March 2026 - phenixbb - phenix-online.org

Issues with zero B-factor and ADP refinement
by sylee00＠snu.ac.kr 06 Jun '26

06 Jun '26

Dear all, I am encountering issues related to B-factors and ADP refinement in Phenix and would appreciate any insights or suggestions. I am currently working on my first PDB file, but I've noticed that many atoms in the PDB file have a B-factor of 0. As far as I understand, B-factor values are calculated by ADP refinement in Phenix real-space refinement, but even after running real-space refinement (with ADP on in refinement settings), the B-factor remains 0 for many atoms. I am currently using Phenix 1.20 on Windows (Newest version available on window). I also attempted to run Phenix 1.21 on a Linux in other computer, but when ADP refinement is enabled, the process starts normally but halts during the ADP refinement step. So I couldn't test whether the issue is fixed in the newest version. Aside from the B-factor issue, I am also experiencing an inssue related to ADP refinement: When I run real-space refinement with ADP refinement enabled, the process starts normally but halts during the ADP refinement step. According to the log file, other refinement steps proceed without issues, but it fails to progress at the ADP refinement stage. Additionally, when I try to pause the process, I receive a "NoSuchProcess" error, so ADP refinement process may have unexpectedly terminated. At first, I thought it's the issue related to system performance or hardware differences, because adp refinement with this pdb file and identical parameters works on some computer but fails on others (the same version of Phenix). Still it's weird because this issue has occurred unexpectedly, as ADP refinement previously worked in my computer under the same conditions without any problems and also other PDB files run without any problems in my computer. I would appreciate any insights or suggestions on how to resolve this. Thanks

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CloudFlare and Spain
by Billy Poon 06 Jun '26

06 Jun '26

Hi everyone, Does anyone in Spain have issues reaching the Phenix website ( https://phenix-online.org)? Our website is behind CloudFlare and it looks like, periodically, some CloudFlare IP addresses are blocked in Spain due to some piracy issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Fax: (510) 486-5909 Web: https://phenix-online.org

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for autobuild full sequence?
by James Holton 06 Jun '26

06 Jun '26

Hey all, Don't worry, nothing is funny today. I have a real question: Is there a way to force phenix.autobuild to build in the entire sequence? As in: the full length of the actual molecule that is in the crystal, such as what is supposed to go into SEQRES, regardless of "visible" density? I am trying to come up with a pipeline for prepping MD simulations of protein crystals. It seems proper to me that the molecule being simulated should be the actual molecular species, disordered bits an all. However, we don't seem to have good technology for building protein chains into "nothingness". Yes, I know Alphafold is a thing, but it is rubbish at clashes in the context of a crystal. I mean, I could write something, but does this tool already exist? Cheers, and happy Tuesday, -James Holton MAD Scientist

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Simulate map from model
by Ricardo Righetto 06 Jun '26

06 Jun '26

Hi, Apologies if I'm missing something obvious, but I was not able to find this in the documentation: is there a PHENIX tool for simulating Coulomb potential maps (aka "cryo-EM maps") from atomic models? I'm looking for something like the molmap <https://www.cgl.ucsf.edu/chimerax/docs/user/commands/molmap.html> command in ChimeraX, but more accurate. One such alternative is the simulate program from cisTEM, but I figured PHENIX might also have something? Thank you! -- Ricardo Diogo Righetto

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Question about geometry outliers in RealSpaceRefine
by Kevin M Jude 06 Jun '26

