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With kind regards, Elisabeth Laurent >>> CCP4BB automatic digest system <lists...@jiscmail.ac.uk> 23.12.23 01:00 >>> There are 4 messages totaling 667 lines in this issue. Topics of the day: 1. Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble 2. Postdoc opportunity at the PSI of Switzerland. 3. Relion issue with MPI 4. Relion issue with MPI ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ---------------------------------------------------------------------- Date: Fri, 22 Dec 2023 10:20:57 +0100 From: Elke De Zitter <elke.de-zit...@ibs.fr> Subject: Two-year postdoctoral position in time-resolved crystallography at IBS in Grenoble Dear all, We have an immediate opening for a two-year postdoctoral researcher in SNaX team of the DYNAMOP group at the Institute for Structural Biology in Grenoble (France). The successful candidate will work on the development and optimization of bio-scavengers towards toxic organophosphorus compounds. To attain this goal, the researcher will use time-resolved crystallography and in silico protein design methods. The position is funded by the French National Research Agency via the University Grenoble Alpes, and is open for a young researcher. Applicants must have obtained a Ph.D. in structural biology, biochemistry, biophysics, physics, chemistry, or a related field, no more than two years before the start of the project. The candidate must show a track-record of publications in peer-reviewed journals, and is expected to be proficient in English and highly motivated to learn new skills. The candidate will work in the multidisciplinary DYNAMOP group and thus needs to be a good team player as well as being capable of working independently. While the research will be carried out in English, non-French-speaking candidates are expected to learn the basics of French in order to facilitate communication and integration into the laboratory. Experience with one or more of the following skills would be highly evaluated: protein design or the usage of artificial intelligence for structural biology, protein expression and purification, protein crystallization and macromolecular crystallography, serial crystallography, programming or scripting. Interested candidates can apply via [ https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996 | https://emploi.univ-grenoble-alpes.fr/offres/doctorants/postdoctoral-researcher-in-time-resolved-crystallography-1357683.kjsp?RH=1135797159702996 ] . We advice to contact Elke De Zitter (elke.de-zit...@ibs.fr) to obtain more information about the postdoctoral position and application procedure. All the best, Elke Elke De Zitter Institut de Biologie Structurale - IBS group DYNAMOP 71 avenue des Martyrs 38044 Grenoble Cedex 9, France +33 4 57 42 86 56 elke.de-zit...@ibs.fr ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ------------------------------ Date: Fri, 22 Dec 2023 12:11:40 +0000 From: Panneels Valérie <valerie.panne...@psi.ch> Subject: Postdoc opportunity at the PSI of Switzerland. Dear Colleagues, The Laboratory of Biomolecular Research at the Paul Scherrer Institute (PSI), Switzerland, is advertising for a Postdoc position from the NanoArgovia Programm of the Swiss Nanoscience Institute (SNI). This project is granted for one year and extendable to 2 years. The project is based on Electron Diffraction Crystallography on proteins either photosensitive or involved in pharma applications. The PSI is the largest research institute for natural and engineering sciences in Switzerland (https://www.psi.ch/en) and hosts a synchrotron, the X-ray free electron laser SwissFEL and an electron microscopy facility (https://www.psi.ch/en/emf). The BIO division together with our PSI detector group has developed a unique instrument for electron diffraction with a dedicated ED-detector based on PSI detector technology. Our laboratory (please consult https://www.psi.ch/en/lbr) is focused on studying the mechanism of action of membrane proteins, including structural dynamics, as well as studying the structural and functional role of tubulin in the cell, with a focus on developping personalized medecine tools/strategies. A selection of recent publications can be found here: https://www.psi.ch/en/lbr The project will focus on the structural determination of proteins using electron diffraction. Although most structures are determined at high resolution using X-ray diffraction, the properties of electrons give them the advantage to deliver even higher