May 2024 - phenixbb - phenix-online.org

Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 06 Jun '26

06 Jun '26

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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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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Ordered solvent in phenix.refine
by Oliver H. Weiergräber 11 Sep '24

11 Sep '24

Hello, after switching from version 1.20 to 1.21, I noticed that the updated list of waters generated by the ordered_solvent option in phenix.refine is no longer numbered sequentially; it seems a final re-numbering step is now skipped. Is this intentional? Of course it can be advantageous to keep waters from changing their numbers, e.g. if they are part of occupancy groups. On a related note, is there a mechanism to protect certain "important" waters from being deleted while all the rest is updated as usual? One obvious option would be a dedicated chain ID, but afaik phenix.refine accepts a chain ID for output but not for input waters ... Best regards, Oliver ================================================== Prof. Oliver H. Weiergräber Institute of Biological Information Processing IBI-7: Structural Biochemistry Forschungszentrum Jülich 52425 Jülich, Germany Tel.: +49 2461 61-2028 Fax: +49 2461 61-9540 ==================================================

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Extra map coefficients in 1.21.1-5286
by Dr. Kevin M Jude 29 Jun '24

29 Jun '24

In my latest installed version of phenix, I find that additional, redundant map coefficients are being added to the output mtz file. I compare an identical refinement originally run in 1.21rc1_5058 and then repeated in 1.21.1-5286. *_filled and *_4 appear to be redundant, and the final sets of coefficients (*_no_fill and *_5), appear to include the test set reflections, even though I’ve selected Exclude R-free set from map coefficients in the gui. This is a little bit confusing, but primarily an annoyance because auto-open mtz in coot can’t figure out which coefficients to use. 1.21rc1_5058 Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -42 41 0 100.00 -3.3 16.0 52.38 1.96 H H 2 NONE 0 28 0 100.00 10.3 10.3 52.38 1.96 H K 3 NONE 0 27 0 100.00 10.3 10.3 52.38 1.96 H L 4 NONE -94.4 13012.5 269 98.44 85.01 85.49 45.63 1.96 J I-obs 5 NONE 0.2 337.4 269 98.44 4.44 4.44 45.63 1.96 Q SIGI-obs 6 NONE 0.0 1.0 269 98.44 0.05 0.05 45.63 1.96 I R-free-flags 7 NONE 10.2 2509.6 321 98.14 129.94 129.94 36.90 1.96 F F-obs-filtered 8 NONE 1.3 35.8 321 98.14 10.11 10.11 36.90 1.96 Q SIGF-obs-filtered 9 NONE 0.1 2250.2 321 98.14 125.18 125.18 36.90 1.96 F F-model 10 NONE -180.0 180.0 321 98.14 4.35 89.81 36.90 1.96 P PHIF-model 11 NONE 0.0 2971.8 1165 93.23 117.81 117.81 36.90 1.96 F 2FOFCWT 12 NONE -180.0 180.0 1165 93.23 4.65 89.89 36.90 1.96 P PH2FOFCWT 13 NONE 0.0 2971.8 0 100.00 117.93 117.93 52.38 1.96 F 2FOFCWT_filled 14 NONE -180.0 180.0 0 100.00 4.85 90.05 52.38 1.96 P PH2FOFCWT_filled 15 NONE 0.0 738.9 1165 93.23 46.86 46.86 36.90 1.96 F FOFCWT 16 NONE -180.0 180.0 1165 93.23 4.75 90.35 36.90 1.96 P PHFOFCWT 1.21.1-5286 Col Sort Min Max Num % Mean Mean Resolution Type Column num order Missing complete abs. Low High label 1 NONE -42 41 0 100.00 -3.3 16.0 52.38 1.96 H H 2 NONE 0 28 0 100.00 10.3 10.3 52.38 1.96 H K 3 NONE 0 27 0 100.00 10.3 10.3 52.38 1.96 H L 4 NONE -94.4 13012.5 269 98.44 85.01 85.49 45.63 1.96 J I-obs 5 NONE 0.2 337.4 269 98.44 4.44 4.44 45.63 1.96 Q SIGI-obs 6 NONE 0.0 1.0 269 98.44 0.05 0.05 45.63 1.96 I R-free-flags 7 NONE 10.3 2535.0 321 98.14 131.25 131.25 36.90 1.96 F F-obs-filtered 8 NONE 1.3 36.1 321 98.14 10.21 10.21 36.90 1.96 Q SIGF-obs-filtered 9 NONE 0.0 2261.4 321 98.14 126.66 126.66 36.90 1.96 F F-model 10 NONE -180.0 180.0 321 98.14 3.96 89.82 36.90 1.96 P PHIF-model 11 NONE 0.0 3119.6 1165 93.23 119.71 119.71 36.90 1.96 F 2FOFCWT_1 12 NONE -180.0 180.0 1165 93.23 4.33 89.89 36.90 1.96 P PH2FOFCWT_1 13 NONE 0.0 3119.6 0 100.00 119.85 119.85 52.38 1.96 F 2FOFCWT_filled 14 NONE -180.0 180.0 0 100.00 4.44 90.05 52.38 1.96 P PH2FOFCWT_filled 15 NONE 0.0 780.4 1165 93.23 45.28 45.28 36.90 1.96 F FOFCWT_2 16 NONE -180.0 180.0 1165 93.23 4.21 90.36 36.90 1.96 P PHFOFCWT_2 17 NONE 0.0 3119.6 0 100.00 119.74 119.74 52.38 1.96 F 2FOFCWT_4 18 NONE -180.0 180.0 0 100.00 4.60 90.01 52.38 1.96 P PH2FOFCWT_4 19 NONE 0.0 3119.6 321 98.14 119.56 119.56 36.90 1.96 F 2FOFCWT_no_fill 20 NONE -180.0 180.0 321 98.14 4.40 89.94 36.90 1.96 P PH2FOFCWT_no_fill 21 NONE 0.0 780.4 321 98.14 45.68 45.68 36.90 1.96 F FOFCWT_5 22 NONE -180.0 180.0 321 98.14 4.12 90.23 36.90 1.96 P PHFOFCWT_5 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 Phone: (650) 723-6431<tel:%28650%29%20723-6431>

