- phenixbb - phenix-online.org

Phenix error in real space refinement with ligand
by Yung-Chieh Chen 04 Dec '24

04 Dec '24

Dear all, I'm trying to refine my model bound with a ligand bearing a -SF5 moiety (-pentafluorosulfanyl). I have used openbabel/Grade web server or REEL to generate/edit the cif file for the ligand. I could obtain the desired octahedral geometry for the -SF5 group. However, both cases failed in real space refinement and I got the following error message: "Number of atoms with unknown nonbonded energy type symbols: 22337...". I would be very grateful if anyone can share experience about how to tackle this issue. Thanks in advance. Best wishes, Yung-Chieh Chen

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Polder map
by jirivitali＠gmail.com 28 Nov '24

28 Nov '24

Dear Phenix user I wanted to create Polder map. I just used single atom or residues and it works fine. There is also a option for the compute box but I am more interested to create map by selecting more than one resides but without using the compute box. Is it possible? and what will be the syntax for this. best J. Vitali

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open position for a 2(+2) year postdoc working on plant hormone transport at Aarhus University, Denmark.
by Bjørn Panyella Pedersen 25 Nov '24

25 Nov '24

Dear colleagues, Please pass this along anyone who might be interested. Thanks! /Bjørn Postdoctoral position in biophysical and structural characterization of auxin transport, Aarhus University, Denmark online posting: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral… We are looking for a highly skilled and motivated postdoc with an interest in working on auxin 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 spring 2025, but starting date is negotiable. Funding is available for at least 2 years of employment, with an extension possible for up to a total of 4 years. The position: The position seeks to strengthen ongoing activities in the our group related to the function and mechanism of hormone-transporting membrane proteins in plants (pedersenlab.dk). Examples of our research can be found in: Schulz & Ung et al. "Transport of herbicides by PIN-FORMED auxin transporters" bioRxiv (2024) Andersen et al. Basis of Glucose and Fructose Selectivity in Sugar Transport Proteins" bioRxiv (2024) Bavnhøj et al. “Structure and sucrose binding mechanism of the plant SUC1 sucrose transporter.” Nature Plants 7 (2023) 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 20. Dec. 2024. See details here: https://international.au.dk/about/profile/vacant-positions/job/postdoctoral…

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PostDoc position in time resolved serial crystallography at ESRF ID29 beamline
by Daniele de Sanctis 16 Nov '24

16 Nov '24

Dear all, We have an exciting opportunity for a Post Doc position at the new ID29 serial crystallography beamline at the ESRF. Cheers Daniele The ID29 beamline is the first serial crystallography beamline for room temperature, time-resolved studies at a high energy 4th generation synchrotron. It delivers an unmatched flux density, enabling diffraction data collection from micro-sized samples in a few microseconds, allowing exploration of structural changes at room temperature. The beamline features state-of-the-art equipment, with fast goniometer for fixed target and liquid sample delivery, a high dynamic range integrating detector and laser probes. A dedicated sample preparation laboratory supports crystal delivery systems like injectors, fixed targets and microfluidic devices. You will focus on developing novel environments for crystal handling and delivery systems for serial crystallography experiments, as well as novel data collection methods and applying them to study time-resolved enzymatic reactions in crystals. You will also participate in beamline operations, support external users as the local contact, and have the opportunity to develop your own research and collaborations. Further information please contact Daniele de Sanctis (tel.: +33 (0)4 76 88 28 69, email: daniele.de_sanctis(a)esrf.fr <XXX(a)esrf.fr>). Applications should be submitted through the ESRF portal https://esrf.gestmax.eu/1816/1/post-doc-on-id29/en_US Expected profile - PhD in chemistry, physics, biophysics, biology or closely related science obtained less than 3 years ago - A strong background in X-ray crystallography and serial crystallography is desirable - A strong interest in new method development - Ability to interact with multi-disciplinary staff and facility users - English proficiency (working language at the ESRF) Working conditions The salary will be calculated on the basis of relevant qualifications and professional experience. Do you recognize yourself in this description? Apply now for your next professional adventure! What we offer: 1. *Join* an innovative international research institute, with a workforce from 38 different countries 2. *Collaborate* with global experts to advance science and address societal challenges 3. Come and live in a *vibrant city*, in the heart of the Alps, and Europe's Green Capital 2022 4. *Enjoy* a workplace designed to support your *quality of life* 5. Benefit from our* competitive compensation* and *allowances* *package*, including *financial support for your relocation to Grenoble* For further information on employment terms and conditions, please refer to https://www.esrf.fr/home/Jobs/what-we-offer.html The ESRF is an equal opportunity employer and encourages applications from disabled persons.

