[ccp4bb] PostDoc Positions in FIB-SEM/cryo-ET in Dortmund
Dear colleagues! I would like to draw your attention to the following job opportunities. Deadline April 7! Best, Stefan PostDoc Positions (m/f/d) in Electron Cryo-Tomography (cryo-ET) There are exciting immediate Postdoctoral positions in the lab of Stefan Raunser in the Department of Structural Biochemistry at the Max Planck Institute for Molecular Physiology in Dortmund, Germany. This is a unique opportunity to become a part of a world-renowned research institute with a diverse faculty with backgrounds in chemistry, biology and physics, and to perform interdisciplinary science in a lively and supportive environment! We seek highly motivated, self-driven and creative thinkers who are prepared to take risks in defining and addressing important scientific problems, and who use quantitative experimental, computational and/or technical approaches in their work. The positions are available immediately in the Department of Structural Biochemistry (Director: Stefan Raunser) and are initially limited to 3 years. Summary: Research projects in the Raunser lab focus on important biological questions concerning the structural organization of muscles, cytoskeletal proteins and bacterial toxin complexes. Our ultimate goal is to understand the mechanisms and structure-function relationship underlying these processes in health and disease in molecular detail. To this end, we employ single particle electron cryo-microscopy (cryo-EM), cryogenic focused ion beam milling (cryo-FIB), electron cryo-tomography (cryo-ET), X-ray crystallography, biochemical and biophysical methods and cell biology. There are several projects available in our lab for talented and outstanding young researchers who are eager to apply cryo-FIB and cryo-ET to look deeper into cells and tissues in order to visualize and understand cellular components that have never been seen before. Requirements: Ideal candidates should hold an excellent PhD in structural biology, biophysics, physics or in an equivalent area with previous experience in single particle cryo-EM or cryo-ET. Strong written and oral communication skills in English are required. Why join us? Being a part of the community at the Max Planck Institute is more than just a job. Our dynamic research environment, distinct culture, and diverse community foster collaboration and excellence in every corner of science. We offer an extensive range of benefits and resources such as: • access to state-of-the-art research facilities • opportunities to collaborate on cutting-edge research • an international and exciting working atmosphere • an integrated training program that includes lectures, advanced scientific workshops, complementary skill courses and opportunities for career development • a mentoring program to guide and promote young scientists Salary: Payment depends on personal conditions and qualification according to the directive of the TVöD. Social benefits correspond to those of the public service. How to Apply: Applicants should submit a CV, a motivation letter outlining research experiences and interests and two reference letters by April 7th, 2023 to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de <mailto:raunser-jobsea...@mpi-dortmund.mpg.de> Additional Information: The Max Planck Society (Max Planck Gesellschaft – MPG) is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. The MPG seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. Furthermore, the MPG strives to foster an inclusive culture and diversity within its workforce. Therefore, all qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, religion, color, national origin, age, sex, sexual orientation, disability status, or any other characteristic protected by applicable law. --- Prof. Dr. Stefan Raunser | Director | Dep. Structural Biochemistry | Max Planck Institute of Molecular Physiology | Otto-Hahn-Straße 11, 44227 Dortmund, Germany | +49 231 133 2300 ___ 3dem mailing list 3...@ncmir.ucsd.edu <mailto:3...@ncmir.ucsd.edu> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem <https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem> To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=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/ smime.p7s Description: S/MIME cryptographic signature
[ccp4bb] PhD and PostDoc Positions in cryo-EM and cryo-ET
