[ccp4bb] Two positions available at DESY in Hamburg
Hi everyone, For people who are interested in programming and software engineering, we have two positions available in the photon science department at the Deutsches Elektronen-Synchrotron DESY in Hamburg. The first position is a scientific role within the Center for Data and Computing in Natural Sciences (https://www.cdcs.uni-hamburg.de/) where you will develop and implement new algorithms for data analysis: Scientist/postdoctoral fellow - computational photon science https://v22.desy.de/e67416/records129838/index_eng.html The second position is a technical role (PhD *not* required) as part of DAPHNE4NFDI (https://www.daphne4nfdi.de/) where you will support large-scale data handling by handling cross-platform software deployment: Scientist for cross-platform software development https://v22.desy.de/e67416/records161181/index_eng.html In addition to the contact details given on the job adverts, you're more than welcome to contact me directly for further details. Best wishes, Tom -- Thomas White 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/
[ccp4bb] Electron microscopy support position @ CSSB, Hamburg
Hi everyone, The CryoEM facility at CSSB in Hamburg is growing (https://www.cssb-hamburg.de/facilities/cryo_em/index_eng.html) We are currently looking for an EM support scientist to complement our Team. A job description is pasted below - however, we are totally aware, that everyone contributes her/his own expertise, and that this may change some of the responsibilities described. For more information, or any other questions, please contact: Carolin Seuring Electron Microscopy Support (m/f/D) - Salary Level 13 TV-L - The position commences as soon as possible and is permanent. This position is also suitable for part time employment. The Centre for Structural Systems Biology (CSSB) was created with the mission to use cutting edge technologies and methods to investigate how pathogens infect humans. Part of this mission are the CSSB Core Facilities that provide access to technology and research services for bio-sciences. Alongside these facilities, the multi-user facility for electron cryo-microscopy (cryoEM) has started its operation in 2017, and is positioned on the Science Campus Bahrenfeld, being also home to the Deutsches Elektronen-Synchrotron DESY. Our facility is currently the most advanced centre for cryoEM in the north of Germany housing five electron microscopes: two Titan Krios instruments equipped with phase plates, energy filters, K3 and Falcon 3 direct detectors, a Talos Arctica with a phase plate and a Falcon 3 direct detector, a Talos L120C and an Aquilos FIB cryo-SEM for preparing lamellae of thick samples, such as vitrified cells or crystals. Auxiliary equipment and nearby lab space for sample preparation and cell culture work complete the workflows. We primarily focus on single particle analysis and electron cryo-tomography. The facility is set up to handle biological samples up to German biosafety level 2. Nature of the job 85% equipment set-up and operation, equipment maintenance, 15% user-training & assistance: Responsible for the day-to-day running and maintenance of the electron microscopes and associated sample preparation equipment Manage and operate the cryoEM instruments and associated equipment, this includes first-fault diagnosis, and maintenance work Assist in improving set-ups for the different cryoEM modalities (SPA, Tomo) and the implementation of additional workflows (correlative microscopy, microED) Work with our computing scientist to ensure a seamless interface between data collection and data processing Establish and implement schedules for microscope hardware and software maintenance, and support alignments and performance checks, to ensure that the facility is operating at peak performance Coordinate repairs with microscope supplier’s service engineers Work with in house engineers and other facilities provide instructions, assistance and consultation to faculty, students, staff members regarding the TEM equipment and optimal processes Perform other related duties incidental to the work described above Your Profile Experience in cryoEM (hardware and/or software), X-ray technology, imaging detectors, or computational work at the interface hardware/software Experience in cryoEM & understanding the basics of electron optics and vacuum systems Previous experience in microscope control and acquisition software packages for single particle analysis or tomography or one of the following programming interfaces/languages: Python, C++, Java, LabView, SerialEM Good English language skills (both written and oral) Experience with managing, analyzing, and improving complex workflows Demonstrated record keeping and organization skills Ability to proactively plan maintenance work and increase microscope uptime & performance Attention to detail A desire to learn, and a willingness to share knowledge Self-driven and organized Your responsibilities within the team can be adjusted to best fit your specific skill-set. For more information please visit: https://www.uni-hamburg.de/uhh/stellenangebote/technisches-bibliotheks-und-verwaltungspersonal/technik-und-service-und-sonstiges/17-02-20-tvp-602-1-en.pdf To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] challenges in structural biology
