- phenixbb - phenix-online.org

Scientist Antibody Production at the Institute for Protein Innovation in Boston, USA
by Christopher Bahl 19 Feb '21

19 Feb '21

Scientist Antibody Production Reports to the Head of Biological Discovery, Dr. Rob Meijers The Institute for Protein Innovation (IPI) is a nonprofit research organization advancing protein science to accelerate research and improve human health. Located on the Harvard Medical School campus in the Boston Longwood Medical Area, IPI is pioneering a new way of doing science that uniquely combines the freedom of academia with the high-throughput scaling of industry to take on transformative projects. IPI has built a robust platform and a repository of synthetic antibodies and other protein tools to share with the biomedical community through licensing and collaboration. The Institute’s deep protein expertise, collaborative spirit and fit-for-purpose antibodies are powering new biomedical and therapeutic discoveries for academic and industrial researchers worldwide. Job Overview IPI’s flagship project, the “Antibody Initiative,” aims to create well-characterized, synthetic antibodies against human cell surface receptors and their ligands, particularly those that are traditionally difficult to target. These antibodies may have high therapeutic and diagnostic potential but will also serve to enable basic biological discovery. The Scientist, Antibody Production will play an essential role in the high-throughput production, characterization and formulation of synthetic antibodies for this Initiative and other key IPI projects. Specifically, the successful candidate will join the Protein Group, a dynamic team generating high-quality antibodies and developing new technologies for conjugation. Having completed a doctorate in protein chemistry, the successful candidate will bring to the job experience in mammalian expression, purification and reagent-grade preparation of glycoproteins. The candidate will be adept in quality control and process management and reliably provide detailed documentation on experiments completed. The Scientist will work in close collaboration with the other Antibody Initiative team members and enjoy the opportunity to contribute to a wide array of novel biological discovery projects. As this position is highly collaborative, strong communication skills are needed. The Scientist will engage with outside collaborators, translate their biological questions into novel protein reagents and share these reagents with the larger research community through abstracts, presentations and publications. Responsibilities and Duties -Express, purify, and characterize glycoproteins from mammalian cells -Leverage robotics and automation to increase the quality and throughput of antibody production at IPI -Formulate and package antibodies for use by collaborators and customers -Supervise research associates and coordinate with other scientists to ensure efficient, high-quality antibody production -Actively lead the experimental design and data production for collaborations and scientific publications -Participate in meetings and conferences to engage and recruit outside research groups to participate in the Antibody Initiative Qualifications -PhD degree in mammalian protein expression, protein biochemistry, or structural biology -Well acquainted with best practices in cell culture and reagent production -Ability to work in a fast-paced, intellectually challenging environment -Enthusiastic team member with a strong commitment to mission and a desire to conduct impactful science -Good organizational and documentation skills -The ideal candidate will have recently completed a PhD and have a desire to explore a more entrepreneurial position IPI is an independent 501(3)(c) nonprofit research organization and an equal opportunity employer. The Institute celebrates diversity and is committed to creating an inclusive environment for all employees. If interested, please email your resume to . -- PLEASE NOTE: This message, including any attachments, may include privileged, confidential and/or inside information belonging to IPI. Any distribution or use of this communication by anyone other than the intended recipient(s) is strictly prohibited and may be unlawful. If you are not the intended recipient, please notify the sender by replying to this message and then delete it from your system. Thank you.

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Autosol help: FOM is great but map is trash
by Alex Johnson 19 Feb '21

19 Feb '21

Hi Phenix team, I am attempting to phase a protein structure from SeMet-labeled crystals and have encountered some issues in using Autosol that appear unusual, as they have not been encountered by any members of my group. The short summary is that while I achieved great statistics from beam line collection and Autosol produces solutions with FOM (>0.4) from multiple crystals processed to ~2.4-3.0 A, the output maps are of poor quality and Autobuild can never build with Rfree <0.5. There is only one methionine for the ~30 kDa protein, but the crystals appear to have good anomalous signal with anomalous multiplicity >15 overall and delanon in the inner shell >0.5. There appears to be translational NCS and the dataset can be processed with good statistics in several space groups (P212121, P21212, P2122, etc) but this doesn’t solve the phase problem. The axis drops by half in processing in the P212121 versus P21212 space groups: from one crystal they are 48.37 101.56 110.39 90 90 90 (in P212121) and 101.62 48.35 55.19 90 90 90 (in P21212). If anyone in the community has encountered similar problems please let me know! I am all ears to any possible solutions and am also installing additional methionine for labeling but unsure whether this will overcome the other issues. Thanks, Alex Johnson Postdoc, Kranzusch lab, Dana-Farber Cancer Institute algejohnson(a)gmail.com <mailto:[email protected]>