PhD and PostDoc Positions (m/f/d) in Electron Cryo-Microscopy (cryo-EM) and Tomography (cryo-ET) There are exciting immediate PhD and Postdoctoral positions in the lab of Stefan Raunser in the Department of Structural Biochemistry at the Max Planck Institute for Molecular Physiology in Dortmund, Germany. This is a unique opportunity to become a part of a world-renowned research institute with a diverse faculty with backgrounds in chemistry, biology and physics, and to perform interdisciplinary science in a lively and supportive environment! We seek highly motivated, self-driven and creative thinkers who are prepared to take risks in defining and addressing important scientific problems, and who use quantitative experimental, computational and/or technical approaches in their work. The positions are available immediately in the Department of Structural Biochemistry (Director: Stefan Raunser) and are initially limited to 3 years. Summary: Research projects in the Raunser lab focus on important biological questions concerning the structural organization of muscles, cytoskeletal proteins and bacterial toxin complexes. Our ultimate goal is to understand the mechanisms and structure-function relationship underlying these processes in health and disease in molecular detail. To this end, we employ single particle electron cryo-microscopy (cryo-EM), electron cryo-tomography (cryo-ET), X-ray crystallography, biochemical and biophysical methods and cell biology. There are several projects available in our lab for talented and outstanding young researchers who are eager to combine these techniques to look deeper into cells and tissues in order to visualize and understand cellular components that have never been seen before. Requirements: Ideal PhD candidates should hold an excellent diploma or master degree in physics, biology, biochemistry, biophysics, or a related field of science. Ideal PostDoc candidates should hold an excellent PhD in structural biology, biophysics, physics or in an equivalent area with previous experience in single particle cryo-EM or cryo-ET. Strong written and oral communication skills in English are required. Why join us? Being a part of the community at the Max Planck Institute is more than just a job. Our dynamic research environment, distinct culture, and diverse community foster collaboration and excellence in every corner of science. We offer an extensive range of benefits and resources such as: • access to state-of-the-art research facilities • opportunities to collaborate on cutting-edge research • an international and exciting working atmosphere • an integrated training program that includes lectures, advanced scientific workshops, complementary skill courses and opportunities for career development • a mentoring program to guide and promote young scientists PhD students will join the International Max Planck Research School for Living Matter (IMPRS-LM), which is a joint PhD Program between the Max Planck Institute of Molecular Physiology in Dortmund, the Technical University Dortmund, the Ruhr University Bochum and the University of Duisburg-Essen. All four institutions are located in the Ruhr Metropolitan Area of Germany, an extremely vibrant and culturally interconnected region. Salary: Payment of Postdocs depends on personal conditions and qualification according to the directive of the TVöD. Social benefits correspond to those of the public service. Employment of PhD students is according to the funding guidelines of the Max Planck Society. How to Apply: Applicants should submit a CV, a motivation letter outlining research experiences and interests and two reference letters by September 20th, 2020 to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de<mailto:raunser-jobsea...@mpi-dortmund.mpg.de> Additional Information: The Max Planck Society (Max Planck Gesellschaft – MPG) is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. The MPG seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. Furthermore, the MPG strives to foster an inclusive culture and diversity within its workforce. Therefore, all qualified applicants are encouraged to apply and will receive consideration for employment without regard to race, religion, color, national origin, age, sex, sexual orientation, disability status, or any other characteristic protected by applicable law. --- Prof. Dr. Stefan Raunser | Director | Dep. Structural Biochemistry | Max Planck Institute of Molecular Physiology | Otto-Hahn-Straße 11, 44227 Dortmund, Germany | +49 231 133 2300 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.
