- phenixbb - phenix-online.org

Potential website disruptions
by Billy Poon 11 Apr '23

11 Apr '23

Hi everyone, We are doing some maintenance on our websites, https://phenix-online.org and https://cci.lbl.gov, over the next few days. There may be some disruptions. Thanks in advance for your patience. -- 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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ALS Webinar April 10th
by Paul Adams 05 Apr '23

05 Apr '23

Dear Colleagues, A reminder that we will be hosting a webinar (registration link below) that provides information for the synchrotron structural biology user community about accessing the resources at the Advanced Light Source in Berkeley. This is timely because of the imminent closure of the Advanced Photon Source for a year for their upgrade. Synchrotron capacity for biosciences research will be significantly impacted, and we want to be sure that the community has information about alternative facilities during the APS dark time. http://als-enable.lbl.gov/wordpress/2023/03/14/als-enable-webinar-april-10t… The webinar will cover capabilities at the beamlines in macromolecular crystallography, small angle X-ray scattering, and X-ray footprinting, as well as information on how to apply for beamtime. While the webinar is of most relevance to the US research community, we welcome participation by anyone who is 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 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 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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Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 03 Apr '23

03 Apr '23

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in structure of sugar and phytohormone transporting membrane proteins at Aarhus University, Denmark. online posting: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-s… We are looking for a highly skilled and motivated postdoc with an interest in working on sugar and hormone transporting membrane transporters and preferably with a proven track record in the area of structural and/or functional analysis of membrane proteins. The position will be open from summer 2023, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of sugar-transporting and hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Bavnhøj et al. “Molecular mechanism of sugar transport in plants unveiled by structures of glucose/H+ symporter STP10” Nature Plants 7 (2021) Ung et al. “Structures and mechanism of the plant PIN-FORMED auxin transporter” Nature 609 (2022). The laboratory's interest is the interplay between structure and function of transmembrane transport processes with a focus on metabolite uptake systems and proton driven transport, and the methods uses are primarily structural biology (cryo-EM, crystallography) and biochemistry. 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. - an exciting interdisciplinary environment with many national, international and industrial collaborators. - 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 “life in Denmark” at Aarhus and surroundings for further details on the city and the university (https://international.au.dk/life/locations/aarhusandsurroundings). Deadline: All applications must be made online and received by 15. May. 2023. See deails here: https://www.au.dk/om/stillinger/job/postdoctoral-position-in-structure-of-s…

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restraints_edits.params -- inquiries -- issues
by p.auffinger 30 Mar '23

30 Mar '23

Hi phenix users, I started to add restraints to a large ribosomal file by using the file (in full) below. I encountered two issues: 1) The first one is: how to use this file in the GUI? It seems to get rejected while its accepted when I run phenix through the command line. 2) The second is: restraints involving water molecules with residue numbers > 9999 get rejected. Could that limit be overcome through a future patch? ### refinement.geometry_restraints.edits { MG_8078 = chain 0 and resname MG and resid 8078 and name MG W_12641 = chain 0 and resname HOH and resid 12641 and name O bond { action = *add atom_selection_1 = $MG_8078 atom_selection_2 = $W_12641 symmetry_operation = None distance_ideal = 2.2 sigma = 0.1 slack = None } } ### Thanks for any thoughts on this, Pascal ----- Pascal Auffinger IBMC/CNRS 15 rue René Descartes 67084 Strasbourg Cedex p.auffinger(a)ibmc-cnrs.unistra.fr -----

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27th Annual SCSB Structural Biology Symposium - Registration NOW OPEN
by White, Mark 21 Mar '23

21 Mar '23

You and your colleagues are cordially invited to join us for the 27th Annual Structural Biology Symposium to be held on April 29, 2023 in Levin Hall, UTMB Galveston. The meeting is organized by the Sealy Center for Structural Biology & Molecular Biophysics and co-sponsored by the Keck Center for Computational & Structural Biology. This year’s speakers include: Yunfeng Chen Ph.D. Univ. of Texas Medical Branch Ruben L. Gonzalez Jr., Ph.D. Columbia University John A. Tainer, Ph.D. University of Texas MD Anderson Cancer Center David W. Taylor, Ph.D. University of Texas Junjie Zhang Ph.D. Texas A&M University To register or for more information, visit https://scsb.utmb.edu/symposium Mark Andrew White, Ph.D. Associate Professor of Biochemistry & Molecular Biology, UTMB, Galveston, TX 409.747.4747 https://xray.utmb.edu ________________________________

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Save the date! “Not the GRC” on Diffraction Methods in Structural Biology 2024
by Winter, Graeme (DLSLtd,RAL,LSCI) 17 Mar '23