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Post-Doctoral Position at the University of Illinois to Study Ribosome Structure
by Yury Polikanov 16 Feb '21

16 Feb '21

*Post-Doctoral Position in Structural Biology at the University of Illinois at Chicago (UIC) to Study the Structure and Function of the Ribosome* The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the available *NIH-funded Post-Doctoral Scholar *position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory 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. More information about Dr. Polikanov research can be obtained from the most recent publications (*https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/50395623/public/?sort=date&direction=descending <https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…>*) or found on the web-page (https://bios.uic.edu/bios/people/faculty/yury- polikanov). The successful candidate will be 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. *Basic qualifications:* - PhD in chemistry, biochemistry , biophysics, or a related field; - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); - Experience in structural biology (X-ray crystallography or cryo-EM); - Experience in the RNA biology field is not required but highly desired; *The successful candidate is also expected to:* - Act independently in terms of planning and executing the experiments; - Compile, analyze, and prepare data for publications; - Assist with training of graduate and undergraduate students. Review of applications will begin immediately and will continue until the position is filled. Interested candidates should apply by 04/16/2021 using the following link: https://jobs.uic.edu/job-board/job-details?jobID=142760 or email directly to Dr. Polikanov - yuryp(a)uic.edu. Please make sure to include CV, cover letter, and contact information for three references. *For full consideration, in **the cover letter, describe** how your previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group.* *The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans, and individuals with disabilities are encouraged to apply.* *Offers of employment by the University of Illinois may be subject to approval by the University’s Board of Trustees and are made contingent upon the candidate’s successful completion of any criminal background checks and other pre-employment assessments that may be required for the position being offered. Additional information regarding such pre-employment checks and assessments may be provided as applicable during the hiring process.* *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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postdoctoral position in cryo-EM at LMB in Jan Löwe's group
by Jan Löwe 16 Feb '21

16 Feb '21

Dear all, My group has a grant-funded job opening for a postdoctoral structural biologist to work on problems in archaeal and bacterial cell biology. The aim is to understand cell division and vesicle formation at the molecular or even atomic scales. The work will involve state-of-the-art cryo-EM, biochemistry and tomography (and who knows, maybe even crystallography and/or NMR). We are surrounded here at LMB by many experts and a lot of exciting instrumentation, and given the current state of the project, only the sky (and our imagination) is the limit. Please find the job advert here: https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-… <https://www.nature.com/naturecareers/job/postdoctoral-scientist-structural-…> Please do get in touch if you would like to know more before applying. Best wishes, Jan Jan Löwe MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH UK email: jyl(a)mrc-lmb.cam.ac.uk website: http://www2.mrc-lmb.cam.ac.uk/groups/jyl

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Re: [phenixbb] rotamer outlier and clash socre
by Pavel Afonine 14 Feb '21

14 Feb '21

Hello Pan, """ I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? """ if you used latest version of Phenix, which is dev-4146 as of today: http://phenix-online.org/download/nightly_builds.cgi?show_all=1 then this is not expected, because phenix.real_space_refine has built-in ability to detect which residues need a fix and does an exhaustive grid-search in chi-torsion angle space to optimize it against the map and local environment. If this happened using the latest version of Phenix, then this is an indication to me that something has gone wrong and we need to investigate. For this I'm asking to send all input files. Residues that phenix.real_space_refine was unable to fix for whatever reason are best to fit manually in Coot. And I can't agree more with Tristan -- all the great tools and automation are to help you not substitute you! So, checking manually is important! """ Another question is the value of clash score are also too high. """ You did not tell us the value, so no answer here! A general guidance: the lower the better, but zero is not the goal. """ When I set the nonbonded_weight to 10000 """ According to study we conducted recently: http://phenix-online.org/presentations/nb_weight.pdf this unlikely to be a great idea. Pavel

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rotamer outlier and clash socre
by xiaowp82＠hotmail.com 14 Feb '21