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Hardware migration
by Billy Poon 18 Jun '24

18 Jun '24

Hi everyone, We are in the process of migrating these bulletin boards to new hardware over the next few weeks. I will make another post once the migration is completed. Nothing will be changed until then. 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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high and low resolution in Phenix 1.21.1-5286-000
by Dominik Oberthuer 30 May '24

30 May '24

Hi, because of an update to Sonoma, I also had to update to Phenix 1.21.1-5286-000. When I'm running phenix.refine from the GUI, use an MTZ with resolution e.g. from 1.65 - 51A, use "High resolution" and "Low resolution" to refine against a specific range of data, phenix.refine does not cut off the data beyond the limits set there, but instead takes all of the data. For sure, I cut the MTZ before, but many times it is about trying out which data to include and not include and this is not really how it should be... Is this known? Is there any way to solve this issue? Thanks! Dominik -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science - DESY Coherent Imaging Division Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de

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NIGMS Mature Synchrotron Program Evaluation
by Paul Adams 20 May '24

20 May '24

Dear Colleagues, Apologies for the US-centric posting, but I think this is of interest to many of the bulletin board subscribers who make use of synchrotron facilities in the US. NIH is seeking feedback on the Mature Synchrotron Program: https://grants.nih.gov/grants/guide/notice-files/NOT-GM-24-019.html This program supports synchrotron-based user resources where the technologies are at an advanced level, including Macromolecular Crystallography, Small-Angle and Wide-Angle X-ray Scattering, fiber diffraction, and other synchrotron-based techniques that generate important data, with an emphasis on structural biology. Responses to the RFI will be accepted through 6/17/2024. All comments will be anonymous and should be submitted electronically via a web form at: https://www.research.net/r/P30_RFI As the Director of one of the resources it has been suggested that I help make the community aware of the RFI, so there is the opportunity to provide feedback in a timely manner. Feel free to pass this on to any of your colleagues who may be interested. Cheers, Paul -- 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) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.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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"<" symbol in reflection mmcif status column
by Kreitler, Dale 17 May '24

17 May '24

Looking at some output reflection cif files from phenix.refine I'm wondering what does "<" mean in the status column and why would F_calc_with_sovlent structure factors also be missing for these reflections? In some cases I can see it coincides with unobserved reflections, but this doesn't seem consistent. Any insight or links to documentation that describe these values would be much appreciated. Thank you, Dale loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent ... 30 0 48 65.2227 18.9183 72.4766 0 5.77152 -2.25565e-14 3 o 77.6435 1.95165e-15 30 0 49 206.068 7.45891 200.645 120 ? ? 19 < ? ? 30 0 50 33.324 17.5773 1.10423 -120 0.328059 -120 10 o 0.916822 -120 30 0 51 23.7705 14.8724 10.7438 180 2.40893 1.88332e-14 6 o 16.3173 180 ... 32 7 2 ? ? 11.4163 118.276 ? ? 5 < ? ? 32 7 3 ? ? 52.373 -121.74 ? ? 10 < ? ? 32 7 4 ? ? 33.1269 -26.1149 ? ? 3 < ? ? 32 7 5 ? ? 106.054 -86.2146 ? ? 19 < ? ? ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318

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ADP refinement in phenix.real _space_refine
by Luca Pellegrini 16 May '24

16 May '24

While refining a protein-DNA complex in a cryoEM map (~2.5-7A), I have noticed the following behaviour of ADP refinement: - If NCS is on for the protein chains, no ADP refinement of the DNA takes place. - If NCS is off, ADP refinement behaves oddly: one strand of dsDNA is refined with atomic ADPs, the other strand with group ADPs (one per nucleotide). The group ADPs take up unphysical values (lower ADPs in poor map regions), whereas the atomic ADPs look sensible. - To get the ADP refinement of DNA to behave normally, I need to both leave NCS out and set nproc=1 explicitly (haven’t tried other values). I wonder if any of this has been seen before or am I not doing this correctly? Phenix-dev-5330 iMac, Catalina 10.15.7, 8-core Intel i9 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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