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Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 01 Nov '24

01 Nov '24

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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Tool to calculate Q-scores?
by Guillaume Gaullier 29 Oct '24

29 Oct '24

Hello phenixbb, It would be convenient to have a tool to calculate Q-scores [1], with suggested command-line name phenix.qscore or phenix.model_map_qscore. It would work just like phenix.model_map_cc but report Q-scores instead (average per chain by default, but if requested also per-residue backbone / side chain / whole residue averages, or per ligand). And phenix.validation_cryoem could report these scores as well, in addition to the CCs that it already reports. There is already a tool to do this in ChimeraX [2], which is very helpful for interactive work. But for automated calculation of these scores from many models and maps, it would be more convenient to have a phenix tool for it. If it already exists, sorry I overlooked it (but I looked up both the latest documentation and phenix command completion and couldn't find anything like it), and I'll be happy if somebody can point me to it! Cheers, Guillaume [1]: https://doi.org/10.1038/s41592-020-0731-1 [2]: https://github.com/tristanic/chimerax-qscore När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy

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MASSIF-1 10 year celebration symposium
by Matthew BOWLER 25 Oct '24

25 Oct '24

Dear CCP4 community, I would like to draw your attention to a one day symposium we are holding here in Grenoble to celebrate 10 years of fully automatic data collection at the ESRF/EMBL beamline MASSIF-1 - from starting with basic characterisation and data collection we now measure crystal volumes, dynamically adapt beam diameters, automatically collect and merge kappa sweeps, helical and multi-crystal data sets and even automatically mount crystals from trays using the EMBL CrystalDirect robot. With a great line-up of speakers we will highlight some of the research enabled by MASSIF-1, how it has inspired other beamlines around the world, as well as some history of the project. You can find more details in the attached flyer and register in the link below. We look forward to seeing you in Grenoble! Matthew Bowler and Didier Nurizzo. https://www.esrf.fr/home/events/conferences/2024/massif-1-symposium.html -- Matthew Bowler Project Leader MASSIF1@ESRF European Molecular Biology Laboratory 71 avenue des Martyrs CS 90181 F-38042 Grenoble France =================================================== Tel: +33 (0) 4.76.20.76.37 Fax: +33 (0) 4.76.20.71.99 http://www.embl.fr/ http://www.esrf.eu/MASSIF1 https://twitter.com/id30_massif1 https://www.embl.org/people/person/mbowler/ ===================================================

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Bursaries available for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 25 Oct '24

25 Oct '24

Standard Student Bursaries As in year’s past, CCP4 has made funding available for students, to help with the costs of attending Study Weekend, in the form of a bursary. All students are eligible for a standard bursary which covers the registration fee plus one night’s accommodation in halls. Bursaries will be given out to all students registering during the early bird registration period – 26th September to 11th November 2024. Students obtaining a standard bursary will only need to pay for any additional night’s accommodation. Students wishing to stay in the hotel rather than Rutland halls, will have 1 nights accommodation subsidised at the halls rate and will therefore pay a reduced rate for this night. Additional nights accommodation will need to be paid at the standard cost. Please also note that should you obtain a bursary and cancel after the latest cancellation date of 6 December 2024 you WILL be liable to pay.  This is because we have had a number of students obtaining bursaries and then cancelling last minute.  Places can be transferred to other people at no charge.  Travel bursaries Limited funds will also be made available to help pay travel costs for students and young post-docs from non-UK laboratories. Please send a separate letter, signed by your supervisor and stating the expected cost of travel in pounds sterling, to justify applications for travel support. Supervisors are asked to nominate only one candidate from their Laboratory. Delegates are expected to travel by the most economic means possible. Candidates from less favoured regions will be given preference. Applications should be e-mailed to ccp4sw(a)stfc.ac.uk<mailto:[email protected]> : Lauren Giles CCP4 Study Weekend Travel Bursary Applications for travel bursaries need to be in by Thursday 31st October 2024. Regards Karen McIntyre CCP4 Project Administrator CCP4 ED&I Champion UKRI-STFC Rutherford Appleton Laboratory Harwell Campus Didcot OX11 0QX Phone: +44 (0) 1235 44 5790 [cid:[email protected]] STFC is part of UK Research and Innovation, a public body funded by the UK government. For more information visit www.ukri.org<http://www.ukri.org/> [A grey circle with red text Description automatically generated] Affiliatated Member of the Institute for Continuous Improvement in the Public Sector ***Please note I only work part-time – hours are Monday to Thursday 08:30 to 13:30 and Friday 10:30 to 15:30**********

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working with composite models
by Dmitry Semchonok 24 Oct '24

24 Oct '24

Dear Colleagues, We're encountering an issue with composite model refinement and would appreciate your advice. Our scenario: 1. We built two separate models based on two subtracted maps of a single complex. 2. We have a lower-resolution map of the full complex. 3. We merged the two models into the full complex and refined it against the full map. The problem: When refining the merged model against the full map using real-space refinement in Phenix, the clashscore progressively worsens. Has anyone experienced similar issues, or can you offer suggestions on addressing this problem? Thank you for your insights. Best regards, Dmitry

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About cryo-EM map sharpening in Phenix
by Shanti Pal Gangwar 17 Oct '24

17 Oct '24

Hello everyone, I'm working on anisotropic map sharpening in Phenix version 1.21-5207-00 with a cryo-EM map of a multiprotein complex. Should I provide the sequence files for each component individually, or would it be better to compile all the sequences into a single file? In addition, shall I provide the full sequence even if a segment of the protein is not resolved in the map? I would appreciate any advice! Shanti Pal

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