October 2024 - phenixbb - phenix-online.org

Re: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models
by Karen McIntyre - STFC UKRI 05 Dec '24

05 Dec '24

Just a reminder that registration is open for the CCP4 Study Weekend taking place in January 2025. Early bird deadline is 11 November so if you want to save some money or are a student wanting a standard bursary register ASAP. Applications for Travel bursaries are now open but close at the end of the month so get your applications in now! Hope to see you there!! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK) From: McIntyre, Karen (STFC,RAL,SC) Sent: 26 September 2024 13:15 To: CCP4 WG2 <ccp4wg2(a)listserv.stfc.ac.uk>; CCP4 WG1 <ccp4wg1(a)listserv.stfc.ac.uk>; ccp4bb(a)jiscmail.ac.uk Subject: Registration now open for CCP4 Study Weekend 2025 - Using software, AI and other methods to advance macromolecular models Importance: High Dear all, Registration is now open for the 2025 CCP4 study weekend entitled " Using software, AI and other methods to advance macromolecular models". This year the CCP4 Study Weekend will be held as a hybrid event from the 7th to 9th January 2025, enabling people to choose whether to attend in-person or virtually. The in-person event will be held at the East Midlands Conference Centre, Nottingham, UK. We would like to invite you to another iteration of the ever-popular CCP4 Study Weekend - to start the year 2025 with a lot of fresh ideas, new insights and (hopefully) new friends and contacts to boost. As always it will be an eclectic mix of bleeding-edge science, in-depth presentations, discussion panel, poster-sessions, hands-on tutorials and plenty of opportunities for social interactions. For full details, programme, logistics and registration, please visit the Study Weekend website<https://studyweekend.ccp4.ac.uk/>. There is no better way to start 2025 than to put participation in that exciting meeting at the top of your "New Year's Resolutions" list! Key Dates: * Early bird registration final date: 11 November 2024; * Standard Student bursaries are open to all students registering during early bird period i.e. now until 11 November which cover the cost of registration plus one night accommodation in halls (1 night in hotel will be subsidised for those students choosing to stay in the hotel); * Travel bursaries are available for students and young postdocs studying at overseas labs to help cover cost of travel to UK. The deadline for applications is 31 October 2024; * Registration for in-person delegates closes 4 December 2023 (or earlier if in-person places sell out although you will be able to join the in-person waitlist). * Registration for virtual delegates will close 9 January 2025. Key Timings Diamond MX user meeting will start at 11:00 on 7TH January 2025 CCP4 study weekend 2025 will start at ~17:30 on 7th January 2025 the event will finish at ~16:30 on 9th January 2025 We hope to see you there! Scientific Organisers: Elke De Zitter (Institut de Biologie Structurale, FRANCE) Deborah Harrus (EMBL-EBI, UK) Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) Administrative Organisers: Karen McIntyre (CCP4, UK)

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RapiData at SSRL 2024
by Smith, Clyde 17 Nov '24

17 Nov '24

Hi everyone, Applications are now open for the 2024 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from April 29 to May 4, 2024. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, Data collection strategies, X-ray light sources, X-ray detectors, Data reduction, Structure solution by MAD, SAD and Molecular Replacement, Complementary methods (spectroscopy and small angle scattering) Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2024/ and use the links on the "Application and Registration" page to apply for the course. The application deadline is January 31, 2024. Successful applicants will be notified early in February 2024 and invited to register and book accommodation at SLAC Stanford Guesthouse at that time. A limited amount of support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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Re: [phenixbb] red blobs (Andrea Smith)
by Kay Diederichs 31 Oct '24

31 Oct '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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AQuaRef - issues with torch-cluster installation
by Martin Malý 16 Oct '24

16 Oct '24

Dear colleagues, I'm trying to install AQuaRef. However, I'm struggling with running `bash config/update_phenix.sh aimnet2` which is part of `bash build_into_phenix.sh aimnet2`. This script wants to install the python package torch-cluster. However, I'm getting the error: /opt/phenix/phenix-dev-5480/conda_base/lib/python3.9/site-packages/torch/include/torch/csrc/python_headers.h:12:10: fatal error: Python.h: No such file or directory 12 | #include <Python.h> | ^~~~~~~~~~ compilation terminated. error: command '/usr/bin/gcc' failed with exit code 1 [end of output] I'm getting the same error when I tried to install only this package using the command `qrefine.python -m pip install torch-cluster`. I have a laptop with Ubuntu 22.04. I have all the usual development packages installed (build-essential, linux-headers, gcc, g++, ...). According Python, I have libpython3-dev, libpython3.10-dev, python3-dev, python3.10-dev. I can see that qrefine.python has a version of 3.9, so I also installed libpython3.9-dev, python3.9-dev and python3.9-distutils from ppa:deadsnakes/ppa but it did not help. I am also attaching a full log from the torch-cluster installation. It seems that the package torch has been installed successfully in prior. Do you have please an idea what is wrong and how to fix it? Thank you. Martin

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help for the 4.3 A dataset
by princeadam＠163.com 15 Oct '24

15 Oct '24

Dear colleagues, I am currently engaged in an endeavor to unravel the crystal structure through molecular replacement techniques. Regrettably, the resolution attained stands at a rather low mark, approximately 4.3 Angstroms, which poses significant challenges. Despite exhaustive efforts directed towards optimizing the crystal conditions, there has been no discernible improvement in the resolution. The structure in question is confined to a specific domain, and we have at our disposal two distinct conformational models sourced from the PDB database: one derived from X-ray data and the other from Cryo-EM. Our prime objective is to meticulously discern which of these two conformations aligns most accurately with our experimental context. To this end, we have employed both structures (X-ray and Cryo-EM) as templates for molecular replacement, yet the refinement process has hit a roadblock, hindering our progress. We are seeking a collaborator with experience in dealing with low-resolution data to assist in solving the structure. We are open to sharing first or corresponding authorships in the near future for this paper. Warm regards Hui

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