14 Feb '21

Hello everyone I refined a cryo-EM data with 3.2 angstrom, the model fit well with the map, but the rotamer outlier is too high, about 8%. How can I decrease the value of rotamer outlier by realspace.refinement in Phenix GUI, and no need to adjust the residues one by one in Coot? Another question is the value of clash score are also too high. When I set the nonbonded_weight to 10000, the clash score get better, but the value of rotamer outlier get worse. The high clash score maybe due to including hydrogens for refinement? Can I exclude hydrogen for refinement and how to do? Thanks ! Pan xiaowp82(a)hotmail.com

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Phenix ligand identification resolve was not able to finish on the first cycle
by Ahmad Khalifa 14 Feb '21

14 Feb '21

Hello, I want to use phenix.ligand_identification to identify a ligand. I used chimera's volume eraser to erase everything except for the ligand density. I then converted it to mtz. in the phenix.ligand_identification gui, I set reflection data type to difference map. When I ran the job, I got a lot of "Sorry, resolve was not able to finish on the first cycle". Regarding the mtz, I have to contour the map to 170rmsd to visualize it in coot, so something have to be wrong. I appreciate any input. Best regards.

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on phenix uninstall
by Smith Lee 13 Feb '21

13 Feb '21

Dear All, In order to install new version of phenix, should I uninstall the older version of phenix first? If needed, what are the command to uninstall the windows version of phenix and to uninstall the linux version of phenix? Smith

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The weblinks for the Daresbury Laue software source code and information
by John R Helliwell 12 Feb '21

12 Feb '21

Dear Colleagues, The weblinks for the Daresbury Laue software source code and information have become hidden from a simple google search. This short article at IUCr Journals makes clear where the software source code and information can now be found. See:- https://journals.iucr.org/s/issues/2021/02/00/me6120/index.html Best wishes, John Emeritus Professor John R Helliwell DSc

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unable to run coot
by Badmalia, Maulik 12 Feb '21

12 Feb '21

hello team phenix, I hope this email finds you well. I recently downloaded phenix for analysing our cryoEM data, before moving to the data analysis I decided to try the tutorial. I decided to use the autosharpen option first, I was able to access the tutorial but when I clicked on coot I repeatedly got a message saying that "Sorry: the 'coot' command could not be located. We have installed Coot to run on a CentOS platform and has the latest version of Coot on the system. I am a novice with linux and phenix. So any help in this regard would be highly appreciated. Do let me know if you have any questions. Regards, Maulik Maulik D. Badmalia Postdoctoral Researcher Laboratory of Medicinal Biophysics Alberta RNA Research and Training Institute Dept. of Chemistry & Biochemistry University of Lethbridge, Lethbridge, AB, Canada

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Re: [phenixbb] unable to run coot
by Werther, Rachel A 12 Feb '21

12 Feb '21

Hello Maulik, Sometimes uninstalling Xquartz and reinstalling it will correct the link between Phenix and Coot, particularly after computer updates. Best of luck, Rachel Rachel Werther / she & her pronouns / Research Technician III / Campbell Lab / Lab A3-201 / 206-667-4189 / Basic Sciences Division / Fred Hutchinson Cancer Research Center / rwerther(a)fredhutch.org<mailto:[email protected]> From: <phenixbb-bounces(a)phenix-online.org> on behalf of "Badmalia, Maulik" <maulik.badmalia(a)uleth.ca> Date: Thursday, February 11, 2021 at 3:37 PM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] unable to run coot hello team phenix, I hope this email finds you well. I recently downloaded phenix for analysing our cryoEM data, before moving to the data analysis I decided to try the tutorial. I decided to use the autosharpen option first, I was able to access the tutorial but when I clicked on coot I repeatedly got a message saying that "Sorry: the 'coot' command could not be located. We have installed Coot to run on a CentOS platform and has the latest version of Coot on the system. I am a novice with linux and phenix. So any help in this regard would be highly appreciated. Do let me know if you have any questions. Regards, Maulik Maulik D. Badmalia Postdoctoral Researcher Laboratory of Medicinal Biophysics Alberta RNA Research and Training Institute Dept. of Chemistry & Biochemistry University of Lethbridge, Lethbridge, AB, Canada

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NIH-funded Postdoc, Membrane Protein Structural Biology (Nebraska, USA)
by Alex Vecchio 11 Feb '21