17 Mar '23

Good afternoon all, “Not the Gordon Research Conference” on Diffraction Methods in Structural Biology 2024 - Experiments and Measurements Organisers: Graeme Winter, Kunio Hirata (NTGRC-chairs) Helena Taberman, Ali Ebrahim (NTGRS-chairs) Local organisers - Arwen Pearson, Ashwin Chari As you will have seen from a message from James Holton last year, the GRC have decided that the 2024 meeting on Diffraction Methods will not be further supported. We are not deterred! A number of the GRC ex-chairs and those nominated for chairing the next meeting feel that this opportunity for the diffraction methods community to come together is important enough that it should continue to happen, even without GRC support. We are therefore delighted to launch the “Not-the-GRC Diffraction methods in Structural Biology”. The topic of the meeting will be “Experiments and Measurements” and we have a great lineup of speakers in mind. Where: https://www.harnackhaus-berlin.mpg.de/en When: 21st - 27th July 2024 i.e. about when the next diffraction methods meeting would have been. Starting with the model of the GRC, since we collectively believe it is a fantastic meeting, we plan to make a few improvements (better accommodation and acoustics, fewer minimum attendees to keep the feel of a small meeting) and we will keep the equivalent of the GRS before the main meeting, as well as the free afternoons for collaborative discussion, and the strong emphasis on being able to talk to everyone. We will also keep the focus on new ideas and so follow the protocol of not recording presentations and encouraging the presentation of unpublished data and ideas. With that in mind, this will be a small meeting (100-120 maximum) so there will be an application process and we will open registration in January 2024. We also want as many early career people as possible - the last GRC was refreshing and fun with a lot of new faces, and this is something we want to build on. So, please hold the date in your calendar and we look forward to sharing the scientific programme with you in the coming months and seeing many of you in Berlin next summer. All the best Graeme, Kunio, Helena, Ali, Arwen and Ashwin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Postdoc positions in cryo-EM development at the MRC Laboratory of Molecular Biology, Cambridge UK
by Jan Löwe 13 Mar '23

13 Mar '23

*Postdoctoral positions available in cryo-EM methods development at the MRC Laboratory of Molecular Biology, Cambridge UK, in the groups of Chris Russo and Jan Löwe* We have one position each available, funded for two years as part of the LMB’s Blue Sky collaboration with AstraZeneca. The project, in collaboration with Kasim Sader at AZ aims to develop novel methods to overcome problems with sample denaturation and preferred orientation during vitrification of thin aqueous films. Ideas involve outrunning the processes involved and modifying the air-water interfaces. The ultimate goal is to make cryo-EM sample preparation a much more universal (and enjoyable) process. Cryo-EM experience will be beneficial and a strong desire to engage deeply in technical developments is a must. The LMB and AZ provide everything required, including a highly collaborative and friendly environment, as well as one of the world’s best institutional cryo-EM setups, including state-of-the-art machine and electronics workshops, a clean room dedicated to grid fabrication, and soon four Titan Krios microscopes. More details and on how to apply are here: https://www.nature.com/naturecareers/job/12796284/postdoctoral-scientist-st… https://www.nature.com/naturecareers/job/12796280/postdoctoral-scientist-st… Chris, Kasim and Jan Jan Löwe MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK Email: jyl(a)mrc-lmb.cam.ac.uk Phone +44 1223 26 7644 Website: http://www2.mrc-lmb.cam.ac.uk/groups/jyl Christopher J Russo  MRC Laboratory of Molecular Biology  Cambridge, CB2 0QH, UK Email: crusso(a)mrc-lmb.cam.ac.uk  Phone +44 1223 26 7535 Website http://www.mrc-lmb.cam.ac.uk/crusso/

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Local restraints
by Luca Pellegrini 07 Mar '23

07 Mar '23

How can I freeze a set of atoms in phenix.real_space_refine? I've got an arginine side chain that is consistently misplaced during refinement, and I’d like to restrain its movement. I notice that refinement.geometry_restraints.edits.scale_restraints is not available anymore, is there another way? Thanks, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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Two postdoctoral positions at CNB-CSIC, Spain
by Carmen San Martin 23 Feb '23

23 Feb '23

Dear all, Please find here information on two open positions on structural biology / protein design: https://saco.csic.es/index.php/s/gFm9EKLMNBWD2G8 Regards, ------------------------------------------------------------- Carmen San Martín, Ph. D. Centro Nacional de Biotecnología (CNB-CSIC) Darwin, 3 28049-Madrid (SPAIN) Email: carmen(a)cnb.csic.es Phone: 34-91-5855450 (internal: 432228) Fax: 34-91-5854506 <http://www.cnb.csic.es/> http://wwwuser.cnb.csic.es/~sanmartinlab http://www.microscopia.org ------------------------------------------------------------

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Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023
by Armando Albert 19 Feb '23

19 Feb '23

Dear all, The registration for the next edition of the Macromolecular Crystallography School in Madrid from the 8th to the 12th of May 2023 is open. The workshop has been organized at Instituto de Química Física Rocasolano CSIC since 2010 and it is meant for 25 graduate students or researchers with previous expertise in crystallography and/or CryoEM who need a deeper insight into the most advanced crystallographic and CryoEM techniques to carry out their research projects. The program traditionally covers aspects such as sample preparation, structure solution, model building, crystallographic refinement, validation, and analysis of the structural results, as well as an overview of the newest structural biology technologies. On top of these subjects, this year's program will include those aspects related to the impact of Artificial Intelligence methods on structure solution and low-resolution refinement. In addition, we will cover dynamic crystallography at XFEL and synchrotron and ligand building for drug discovery. You may find further information on our website (https://www.xtal.iqfr.csic.es/MCCS2023/index.html <https://linkprotect.cudasvc.com/url?a=https%3a%2f%2fwww.xtal.iqfr.csic.es%2…>) Hoping to see you In Madrid Juan and Armando Armando Albert and Juan A. Hermoso Departamento de Cristalografía y Biología Estructural Instituto de Química Física "Rocasolano", Consejo Superior de Investigaciones Científicas Serrano 119, 28006 Madrid Spain

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