06 Jun '26

After a recent RealSpaceRefine run, the Geometry Restraints tab in the gui reports that I have two bond angle outliers > 4 sigma, but only lists one of them: D 180 MET N, D 180 MET CA, D 180 MET CB 114.170 109.342 4.2 So I check the logfile for the job and see: Bond angle restraints: 12582 Sorted by residual: angle pdb=" N MET D 180 " pdb=" CA MET D 180 " pdb=" CB MET D 180 " ideal model delta sigma weight residual 114.17 109.34 4.83 1.14e+00 7.69e-01 1.79e+01 angle pdb=" CA LEU B 79 " pdb=" CB LEU B 79 " pdb=" CG LEU B 79 " ideal model delta sigma weight residual 116.30 127.81 -11.51 3.50e+00 8.16e-02 1.08e+01 angle pdb=" C ASP B 333 " pdb=" N SER B 334 " pdb=" CA SER B 334 " ideal model delta sigma weight residual 122.74 127.19 -4.45 1.44e+00 4.82e-01 9.54e+00 angle pdb=" C GLN D 167 " pdb=" N ARG D 168 " pdb=" CA ARG D 168 " ideal model delta sigma weight residual 121.48 126.80 -5.32 2.04e+00 2.40e-01 6.80e+00 angle pdb=" C ASP B 163 " pdb=" N THR B 164 " pdb=" CA THR B 164 " ideal model delta sigma weight residual 123.47 127.30 -3.83 1.53e+00 4.27e-01 6.27e+00 ValidationCryoEM returns identical results except the gui says only one > 4-sigma outlier (at //D/Met180/). PDB Validation reports only the outlier at //B/Leu79/, which does have the largest sigma in the above log. My questions are: 1. Why does the gui report two 4-sigma outliers but only show one? 2. Why do the sigmas in the log file not correspond to the sigmas in the gui? Best wishes Kevin -- 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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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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Re: coot-1 linked to phenix
by Roberto Steiner 06 Apr '26

06 Apr '26

Hi Chiara I have installed coot-1 using homebrew and using /opt/homebrew/Cellar/coot/1.1.20/bin/coot works for me. Ciao Roberto Roberto A Steiner www.steinerlab.org https://twitter.com/steiner_lab roberto.steiner(a)kcl.ac.uk Randall Centre for Cell and Molecular Biophysics Faculty of Life Sciences and Medicine King's College London Room 3.10A New Hunt's House, Guy's Campus SE1 1UL, London, UK Phone 0044 20 78488216 Fax 0044 20 78486435 roberto.steiner(a)unipd.it Dipartimento di Scienze Biomediche Università degli Studi di Padova Viale G. Colombo 3 35131 Padova, Italia Telefono 0039 049 8276409 Responses to emails are not expected outside of your normal working hours. On 28/01/2026, 13:27, "Rapisarda, Chiara /FR via phenixbb" <phenixbb(a)phenix-online.org <mailto:[email protected]>> wrote: Hello, I have a Mac that I upgraded to Tahoe, and now coot 0.9 isn’t working any more. I would like to link phenix to coot-1. I can do that by adding: /Applications/ccp4-9/coot_py3/bin/coot To the coot path in preferences, but after a refinement when I open coot , it is open but it is not connected to the phenix refine job and no PDB nor map is open. I am aware that I can manually open the map and pdf, I would like to know if coot-1 can be opened in a way that will allow me to navigate the structure using phenix. When I ask gemini it tells me that I should point it to: /Applications/ccp4-9/bin/coot-py3 But it doesn’t exist in my ccp4 installation. Has anyone successfully managed to link coot-1 to phenix using a good bridge? Any help will be greatly appreciated. Best, Chiara _______________________________________________ phenixbb mailing list -- phenixbb(a)phenix-online.org <mailto:[email protected]> To unsubscribe send an email to phenixbb-leave(a)phenix-online.org <mailto:[email protected]> Unsubscribe: phenixbb-leave@%(host_name)s

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Issues refining a cyclic peptide with non-natural residues
by Dayna Louise Holroyd 31 Mar '26

31 Mar '26

Hi all, I am currently refining a cyclic peptide which I have modelled into my 3A crystal structure. The peptide contains multiple non-natural amino acids, two of which haven't been defined in the PDB before by a three letter code (made cif files with elbow for these). I have been adding custom restraint files each refinement round to connect residues at the ends and maintain cyclisation. I am encountering various issues during refinement: 1. Certain pairs of non-natural residues drift apart after refinement if I do not include restraints between the two residues. 2. Some backbone dihedral angles are much smaller than expected, while other angles appear unusual or physically implausible, even after defining particular angles in the restraint files. I suspect that some of these issues may be related to the compact nature of the cyclic peptide and the presence of undefined residues, but I am unsure how to address them effectively. Has anyone refined similar cyclic peptides with non-natural residues and can offer advice on my problems with restraints, compact backbone angles, non-natural residues, etc? Any guidance or ideas would be greatly appreciated. Many thanks, Dayna Holroyd PhD Candidate Protein Crystallography and Structural Biology Laboratory School of Biological Sciences | College of Science ADELAIDE UNIVERSITY

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