11 Feb '21

Dear phenixbb Community, I would like to bring your attention to a posting for a 5-year NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska. We are looking for a recent or soon-to-be Ph.D., with experience in membrane protein biochemistry and one structural technique. Our program is established and has capabilities in X-ray crystallography, SAXS, cryo-EM, and now, microED. For more information, please read our ad HERE <https://jobrxiv.org/job/university-of-nebraska-lincoln-27778-membrane-prote…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -- *Alex J. Vecchio, Ph.D.* *Assistant Professor* University of Nebraska–Lincoln Department of Biochemistry Center for Integrated Biomolecular Communication 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Call for abstracts (Deadline Feb 18): Michael G. Rossmann Memorial Symposium at the Microscopy & Microanalysis 2021
by Hasan, Syed Saif 11 Feb '21

11 Feb '21

*** MICROSCOPY & MICROANALYSIS 2021 ABSTRACT DEADLINE FEBRUARY 18 *** Dear All, Please note that the deadline for submitting abstract for the Michael Rossmann Memorial Symposium at The Microscopy & Microanalysis conference, held in Pittsburgh, Aug 1-5, 2021 is coming up soon: February 18. So get your abstracts in now! ********************************************************************************************************* We cordially invite you to the “Michael G. Rossmann Memorial Symposium” at the Microscopy & Microanalysis 2021 conference, to be held in Pittsburgh, PA, Aug 1-5, 2021. This symposium focuses on the application of hybrid methods in electron microscopy of viruses, enzymes and other macromolecules, areas in which Michael was a pioneer. The symposium will feature invited talks from Prof. Hao Wu (Harvard Medical School), Prof. Rui Zhao (University of Colorado School of Medicine), and Prof. Chuan (River) Xiao (University of Texas El Paso). We invite abstracts from speakers in academics and industry at all career levels who develop and apply cutting-edge structural biology approaches to the study of viruses, viral proteins, enzymes, membrane proteins, and other systems. Ten abstracts will be selected for 15-minute oral presentations whereas the remaining abstracts will have the opportunity to be selected for poster presentations. Please note that the deadline for abstract submission is February 18, 2021. You will have the opportunity to select your preference for either in-person or virtual presentation. For additional meeting information and to register and submit your abstract, visit: https://www.microscopy.org/MandM/2021/ Deadline for abstract submission: February 18, 2021 We look forward to hosting you and learning about your exciting science at the M&M 2021 meeting. Sincerely, Terje Dokland (University of Alabama at Birmingham, Birmingham AL) S. Saif Hasan (University of Maryland School of Medicine, Baltimore MD)

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phenix.polder how to select atoms by _struct_asym.id
by Agnieszka Kiliszek 11 Feb '21

11 Feb '21

Hi everyone, I would like to generate polder maps in phenix of selected ligand molecules using mmCIF files. For me, the most convenient way of selecting atoms of ligand was to use "_struct_asym.id". Therefore I tried syntax selection segid but I received error "no atoms selected". In pymol similar syntax "segi" works for the same mmCIF file. What can be the reason of the error? Is it a way to select atoms of ligand using "_struct_asym.id" in phenix.polder? Best regards, Agnieszka

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Cryo_fit
by Reza Khayat 10 Feb '21

10 Feb '21

Hi, The gaussian filter used to prepare cryo-EM maps for cryo_fit is equivalent to a low pass filter. Can anyone suggest a resolution to low pass filter the map to? Or is this value empirically determined by screening through a number of resolutions? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Re: [phenixbb] Cryo_fit
by Kim, Doo Nam 09 Feb '21

09 Feb '21

Hi Reza, Can anyone suggest a resolution to low pass filter the map to? Or is this value empirically determined by screening through a number of resolutions? ==> Yes, this is somehow empirically determined. I think that my predecessors of cryo_fit used to use 15 A, 10 A, 5 A resolution cryo-EM maps successively to avoid being trapped in local minima when they fit ribosome atomic structure into these. Relevant references: https://www.phenix-online.org/documentation/faqs/cryo_fit2_FAQ.html#how-can… cascade mdff in https://elifesciences.org/articles/16105 best, Doo Nam From: <phenixbb-bounces(a)phenix-online.org> on behalf of Reza Khayat <rkhayat(a)ccny.cuny.edu> Date: Tuesday, February 9, 2021 at 11:51 AM To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] Cryo_fit Check twice before you click! This email originated from outside PNNL. Hi, The gaussian filter used to prepare cryo-EM maps for cryo_fit is equivalent to a low pass filter. Can anyone suggest a resolution to low pass filter the map to? Or is this value empirically determined by screening through a number of resolutions? Thanks. Best wishes, Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031

