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latest nightly build that runs on windows flawless
by Georg Mlynek 31 Jul '23

31 Jul '23

Hi community members, what is the latest latest nightly build that runs on windows flawless? I tried several versions after dev 4815 in the last year but all of them had different bugs. Most importantly the import of old projects should work. Many thanks, br Georg.

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General interest
by John R Helliwell 17 Jul '23

17 Jul '23

Dear Colleagues, I imagine that this book on the History of Scientific Journals: Publishing at The Royal Society 1665-2015, which I have reviewed in the current issue of J Appl Cryst will be of interest:- https://journals.iucr.org/j/issues/2023/04/00/xo0198/index.html My review is open access. The book itself is also open access:- https://www.jstor.org/stable/j.ctv2gz3zp1 Best wishes, John Emeritus Professor John R Helliwell DSc

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Phenix Phaser Question
by hyun4867 11 Jul '23

11 Jul '23

Dear, Everyone Hi all, I am Hyun Jeong. I want to ask you about phenix phaser problem. I obtain diffraction pattern of crystal that is complex. I tried to solve the phase based on the Apo structure i previoulsy solved. Using full-featured phaser, i obtain 18 Phaser solution. This is really strange number. But, the map obtained 18 Phaser solution is fitted in electron density map. May I proceed with processing using the discovered electron map with 18 Phasers? Is it necessary to redo the scaling? I appreciate your request for advice. Best regards, Hyun Jeong

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symmetry finding question
by Dmitry Semchonok 06 Jul '23

06 Jul '23

Dear colleagues, I have a chaperone map with D7 symmetry. But the Phenix «Map symmetry» tool finds only C7. Is there a way to make the software see the D7 symmetry of my protein? Many thanks for considering my request. Sincerely, Dmitry

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Discrepancy between Phenix GUI and command line for MR
by Xavier Brazzolotto 04 Jul '23

04 Jul '23

Dear Phenix users I’ve noticed that molecular replacement was clearly slower while running from the GUI compared to using the command line (phenix.phaser). Did you also observe such behavior? Best Xavier

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General interest, education article
by John R Helliwell 04 Jul '23

04 Jul '23

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Young Crystallographers Meeting in Strasbourg
by Triantafyllidis, Dimitrios P. 29 Jun '23

29 Jun '23

Dear all, We are pleased to announce that the first joint Franco-German Young Crystallographers's Meeting (YCM1) will be held from September 26-29 in Strasbourg. The collaboration of the French and German crystallographic associations and the IB-ID doctoral college will bring a bi-national and international dimension, with the opportunity for participants to present their work in English, either orally (over thirty slots available) or in poster form. The deadline for abstract submission is July 15. The scientific committee, mainly made up of young researchers, is preparing a rich, multidisciplinary program, including meetings with industrialists working in the field of crystallography. We will be delighted to welcome a prestigious guest in the person of Professor Jean-Pierre Sauvage, winner of the 2016 Nobel Prize in Chemistry. Other guests will be announced shortly on our website: https://ycm1.xyz Full details of the spirit of the event and practical details are available online. A special effort has been made to offer very attractive registration fees (140 EUR) including meals and accommodation. This offer is limited to the first 50 registrants, so don't delay your registration! For any question, feel free to contact us at: ycm1.communication(a)gmail.com Please spread the word around, especially to our young colleagues, and we look forward to seeing you in the beautiful city of Strasbourg this autumn! On behalf of the YCM1 organizing committee, Dimitris Triandafillidis ______________________________ Dimitris P. Triandafillidis Hamburg Centre for Ultrafast Imaging Universität Hamburg HARBOR (Building 610) Luruper Chaussee 149, DE-22761 Hamburg, Germany

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Apply NFC operators to get identical 14 homo oligomeric model
by Dmitry Semchonok 28 Jun '23

28 Jun '23

Dear colleagues, I use the «Apply NFC operators» tool and would like to use the option described under the "Configuration" sign. But when I follow these instructions, the outcome model is still a single subunit. Initially, I want to get 14mer (with D7 symmetry) with identical 14 monomers. Could you please prompt how to get it with the «Apply NF operators»? Additionally, the resulting model doesn't contain description information in the newly created PDB file. Would you happen to know how to get the correct PDB file? Thanks in advance. Kind regards, Dmitry

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Postdoctoral position in method development (York Structural Biology Laboratory)
by Jon Agirre 27 Jun '23