[ccp4bb] PostDoc Positions in Cryo-EM
Dear colleagues, I would like to draw your attention to the following job opportunities. Best Stefan PostDoc Positions (m/f/d) in Cryo-EM SCIENTIST DORTMUND Structural and Cell Biology Max Planck Institute of Molecular Physiology seeks to fill PostDoc Positions in Cryo-EM (m/f/d). The positions are available immediately in the Department of Structural Biochemistry (Director: Stefan Raunser) and are initially limited to 2 years. Job description: Our research focuses on structural and functional studies of macromolecular protein complexes by single particle electron cryo-microscopy (cryo-EM), electron cryotomography (cryo-ET), X-ray crystallography, biochemical and biophysical methods. There are three projects available in the lab concentrating on the structural organization of muscles, cytoskeletal proteins and bacterial toxin complexes using single particle cryo-EM and/or cryo-ET. Requirements: The successful candidates hold an excellent PhD in structural biology, biochemistry, biophysics or physics. Experience in electron microscopy, in particular single particle cryo-EM or cryo-ET is not essential but will be considered highly advantageous. Strong written and oral communication skills in English and excellent computational skills are required. Payment: Payment of Postdocs depends on personal conditions and qualification according to the directive of TVöD. Social benefits correspond to those of the public service. Application: The Max Planck Society (MPG) is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. The MPG seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourage women to apply. Furthermore the MPG strives for gender equality and diversity within its workforce. Please send your CV, two references and a statement outlining your interests and relevant work experience until November 08, 2019 to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de<mailto:raunser-jobsea...@mpi-dortmund.mpg.de> <mailto:raunser-jobsea...@mpi-dortmund.mpg.de> --- Prof. Dr. Stefan Raunser | Director | Dep. Structural Biochemistry | Max Planck Institute of Molecular Physiology | Otto-Hahn-Straße 11, 44227 Dortmund, Germany | +49 231 133 2300 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] job offer: Software Architects / Engineers - MPI Dortmund
Dear colleagues, I would like to draw your attention to the following job opportunity. Best Stefan The Max Planck Institute of Molecular Physiology<https://www.mpg.de/151484/molekulare_physiologie> (MPI) is in search of two experienced Software Architects / Engineers to join the development team of SPHIRE, which is a software for the semi-automated processing of single particle electron cryo-microscopy (cryo-EM) data. Further information on SPHIRE is available at: http://sphire.mpg.de<http://sphire.mpg.de/>. Joining this team will provide you with the benefit of working closely in a dynamic and international environment involving scientists from a variety of academic fields. You will be expected to work on existing SPHIRE modules, as well as introducing new innovations to the framework. In particular, you will have the opportunity to contribute to the research and development of topics including: machine/deep learning, image processing, parallel processing and data visualization. Our code is primarily written in Python but individual modules may also require C++ or CUDA integration. Qualifications and Experience You hold a postgraduate degree in computer science or in an equivalent discipline with at least four years of experience as a professional software developer. You apply best practices of modern software development such as unit testing, source control (git), and build management. You communicate fluently in English, both written and verbal. You routinely produce clean and maintainable code and appreciate the value of clear documentation. Previous experience in scientific software development and handling of biological data would be an advantage. Your responsibilities Your primary responsibilities include: * Revising and modernizing the internal software architecture of SPHIRE * Identifying and implementing new cutting-edge algorithms * Designing new SPHIRE modules * Maintaining existing SPHIRE modules Working at the MPI The internationally renowned MPI of Molecular Physiology in Dortmund is well-equipped and will provide you with all the high-end gadgets you need for your work as a developer. The SPHIRE framework is currently used to produce results on the cutting edge of structural biochemistry. You will be surrounded by highly motivated developers and scientists from all over the world, employing a wide range of both technical and scientific expertise. Payment We offer full-time employment in a modern, international