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Postdoctoral positions at the Massachusetts Institute of Technology
by Thomas Schwartz 07 Feb '21

07 Feb '21

The Schwartz lab <http://schwartzlab.mit.edu/> at Massachusetts Institute of Technology currently has two open positions for postdocs to work on federally funded projects elucidating structure and function of nucleo-cytoplasmic communication. One project involves the structure of the nuclear pore complex (NPC), in particular with the goal to reduce the resolution gap between crystal structures of NPC components and cryo-ET assembly structures. We work at the interface of bio-engineering and structural biology to solve this problem with innovative methods. The second project centers on the mechanical connections between nucleo- and cytoskeleton via LINC complexes. Here, we want to understand the details for LINC complex engagement, with the lamin layer and with actin filaments, in particular. For both projects, the lab has a vast array of reagents, tools, and expertise to build on. MIT has a brand-new, state-of-the-art, fully-staffed cryo-EM facility <https://nanousers.mit.edu/characterizenano-0/automated-cryogenic-electron-m…> equipped with a Talos Arctica / Falcon 3 and a Titan Krios equipped with a Bioquantum/K3 detector and phase plate. We also have cryo-FIB milling capacity. https://nanousers.mit.edu/characterizenano-0/automated-cryogenic-electron-m… <https://nanousers.mit.edu/characterizenano-0/automated-cryogenic-electron-m…> We seek highly motivated individuals with a passion for structural cell biology. A Ph.D. degree in the life sciences with emphasis on biochemistry/structural biology is desired. Candidates should send their application to Thomas Schwartz at tus(a)mit.edu <mailto:[email protected]?subject=postdoc%20position>.

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Open-rank, tenure-line faculty position
by Hasan, Syed Saif 05 Feb '21

05 Feb '21

Dear Colleagues, The Institute for Bioscience & Biotechnology Research (IBBR) and the University of Maryland, College Park Department of Chemistry & Biochemistry invite applications for an open-rank, tenure-line faculty position in structural biology, with an emphasis in the area of biomolecular cryo-electron microscopy (cryoEM), starting August 2021. The faculty member will base their research program on the IBBR campus in Rockville, Maryland, and hold joint appointments with IBBR and the Department of Chemistry & Biochemistry at College Park. The criteria for selection will be proven excellence and potential for impact through original research, scholarship, and teaching. Successful candidates will be expected to develop a vigorous externally funded research program and have a demonstrated commitment to teaching and mentorship at the undergraduate and graduate levels. IBBR is a joint research institute of the University of Maryland and the National Institute of Standards and Technology (NIST), centrally located in Maryland’s biotechnology corridor. The Institute’s mission is to conduct groundbreaking research in the field of biotechnology that generates innovative solutions to major scientific and engineering challenges. The Institute has a long history of excellence in biomolecular structure-function relationships. Current research programs center on the biomolecular engineering of vaccines, biotherapeutics, and diagnostics; biomolecular measurement science; and disease pathways and biomolecular targets. The available instrumentation at IBBR includes a 200 kV Talos Arctica cryoEM with a Falcon 3EC direct electron detector and a 200 kV Glacios cryoEM with a Gatan K3 direct electron detector and a Volta phase plate. The University of Maryland College Park has a Zeiss EM 10 CA TEM equipped with a tilt stage and a JEOL 100CX II TEM. IBBR instrumentation for sample preparation was recently upgraded with a Thermo Fisher Scientific Vitrobot Mark IV and a Gatan cryoplunge 3. IBBR also maintains a high-performance computing cluster with a dedicated 750 TB parallel file system, and two dedicated 8-GPU nodes. These cryo-EM facilities complement other state-of-the-art instrumentation and expertise at IBBR, including NMR, X-ray crystallography, mass spectrometry, and solution X-ray scattering. For details, please see this advertisement: https://ejobs.umd.edu/postings/80583 Best wishes, Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Postdoc position, Plant Hormone Transporting Membrane Proteins (Denmark)
by Bjørn Panyella Pedersen 05 Feb '21

