gov<mailto:[email protected]> w https://www.bnl.gov/ps/lifesciences/<https://www.bnl.gov/ps/lsbr/> Address: Center for Biomolecular Structure National Synchrotron Light Source II Building 745 Brookhaven National Laboratory Upton NY 11973

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real space refinement with a reference model
by Valérie Biou 29 Apr '26

29 Apr '26

Dear all, I would like to use a reference model to try to improve my cryo-em refinement geometry. I have an AF3 model that superposes with an RMSD of 1.4Å wrt my structure, and I renumbered the residues so they match with my structure. however, I get the message Reference Model Matching Summary: reference file: renumbered.pdb Model: Reference: Total # of matched residue pairs: 0 Total # of reference model restraints: 0 input file list (truncated from the root) default_model = "RealSpaceRefine_72/rsr71_isolde1_real_space_refined_072.pdb" real_map_files = /cryosparc_P29_J343_010_volume_map_sharp.mrc" default_real_map = cryosparc_P29_J343_010_volume_map_sharp.mrc" restraint_files = eLBOW_46/elbow.P.P_pdb.001.cif" default_restraint = eLBOW_46/elbow.P.P_pdb.001.cif" phil_files = Phenix/.phenix/project_data/real_space_refine_88.eff" default_phil = Phenix/.phenix/project_data/real_space_refine_88.eff" then : reference_model { enabled = True file = "renumbered.pdb" side_chain = False secondary_structure_only = True search_options { chain_max_rmsd = 3.0 Can you please help me with this? Kind regards Valérie

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