work environment. The position is to be filled immediately and is initially limited for three years. Remuneration is paid in accordance with the collective agreement of the public service (TVöD Bund), taking account your qualifications and professional experience. In addition, social benefits correspond to those of public service. Application The Max Planck Society is committed to increasing the number of individuals with disabilities in its workforce and therefore encourages applications from such qualified individuals. The Max Planck Society seeks to increase the number of women in those areas where they are underrepresented and therefore explicitly encourages women to apply. Please send your CV, two references, and a statement outlining your relevant work experience until September 30 to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de<mailto:raunser-jobsea...@mpi-dortmund.mpg.de> Prof. Dr. Stefan Raunser, Max Planck Institute of Molecular Physiology, Department of Structural Biochemistry, Otto-Hahn-Str. 11, 44227 Dortmund --------- Stefan Raunser Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Computer scientist position - MPI Dortmund
Dear colleagues, I would like to draw your attention to the following job opportunity. Best Stefan Computer scientist position at Max Planck Institute of Molecular Physiology Job description: Our research focuses on the structural analysis of macromolecular protein complexes using single-particle cryo-electron microscopy and cryo-electron tomography. For the processing of the electron microscopic pictures we develop in our laboratory the image processing software package SPHIRE. The successful candidate will work in a team of five software developers and develop algorithms, write scripts and software for image processing in single particle cryo-EM as well as cryo electron tomography and maintain the software package SPHIRE. As part of the team she/he will teach the usage of the program in workshops and support users. Requirements: The successful candidate has an excellent PhD in computer science, computational biology, physics or related areas. Proficiency in scripting is expected. Experience in deep learning and other machine learning techniques would be advantageous. Previous experience in single particle electron cryo-microscopy or electron tomography is a bonus but not a prerequisite. Strong written and oral communication skills in English are required. Payment: We offer full-time employment in a modern, international work environment. The position is to be filled immediately and initially limited to two years but can be extended to up to 5 years. Remuneration is paid in accordance with the collective agreement of the public service (TVöD Bund), taking account of your qualifications and professional experience. In addition, other social benefits are granted in accordance with the regulations of the public service. Application: The Max Planck Society (MPG) is committed to employing more handicapped individuals and especially encourages them to apply. The MPG aims to increase the percentage of women on its scientific staff and therefore strongly encourages women to apply. Please send your CV, two references and a statement outlining your relevant work experience until June 24 to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de. Stefan Raunser, Max Planck Institute of Molecular Physiology, Department of Structural Biochemistry, Otto-Hahn-Str. 11, 44227 Dortmund - Stefan Raunser, Ph.D. Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 and Adjunct Professor, Faculty of Chemistry and Chemical Biology Technical University Dortmund Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology University Duisburg-Essen
[ccp4bb] release of SPHIRE 1.0
Dear colleagues, We are excited to announce the release of the latest version of our SPHIRE software suite (SPHIRE 1.0) (co-distributed with EMAN 2.21), which is now available from our website: http://sphire.mpg.de<http://sphire.mpg.de/> Main new components and updates: - SORT3D – A novel 3D sorting program based on novel concepts of reproducibility. We tested it on several high-resolution projects in our lab and were able to gain valuable and unparalleled insight into data heterogeneity. - MERIDIEN – Rapid ML 3D refinement. We have introduced initialization of the program directly from 3D orientation parameters, as opposed to standard mode, which is initiated by an initial template structure. The new mode allows the user to rapidly perform local refinements of data subsets obtained with SORT3D. The two programs, MERIDIEN and SORT3D, thus serve as a perfect tool for exploration of data set heterogeneity. - We have streamlined the processing workflow and the GUI interface facilitating users’ interactions with the system. - The new release is accompanied by extensive documentation including tutorials explaining the underlying concepts. For any issues and inquiries, the SPHIRE team is accessible 24/7 via the mailing list. We sincerely hope that the updated SPHIRE 1.0 will meet your expectations and be a helpful advance in high-resolution cryo-EM. Your SPHIRE development team Toshio, Markus, Felipe, Thorsten, Christos, and Stefan – MPI Dortmund Zhong and Pawel - UTH Texas (Follow us on Twitter: https://twitter.com/SPHIRE_Package)<https://twitter.com/SPHIRE_Package> ----- Stefan Raunser, Ph.D. Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 and Adjunct Professor, Faculty of Chemistry and Chemical Biology Technical University Dortmund Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology University Duisburg-Essen
[ccp4bb] release of SPHIRE 1.0
Dear colleagues, We are excited to announce the release of the latest version of our SPHIRE software suite (SPHIRE 1.0) (co-distributed with EMAN 2.21), which is now available from our website: http://sphire.mpg.de<http://sphire.mpg.de/> Main new components and updates: - SORT3D – A novel 3D sorting program based on novel concepts of reproducibility. We tested it on several high-resolution projects in our lab and were able to gain valuable and unparalleled insight into data heterogeneity. - MERIDIEN – Rapid ML 3D refinement. We have introduced initialization of the program directly from 3D orientation parameters, as opposed to standard mode, which is initiated by an initial template structure. The new mode allows the user to rapidly perform local refinements of data subsets obtained with SORT3D. The two programs, MERIDIEN and SORT3D, thus serve as a perfect tool for exploration of data set heterogeneity. - We have streamlined the processing workflow and the GUI interface facilitating users’ interactions with the system. - The new release is accompanied by extensive documentation including tutorials explaining the underlying concepts. For any issues and inquiries, the SPHIRE team is accessible 24/7 via the mailing list. We sincerely hope that the updated SPHIRE 1.0 will meet your expectations and be a helpful advance in high-resolution cryo-EM. Your SPHIRE development team Toshio, Markus, Felipe, Thorsten, Christos, and Stefan – MPI Dortmund Zhong and Pawel - UTH Texas (Follow us on Twitter: https://twitter.com/SPHIRE_Package)<https://twitter.com/SPHIRE_Package> ----- Stefan Raunser, Ph.D. Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 and Adjunct Professor, Faculty of Chemistry and Chemical Biology Technical University Dortmund Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology University Duisburg-Essen
[ccp4bb] Postdoc positions in cryo-ET and single particle cryo-EM
Dear colleagues, I would like to draw your attention to the following job opportunities. Best Stefan PostDoc Positions in Electron Microscopy at Max Planck Institute of Molecular Physiology The positions are available immediately in the Department of Structural Biochemistry (Director: Stefan Raunser) and are initially limited to 3 years. Job description: Our research focuses on structural and functional studies of macromolecular protein complexes by single particle electron cryo-microscopy (cryo-EM), electron cryo-tomography (cryo-ET), X-ray crystallography, biochemical and biophysical methods. As part of a project that is funded by a Wellcome Trust Collaborative Award grant, one successful candidate will determine the structural organization of cellular components using cryo-ET. The other candidate will be involved in the structural elucidation of cytoskeletal proteins using single particle cryo-EM. Equipment at the institute: 2 FEI Krios equipped with Volta phase plate, energy filter, K2, and Falcon3; JEOL3200FSC with in-column energy filter; FEI Scios2 Dual Beam; 2 120 kV screening EMs, FEI CorrSight and all necessary equipment for cryo-EM Requirements: The successful candidate holds an excellent PhD in biochemistry, structural biology, biophysics or physics and has sufficient specialist knowledge in electron microscopy, in particular electron cryotomography (cryo-ET) and correlated light and electron microscopy (CLEM) or single particle cryo-EM. Strong written and oral communication skills in English and strong computational skills are required. Payment: Payment of Postdocs depends on personal conditions and qualification according to the directive of TVöD. Social benefits correspond to those of the public service. Application: The Max Planck Society (MPG) is committed to employing more handicapped individuals and especially encourages them to apply. The MPG aims to increase the percentage of women on its scientific staff and therefore strongly encourages women to apply. Please send your CV, two references and a statement outlining your interests and relevant work experience to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.de<mailto:raunser-jobsea...@mpi-dortmund.mpg.de>. Deadline is September 30 2017. - Stefan Raunser, Ph.D. Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 and Adjunct Professor, Faculty of Chemistry and Chemical Biology Technical University Dortmund Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology University Duisburg-Essen ___ 3dem mailing list 3...@ncmir.ucsd.edu<mailto:3...@ncmir.ucsd.edu> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