05 Feb '21

Dear colleagues, I have an open postdoc position funded by the ERC (details below). Please pass this along to anyone who might be interested. Thanks! /Bjørn Postdoctoral position in Structure of Plant Hormone Transporting Membrane Proteins at Aarhus University, Denmark. online posting: https://tinyurl.com/MBGpostdoc We are looking for a highly skilled and motivated postdoc with an interest in working on plant hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins and an interest for plant biology. Starting date is negotiable. Funding is available through an ERC grant for at least 2 years of employment. An extension is possible for up to a total maximum of 4 years of employment as a postdoc. The position: The position seeks to strengthen ongoing activities in the laboratory of Bjørn P. Pedersen on structure, related to the function and mechanism of plant hormone-transporting membrane proteins as defined by the ERC project MUM-GROW (pedersenlab.dk). Exact project will be shaped out in dialogue with top runners. The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems, and the methods uses are primarily crystallography and cryo-EM. The group is part of the Section of Structural Biology at Aarhus University. The candidate: A successful candidate has a relevant Ph.D. degree and a solid and documented background in structural biology, biochemistry and/or biophysics. Experience with membrane protein expression and purification is favored, and the candidate must demonstrate an ability and interest to work with membrane proteins with a structural aim. Applicants should be ambitious, show strong collaborative skills, and be able to take initiatives and responsibility within the work environment. The successful candidate is offered: - access to a well-developed research infrastructure. - a research climate inviting lively, open and critical discussion within and across different fields of research. - a working environment with teamwork, close working relations, network activities among young scientists and social activities. - a workplace characterized by professionalism, equality and a healthy work-life balance. The city: In Aarhus you have easy access to beautiful nature, an exciting culture and city life as well as a safe environment for children - a great place for the whole family. The city of Aarhus has everything you need: exciting national and international jobs, delightful residential areas, a rich cultural life, and beautiful surrounding landscape of woods and coastline that make Aarhus a wonderful place to live and work. See https://international.au.dk/life/ for details. Aarhus University offers relocation service to international researchers. You can read more about it at https://international.au.dk/life/researcherscomingtoau/. Deadline: All applications must be made online (https://tinyurl.com/MBGpostdoc) and received by March 1st 2021.

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Re: [phenixbb] refinement with translational ncs
by Jorge Iulek 31 Jan '21

31 Jan '21

Dear Esko, Thank you for your input. I must also look into these papers. Jorge On 1/27/21 10:02 AM, Esko Oksanen wrote: > Dear Jorge, > > With significant translational pseudosymmetry, at least close to a > pseudo-centerering vector, will inevitably lead to higher R-values. > Basically the R-value isn’t a very good indicator of the structure > correctness any more and the expected values for an acentric structure > are no longer really valid. I had a somewhat similar case long ago > (https://doi.org/10.1107/S0907444906031519) and since then there is a > nice paper summarising the effects of pseudosymmetry > (https://doi.org/10.1107/S090744490705531X). > > HTH, > Esko > *_____________________* > * > * > *Esko Oksanen, PhD* > Instrument Scientist - Neutron Macromolecular Crystallography > > European Spallation Source ERIC > P.O Box 176, SE-221 00 Lund, Sweden > Visiting address: Odarslövsvägen 113 224 84 Lund Sweden > Switchboard: +46 46 888 00 00 > Phone: +46 721 79 20 36 > E-mail: esko.oksanen(a)ess.eu <mailto:[email protected]> > > www.ess.eu <http://www.esss.se/> > > > > > > > > >> On 27 Jan 2021, at 11:46, Jorge Iulek <iulek(a)uepg.br >> <mailto:[email protected]>> wrote: >> >> Dear all, >> >> >> I have a dataset at 2.98 A resolution, images processed to CC_1/2 >> at circa 50% in the last resolution shell, tetramer in the asymmetric >> unit, local (rotational) symmetry 222. Xtriage indicates a peak in >> the Patterson function at 20% height of origin peak, at fractional >> coordinates of 0.0000 0.0000 0.3177. Space group is P21. >> >> I am aware that this brings problems to refinement , as even >> stated at xtriage output "Translational pseudo-symmetry is very >> likely present in these data. Be aware that this will change the >> intensity statistics and may impact subsequent analyses, and in >> practice may lead to higher R-factors in refinement.", and so I can't >> lower my R and R-free below ~31 and 36 % , respectively. >> >> At phenix.refine, setting "tncs_correction = True" brings little >> benefit (what does this actually do? points to references are >> welcome). I wonder nevertheless if some strategy might help in on >> lowering these R's and, of course, allow me to build a better model >> (in spite of the resolution). I tried some combinations of other >> types of ncs and tls groups, with little success. Particularly, it >> seems that the refinement of ADPs are a kind of unstable (what I >> would understand come from the - partial - modular nature of the >> intensities - due to tncs - and these - ADP - would be reflected by >> the intensity fall-off with resolution). What about refining ADPs >> only to a zone which is not affect by data modulation? How to do >> that? Any other ideas? >> >> Thanks, >> >> >> Jorge >> >> >> >> >> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org <mailto:[email protected]> >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org >