27 Jun '23

Dear all, Applications are invited for a Postdoctoral Research Associate position, funded by the Royal Society, for up to 30 months to work with Dr Jon Agirre in the Department of Chemistry. The successful applicant will join a vibrant team of researchers at the heart of the world-leading York Structural Biology Laboratory (YSBL). The work of the laboratory over the years has included the delivery of world-leading methods and experimental discoveries, training and nurturing hundreds of outstanding scientists in the process. Role The AlphaFold software for protein model prediction has revolutionised workflows in structural biology. However, while high-accuracy models are now available for most human proteins of medical relevance, up to 50% of those proteins are expected to be glycosylated – a modification whose structure AlphaFold does not predict. Protein glycosylation is greatly important, with implications for protein folding and molecular recognition including, as evidenced by the spike glycoprotein of SARS-CoV-2, viral infection. In collaboration with other scientists, we have extended the Privateer software to interactively build missing glycosylation onto precalculated AlphaFold models. In parallel, we have developed analyses that allow us to get a clear picture of glycans and their interactions, including H-bonds and XH-Pi interactions. We expect that these methods will enable us to, based on existing glycobiological knowledge, extend the Privateer software to automatically complete AlphaFold models with crucial missing glycosylation components. We are seeking a person with an interest in both biology and coding, who can collaborate with others in a very diverse team with a mission to further our knowledge of glycobiology and seize the opportunities presented by a deeper understanding of it. Main duties and responsibilities To develop and extend the Privateer software to complete AlphaFold models with the missing glycan components. To further our existing collaborations with CCP4, CCP-EM, PDB-REDO, the Protein Data Bank and the AlphaFold Protein Structure Database. Department The Department of Chemistry is one of the largest and most successful departments at York and we are renowned internationally for our research. As a department, we strive to provide a working environment that allows all staff and students to contribute fully, to flourish, and to excel. We are proud of our Athena Swan Gold Award. The Department of Chemistry values all employees for the qualities and skills they bring to the workplace and aims to be a diverse and egalitarian community in which all can thrive. For informal enquiries: please contact Dr Jon Agirre, jon.agirre(a)york.ac.uk To apply: https://jobs.york.ac.uk/vacancy/research-associate-529961.html Deadline for applications: 20 August 2023. Many thanks for making it this far in the advert! With best wishes, Jon -- Dr Jon Agirre Royal Society University Research Fellow (assistant professor) CCP4 WG2 co-chair | instruct-ERIC representative @ 3D-Bioinfo SC (Elixir) York Structural Biology Laboratory, Department of Chemistry University of York, Heslington, YO10 5DD, York, UK

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problems in running Phenix
by Gianluca Cioci 26 Jun '23

26 Jun '23

Dear All, I am experiencing difficulties in installing Phenix in my Linux system based on Ubuntu 20.04.6 LTS (GNU/Linux 5.15.0-75-generic x86_64) Installation is completed, but when I try tu run phenix I get the message: 12:57:27: Cannot set locale to language "English". 12:57:27: locale 'en_GB' cannot be set. and in the terminal I get: Error in sys.excepthook: Traceback (most recent call last): File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 898, in _excepthook Error.show_exception_dialog(type, value, traceback) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/Error.py", line 76, in show_exception_dialog if (app.bug_timer.IsRunning() is False): AttributeError: 'PhenixApp' object has no attribute 'bug_timer' Original exception was: Traceback (most recent call last): File "/data/software/phenix/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 23, in <module> run(sys.argv[1:]) File "/data/software/phenix/phenix-1.20.1-4487/build/../modules/phenix/wxGUI2/command_line/main.py", line 17, in run wxapp = App.PhenixApp(args) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 74, in __init__ wx.App.__init__(self, 0) File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8628, in __init__ self._BootstrapApp() File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_core.py", line 8196, in _BootstrapApp return _core_.PyApp__BootstrapApp(*args, **kwargs) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 108, in OnInit show_splash_screen(timeout=2000) File "/data/software/phenix/phenix-1.20.1-4487/modules/phenix/wxGUI2/App.py", line 952, in show_splash_screen dlg,-1,citations.format_citation(citations.citations_db.get("phenix"))) File "/data/software/phenix/phenix-1.20.1-4487/conda_base/lib/python2.7/site-packages/wx-3.0-gtk2/wx/_controls.py", line 997, in __init__ _controls_.StaticText_swiginit(self,_controls_.new_StaticText(*args, **kwargs)) UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 40: ordinal not in range(128) Anyone has a working solution for this ? We have tried to change the locale to en_GB, but still it's not working. With many thanks, GIA -- Dr. Gianluca CIOCI Toulouse Biotechnology Institute (TBI) https://www.toulouse-biotechnology-institute.fr/en/poles/equipe-cimes/ PICT - Plateforme Intégrée de Criblage de Toulouse http://www.pict.ipbs.fr/ Tel: +33 (0)5 61 55 97 68 E-mail: cioci(a)insa-toulouse.fr TBI - INSA Toulouse 135 avenue de Rangueil 31077 Toulouse CEDEX 04 http://www.toulouse-biotechnology-institute.fr

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