[ccp4bb] Release of the latest version of SPHIRE
Dear EM community, We are excited to announce the release of the latest version of our SPHIRE software suite (SPHIRE Beta Patch 1) (co-distributed with EMAN 2.2 and SPARX) , which is now available from our website: http://sphire.mpg.de<https://urldefense.proofpoint.com/v2/url?u=http-3A__sphire.mpg.de=DwMGaQ=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI=33GhWmUzxWDoNEEn95TH3nVcJvAy4a6HebLeBCyb3z4=04Ujzq5G-7aHzNO3rcVP6wb1Ky6TLXcYMuYf4-aaFC0=> Main new components and updates: - ISAC2 – Rapid and stable 2D Clustering We optimized the popular ISAC algorithm for 2D Clustering (Yang et al., Structure, 2012). ISAC yields now validated 2D class averages > 10-15x faster than before. In addition, the new Beautifier tool allows further refinement and sharpening of the ISAC 2D class averages in order to reveal high-resolution features in 2D. - MERIDIEN – Rapid ML 3D Refinement We introduced the polar coordinates methodology (Penczek et al., 1992) and optimized the parallelization of the program to speed up the structure refinement, reduce the memory requirements and enable calculation on single nodes. MERIDIEN is now > 10-15x faster than the previous version. Cryo-EM structure determination with SPHIRE is now possible within a few days on small clusters and desktop machines. - RSORT3D – Reproducible 3D sorting We re-implemented and improved the 3D sorting procedure and methodology. The updated RSORT3D is 3-4x faster and capable to run on desktop machines. More importantly, it produced better results for several high resolution projects in our lab. - Icosahedral, Tetrahedral and Octahedral Symmetry Refinement of particles with icosahedral, tetrahedral, and octahedral symmetries is now supported. - Easy installation The release of SPHIRE Beta Patch 1 is synchronized with the release of EMAN 2.2. The new Anaconda Installer allows a fast and smooth co-installation of both programs. At the moment we only support CentOS, but we work hard on developing a MacOS Installer for the upcoming stable release. For any issues and inquiries, the SPHIRE team is accessible almost 24/7 via the mailing list.<https://urldefense.proofpoint.com/v2/url?u=https-3A__listserv.gwdg.de_mailman_listinfo_sphire=DwMGaQ=6vgNTiRn9_pqCD9hKx9JgXN1VapJQ8JVoF8oWH1AgfQ=vDDf9rsFxPMXm8JgJa6hc4B9V4qKr7wftnDkLIRdshI=33GhWmUzxWDoNEEn95TH3nVcJvAy4a6HebLeBCyb3z4=yUJ84BmoBfUZa5j2o-lur1OlwjeDwOroamLEgH_Ic-o=> We sincerely hope that the updated SPHIRE Beta Patch 1 version will meet your expectations and be a helpful advance in high-resolution cryo-EM. Your SPHIRE development team Toshio, Markus, Felipe, Thorsten, Michael, Christos, and Stefan – MPI Dortmund Zhong and Pawel - UTH Texas (Follow us on Twitter: https://twitter.com/SPHIRE_Package) --------- Stefan Raunser, Ph.D. Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 and Adjunct Professor, Faculty of Chemistry and Chemical Biology Technical University Dortmund Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology University Duisburg-Essen
[ccp4bb] Reminder: SPHIRE workshop in Dortmund
Dear colleagues, This is just a reminder for the upcoming SPHIRE workshop to be held on 8-10 May, 2017 at the Max Planck Institute of Molecular Physiology (Dortmund, Germany) Registration is open until April 1, 2017. You can find more information and register at: http://sphire.mpg.de<http://sphire.mpg.de/> We look forward to seeing you in Dortmund. On behalf of the organizers Stefan Raunser - Stefan Raunser, Ph.D. Director, Department of Structural Biochemistry Max Planck Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany tel: +49-231-133-2300 and Adjunct Professor, Faculty of Chemistry and Chemical Biology Technical University Dortmund Honorary Professor, Centre for Medical Biotechnology, Faculty of Biology University Duisburg-Essen
[ccp4bb] SPHIRE beta release
