- phenixbb - phenix-online.org

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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