resolution and the possibility to see hydrogens. The project will address several questions around mechanisms involving hydrogen bond displacements in enzymes and membrane proteins. The selected postdoc will crystallize the proteins, a soluble one and a membrane protein, with already established protocols, optimize the crystal size using focused ion beam scanning electron microscopy (FIB-SEM) milling and collect the data at the transmission electron microscope in diffraction mode. Similar experimental data will be compared to the performance of a table top electron diffractometer prototype used in the pharma field. All devices and state of the art equipment for protein expression, purification and crystallisation are located at the Paul Scherrer Institute, including the FIB/SEM device and a dedicated cryo-electron diffraction microsocope. The tabletop electron diffractometer is close to it, in the region of Bale in Switzerland. The position is intended for 2 years and to be filled as soon as possible. Experience in FIB/SEM-lamellae preparation, electron diffraction and/or crystallography would be beneficial. The applicants should send their CV and a cover letter to: valerie.panne...@psi.ch<mailto:valerie.panne...@psi.ch> Informal inquiries can be also addressed to the same e-mail. Best wishes and happy time in this end of the year, Valérie Panneels __________________________________________ Valerie Panneels Projects Leader Paul Scherrer Institute Forschungsstrasse 111 OSRA/005 5232 Villigen PSI Switzerland Tel: +41 56 310 21 04 E-Mail: valerie.panne...@psi.ch<mailto:valerie.panne...@psi.ch> https://www.psi.ch/en/lbr/people/valerie-panneels ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ------------------------------ Date: Fri, 22 Dec 2023 18:31:01 +0000 From: "Srivastava, Dhiraj" <dhiraj-srivast...@uiowa.edu> Subject: Relion issue with MPI Hi I am trying to use relion and I am getting error when trying to use mpi (for 3d classification and 3D auto-refine). ERROR: out of memory in /home/lvantol/relion5/relion/src/acc/cuda/custom_allocator.cuh at line 436 (error-code 2) in: /home/lvantol/relion5/relion/src/acc/cuda/cuda_settings.h, line 65 ERROR: A GPU-function failed to execute. 2D classification is working fine with significant GPU usage. I tried 3 different versions (4, 4 beta and 5 beta), one installed by vendor (Exxact) and all have the same issue. I am able to do 3D auto-refine and 3D classification on the same data set using our cluster without any problem. did anyone encounter a similar issue earlier? How can I fix this problem? Thank you Dhiraj ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ------------------------------ Date: Sat, 23 Dec 2023 08:35:34 +0900 From: Takanori Nakane <tnakane.prot...@osaka-u.ac.jp> Subject: Re: Relion issue with MPI Hi, First of all, please report details of your hardware and your job. - Type of GPU - Number of GPU - GPU memory size - Box size - Number of threads - Number of MPI processes - Full command line Do you get the same error in ALL datasets (including our tutorial dataset) or only on this particular dataset? A very similar issue was reported in https://github.com/3dem/relion/issues/1056 but I do not know what is the cause at the moment. Best regards, Takanori Nakane On 12/23/23 03:31, Srivastava, Dhiraj wrote: > Hi > I am trying to use relion and I am getting error when trying to use mpi > (for 3d classification and 3D auto-refine). > > > ERROR: out of memory in > /home/lvantol/relion5/relion/src/acc/cuda/custom_allocator.cuh at line > 436 (error-code 2) > > in: /home/lvantol/relion5/relion/src/acc/cuda/cuda_settings.h, line 65 > > ERROR: > > A GPU-function failed to execute. > > > 2D classification is working fine with significant GPU usage. I tried 3 > different versions (4, 4 beta and 5 beta), one installed by vendor > (Exxact) and all have the same issue. I am able to do 3D auto-refine > and 3D classification on the same data set using our cluster without any > problem. did anyone encounter a similar issue earlier? How can I fix > this problem? > > > Thank you > > Dhiraj > > > > ------------------------------------------------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > <https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1> > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ------------------------------ End of CCP4BB Digest - 21 Dec 2023 to 22 Dec 2023 (#2023-324) ************************************************************* ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/