- phenixbb - phenix-online.org

math behind beamstop_shadow_outliers
by Gao, Yunyun 13 Dec '23

13 Dec '23

Hi everyone, While I can find references for other outlier rejection options in scaling.outlier_rejction, there is none for beamstop_shadow_outliers. I am wondering what is the math behind z_lim_ac and z_lim_c. Another question would be: Does the same criteria also apply for the medium-resolution (e.g. 6-8 A) reflections? (like reflections under the beamstop support) Thanks! Best regards, Yunyun ------------------------------------ Yunyun Gao, Dr HARBOR Universitaet Hamburg Tel +49 (0)40 42838-3685

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Bug in optimize weights
by Mark Saper 08 Dec '23

08 Dec '23

I am running build 5156 on macOS 13.6.1. I am refining a multi-molecule with imperfect NCS. When I tried to use "Optimize X-ray/sterochemistry" and "Optimize X-ray/ADP weight” the program aborted with an error during the first cycle. The error was: ====================== XYZ individual (reciprocal space) ====================== AttributeError I submitted a bug report via the internal bug report system. I would appreciate how to get around this problem. Should I try the previous stable version? Many thanks, Mark _____________________ Mark A. Saper, Ph.D. Visiting Professor Dept of Microbiology and Molecular Genetics Hebrew University Faculty of Medicine Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu <mailto:[email protected]> | +972 52 815-0480

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Reference model problem
by Luca Pellegrini 06 Dec '23

06 Dec '23

I am trying to use a reference model in real_space_refinement, but phenix stops with the message: “Cannot not restrain working model to self and a reference model simultaneously” (see below). The reference and working models are identical but bound to different ligands. As far as a I can see, all I am doing is adding the reference model in the input window and ticking the box for reference model restraints (phenix 1.21rc1-4985). Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK [cid:[email protected]]

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Research Specialist Position at the University of Illinois to Study Ribosome Structure | POLIKANOV Lab
by Yury Polikanov 04 Dec '23

04 Dec '23

*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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Error 1.21rc1-5156 macOS and cross special position
by Xavier Brazzolotto 01 Dec '23

01 Dec '23

Dear Phenix developers, I have recently updated to macOS Sonoma and updated Phenix to the latest RC (1.21rc1-5156). I do have recent data where a residue gets a bit too close to its symmetric mate. In order to be able to start the refinement, I have to select the model interpretation option « allow_polymer_cross_special_position=True » In this case, the refinement process starts and does my 3 refinement cycles. However, the UI gives me a final error message stating that I have to enable the « cross-special position » (which is already True). The refined data are present (pdb, mtz, log, cif, eff, geo) but I do not get any analysis on these data. No _info.txt, no .kin files. The log ends with a « Sorry » If I deliberately move the faulty residue a bit out of its position (no more clashing with its symmetric mate) and NOT allow the cross-special position, then the refinement ends well with the correct final data analysis. Not a big deal per se, but but I suspect a small issue in the initiation of the analysis programs (Molprobity / King / etc…). Xavier

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Re: [phenixbb] CCP4 Study Weekend 2024 - Early bird registration including standard student bursary deadline coming soon!
by Karen McIntyre - STFC UKRI 01 Dec '23

01 Dec '23

Dear all, Registration is open for the 2024 CCP4 study weekend entitled "Decision making in MX - how to be a productive structural biologist". This year we are focusing on decision-making in macromolecular crystallography: when to use what automated tool, how to interpret the output and when you need to get your hands dirty instead. The frontiers of crystallography now involve massive multi-crystal and multi-dimensional experiments. This means the more that you can leave to the automated pipelines, the more you can focus on the novel elements of your experiment. Sometimes those automated tools work, and sometimes they fail (but have maybe not told you exactly why or how). Sometimes they don't even exist. In that case, how can you return to the basics and develop new strategies to break down the barriers to publication? Once again, this year the CCP4 Study Weekend will be held as a hybrid event from the 3rd to 5th January 2024, 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 2024 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 including the ceilidh. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. Important Key Dates: * Early bird registration final date: 19 November 2023; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 19 November which cover the cost of registration plus one night accommodation; * 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). We hope to see you there! Scientific Organisers: Helen Ginn (Deutsches Elektronen-Synchrotron, DESY, Germany) Nick Pearce (Linköping University, Sweden) Clemens Vonrhein (Global Phasing Ltd, UK) Administrative Organisers: Karen McIntyre (CCP4, UK)

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The experiment is still very much needed (though AlphaFold helps a lot)
by Tom Terwilliger 01 Dec '23

01 Dec '23

Hi Structural biologist colleagues! Our article that helps you make the case that the experiment is still very much needed is now out: https://www.nature.com/articles/s41592-023-02087-4 "AlphaFold predictions are valuable hypotheses and accelerate but do not replace experimental structure determination." Nature Methods (2023) Also, here is a video on the Phenix Tutorials YouTube channel that describes this analysis: https://www.youtube.com/watch?v=ugMPYdPo8Bc (I hope you will be happy to see that you and your structural biology colleagues get the credit for making AlphaFold possible at 2:35 in the introduction of this video! Keep up the fantastic structural biology work!) All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Possible problem with eLBOW in version 1.21rc1.5058 using smiles string
by Francisco Javier Medrano 30 Nov '23

30 Nov '23

Dear developers: I have tried to use eLBOW in version 1.21rc1.5058 to generate a cif file for a ligand and the program give me the following error: SMILES parser error:"Unable to load parsing table". The smiles string used was OP(OP(O)(O)=O)(O)=O, but it does not work for other strings. It does work if you supply a pdb file with connect records. If I use version 1.20.1-4487 with the same smiles string it does work properly. Is there any bur in the 1.21 version? Best regards -- Fº Javier Medrano Cristalografía de Macromoléculas Centro de Investigaciones Biológicas Margarita Salas C/ Ramiro de Maeztu, nº 9 Madrid - Spain

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issue with restrains
by Dmitry Semchonok 22 Nov '23

22 Nov '23

Dear colleagues, The issue with the refinement (Phenix 1.21rc1-5130) The refinement does not recognize the phil parameters prepared with ReadySet. [cid:5bb12054-9715-417b-a68d-58c1228ffe56] Please prompt me on how to proceed. Thank you Kins regards, Dmitry

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Errors in atomic coordinates and B factors in MX
by John R Helliwell 20 Nov '23

20 Nov '23

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