Dear EM-community, We are happy to bring our new software package SPHIRE to the world of cryo-EM. We announced SPHIRE (SParx for HIgh Resolution Electron Microscopy) at this year’s GRC conference in Hong Kong and, in response to the interest of the community we deliver now the early version of the package. SPHIRE embodies a single-particle pipeline supported by ten modules of the previous SPARX system that are accessible through an easy-to-use GUI (Graphical User Interface). It is designed for easy immersion into cryo-EM with the stress on validation and reproducibility of results by using concepts of statistical resampling and provides powerful algorithms that encompass all steps of a typical cryo-EM project. Advanced users have the luxury of easy access to all process parameters through ‘advanced’ tabs and can easily customize the code, which is written in transparent Python! THE TESTS During the last months we worked day and night to extensively test the workflow. We used our in-house datasets and also processed a number of EMPIAR datasets (e.g. TRPV1 (ID: 10005), T20S proteasome (ID: 10025), beta-galactosidase (ID: 10061)) and are happy to report that in all cases we were able to reproduce published results. The SPHIRE pipeline comprises the following major steps: - Frame movie alignment, supported by a graphical drift assessment tool. - CTF estimation and its error assessment tool providing utilities for automated sorting out of inferior data. - Reproducible 2-D classification. - Validated ab initio 3-D reconstruction yielding a perfect starting point for 3-D refinement. - Efficient 3-D structure refinement utilizing maximum likelihood methodology. - Tools for assessing data heterogeneity, including computation of local variance, local resolution providing the necessary validation for our 3D sorting program. THE INFO To find out more about SPHIRE and its team please consult http://sphire.mpg.de The SPHIRE team is accessible almost 24/7 via mailing list. To subscribe please visit: https://listserv.gwdg.de/mailman/listinfo/sphire where you can also browse through the archive of already discussed subjects. In order to facilitate smooth immersion into the SPHIRE world, we prepared an extensive step-by-step tutorial that is supported by a test dataset. Both can also be downloaded from the SPHIRE homepage. THE RELEASE And now the most important part, the release. We have decided to release SPHIRE as a public beta version and here is why: Despite the substantial testing, as a developer team we are only able to test a limited number of datasets so it is reasonable to expect the unexpected. We hope for the community input that will allow us to find problems we did not anticipate and solve them quickly. This phase will be followed by a stable release of SPHIRE within the next year. THE FUTURE We believe that increasing the number of cryo-EM software packages will benefit our community by providing alternative solutions to challenges of cryo-EM structure determination. We sincerely hope SPHIRE will meet your expectations. More importantly, we hope for community feedback, however enthusiastic or critical it may be, to stimulate us for the future developments to carry us into the next quarter of the century. Your SPHIRE development team [cid:D58434BF-44E4-43F0-81A3-928977BCAE42@client.mpi-dortmund.mpg.de]
[ccp4bb] PostDoc position in X-ray crystallography
The Max Planck Institute of Molecular Physiology seeks to fill a Postdoctoral Position in X-ray crystallography The position is available immediately in the newly established Department of Structural Biochemistry (Director: Stefan Raunser). It is initially limited to 3 years. Job description: Our research focuses on structural and functional studies of macromolecular complexes by single particle electron cryo-microscopy (cryo-EM), X-ray crystallography, biochemical and biophysical methods. As part of a project that is funded by an ERC consolidator grant, the candidate will determine the structural organization of bacterial toxin complexes using X-ray crystallography. Requirements: The successful candidate should be highly motivated and have an excellent PhD in structural biology, biophysics or physics and previous experience in X-ray crystallography and in membrane protein biochemistry. Strong written and oral communication skills in English are considered. Payment: Payment depends on personal conditions and qualification according to the directive of TVöD. Social benefits correspond to those of the public service. Application: The Max Planck Society (MPG) is committed to employing more handicapped individuals and especially encourages them to apply. The MPG aims to increase the percentage of women on its scientific staff and therefore strongly encourages women to apply. Please send your CV, two references and a statement outlining your interests and relevant work experience to Stefan Raunser at raunser-jobsea...@mpi-dortmund.mpg.demailto:raunser-jobsea...@mpi-dortmund.mpg.de - Stefan Raunser Max-Planck-Institute of Molecular Physiology Otto-Hahn-Str. 11 44227 Dortmund, Germany