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refinement with translational ncs
by Jorge Iulek 31 Jan '21

31 Jan '21

Dear all, I have a dataset at 2.98 A resolution, images processed to CC_1/2 at circa 50% in the last resolution shell, tetramer in the asymmetric unit, local (rotational) symmetry 222. Xtriage indicates a peak in the Patterson function at 20% height of origin peak, at fractional coordinates of 0.0000 0.0000 0.3177. Space group is P21. I am aware that this brings problems to refinement , as even stated at xtriage output "Translational pseudo-symmetry is very likely present in these data. Be aware that this will change the intensity statistics and may impact subsequent analyses, and in practice may lead to higher R-factors in refinement.", and so I can't lower my R and R-free below ~31 and 36 % , respectively. At phenix.refine, setting "tncs_correction = True" brings little benefit (what does this actually do? points to references are welcome). I wonder nevertheless if some strategy might help in on lowering these R's and, of course, allow me to build a better model (in spite of the resolution). I tried some combinations of other types of ncs and tls groups, with little success. Particularly, it seems that the refinement of ADPs are a kind of unstable (what I would understand come from the - partial - modular nature of the intensities - due to tncs - and these - ADP - would be reflected by the intensity fall-off with resolution). What about refining ADPs only to a zone which is not affect by data modulation? How to do that? Any other ideas? Thanks, Jorge

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Postdoctoral Fellow Position in CFTR biology at AbbVie
by Jain, Rinku 26 Jan '21

26 Jan '21

Hello Everyone, A postdoctoral position is available immediately in the Cystic Fibrosis Group led by Dr. Ashvani Singh at AbbVie Inc, in Illinois, USA. Successful candidate will work with a cross-functional team of researchers to Investigate the Structure-Function Relationship of CFTR Using CFTR Modulators and Understand their Clinical Translation. Qualified candidate should have a PhD in Biochemistry (Biochemistry/Pharmacology/Cell and Molecular Sciences/Structural Biology) with no more than 3 years of prior postdoctoral experience. Experience in membrane protein expression, purification and biochemistry is required and a strong background in CFTR pharmacology is preferred. Key responsibilities include expression and purification of disease mutants and biochemical, biophysical, and structural studies. Previous experience in Cryo-EM is preferred but not essential. Selected candidate will have the opportunity to learn Cryo-EM. For more information and to apply online, please visit: https://careers.abbvie.com/jobs/2007216?lang=en-us#.X48n8qJQthg.mailto Req ID: 2100410 Thanks, Rinku

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Phenix version 1.19.1 released
by Paul Adams 26 Jan '21

26 Jan '21

The Phenix developers are pleased to announce that version 1.19.1 of Phenix is now available (build 1.19.1-4122). This fixes bugs in the 1.19 release. If you have previously downloaded 1.19 we recommend upgrading to 1.19.1. Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.19.1 version of Phenix: - phenix.real_space_refine - Fix bug in restoring previous jobs - Clarify NCS options Please note that this new 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 is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) 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) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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real space rotamer restrains
by Leonid Sazanov 22 Jan '21

22 Jan '21

Hi, Is there somewhere a description of all the new parameters in phenix.real_space_refine rotamer restrains? I mean rotamers { fit = all *outliers_or_poormap outliers_and_poormap outliers poormap restraints { enabled = True sigma = Auto target = max_distant min_distant exact_match fix_outliers } tuneup = outliers outliers_and_poormap } What is poormap? What is the range of Sigma? What are those types of target? With the latest nightly build, with default parameters starting model with 1% of rotamer outliers ends up with 10% (not using local_search, as it was done before). To minimise number of outliers, which parameters can be changed? Lower Sigma? Switch on tuneup? Thanks for any info! Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at

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phenix.ligandfit, specifiy already generated cif file
by Guenter Fritz 22 Jan '21

22 Jan '21

Dear all, I would like to run phenix.ligandfit with a cif file I have already generated with acedrg or grade. This is not really required, just for comparison reasons. Would be nice. There is the parameter cif_already_generated= False / True But how do I define the cif file? Many thanks and best regards! Guenter

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