On Tue, 16 Jul 2019 18:02:20 + "selina.st...@diamond.ac.uk" wrote: > following up on Kay's point, I think it might be worth to discuss > what we as a community understand by serial crystallography and what > makes it different from multiple crystal crystallography. I recently > gave a talk about multiple-crystal and serial crystallography at a > course and I could not find any textbook definition. Kay's email > suggests that my understanding differs from his... I think the usage of the term "serial crystallography" to refer to cases where you record a small number of rotation exposures from one crystal isn't very helpful. I think it's better to reserve "serial" for the limiting case where one crystal gives only ONE pattern and that's it, whether because of radiation damage or just the scanning method being used. There might be some rotation or oscillation of the crystal during that time, but never measurements across more than one detector frame [1]. Anything else is "just" an extreme case of multi-crystal data acquisition. I think this usage of the term comes from extending the definition "one frame per crystal" to "one small wedge per crystal". It sounds innocuous, but as has already been mentioned the difference in data processing between these two cases is absolutely enormous. On top of that, there's the question of whether the exposures are snapshots (stills) or have some rotation or oscillation. This is why many of my papers, e.g. the first CrystFEL paper [2], refer to "snapshot serial crystallography" - I meant specifically both "one exposure per crystal" AND "no rotation at all". However, the term actually originated from some much earlier work in the Spence group at ASU, which didn't involve crystals at all. The idea was to do the work of "crystallography" (i.e. determining structures), but to put the molecules through the beam one by one (serially) rather than side-by-side in a crystal (which I guess would be "parallel crystallography"): https://www.ncbi.nlm.nih.gov/pubmed/15169448 However, that technique didn't work out, and the term got co-opted for the stuff we do nowadays. It's also been commented that the days of getting an entire data set (or anything close to it) from a single protein crystal may just be a short period in the middle of crystallographic history, with multi-crystal/serial techniques dominating in early work (pre 1990 ish) and modern work. Therefore, maybe before too long we'll be calling it simply "crystallography" anyway. Tom [1] Ok, multiple frames per crystal might happen by accident, see for example the last paragraph of section 3.2 of this paper: http://journals.iucr.org/m/issues/2015/02/00/jt5008/index.html However, this shouldn't be the point of the technique. [2] http://scripts.iucr.org/cgi-bin/paper?S0021889812002312 [3] https://www.nature.com/articles/nature09750 -- Thomas White 4E1F C14D 0E0A A014 FE5D 3FC6 C628 75D1 D4CA 4C30 Direct telephone: +49 (0)40 8998-5786 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Electron Cryo-microscopy support technician at CSSB (Hamburg, DE)
The Department of Chemistry, Biochemistry and Molecular Biology of the Faculty MIN (University of Hamburg) invites applications for employment as: Electron cryo-microscopy Support (m/f/D) Salary Level 13 TV-L The position commences as soon as possible and is permanent. This position is also suitable for part time employment. The Central Facility "Electron cryo-microscopy" (CryoEM) at the Centre for Structural Systems Biology (CSSB) Hamburg, a multi-user-facility, provides essential structural information for research groups of the UHH and other research groups participating in the CSSB co-operation. These insights are of fundamental importance for Bachelor, Master and doctoral theses as well as for publications. The facility currently comprises five electron cryo-microscopes: two Titan Krios instruments with phase plate, energy filter, K2/3 and Falcon 3 direct detectors, a Talos Arctica with phase plate and Falcon 3 direct detector, a Talos L120C and an Aquilos FIB cryo-SEM for preparing lamellae of vitrified cells plus auxiliary equipment to complete the workflows. Independent scientific research in the area of structural and cell biology, especially in the field of infection biology, as part of scientific collaborations and involvement in electron microscopy method development for structural biology applications are highly encouraged. Responsibilities: The post holder will have responsibility for ensuring the day-to-day running of the electron microscopes and of the related auxiliary and preparatory equipment to the level of optimal system performance at the Facility in accordance with the Senior Staff Scientist CryoEM. This includes initial fault diagnosis, participation in repair and maintenance work, coordination with home technology, installation and update of the data collection software (both manufacturer provided and academic alternative developments) in collaboration with the Facility's data processing scientist. As part of the team, the post holder will assist with the establishment, optimisation and expansion of dedicated workflows for the different cryoEM modalities (in particular single particle analysis and tomography) including the regular implementation of significant new developments. A particular local emphasis is put on correlative microscopy, and close interaction with the Advanced Light and Fluorescence Microscopy Facility at CSSB is desired. Another responsibility of the job holder is to support the other staff members with the development and implementation of the training and induction concept for academic users. Requirements: A university degree in chemistry, biology, physics or another relevant subject Required skills and personal qualities: * Sound research experience and knowledge in electron cryo-microscopy, and the corresponding underlying theoretical and technical principles (e.g. electron optics, vacuum systems etc.) and procedures * Extensive knowledge of the relevant control software of electron microscopes * Solid experience in fault finding of complex electron microscopes and in user training for electron microscopic and auxiliary equipment * Excellent English language skills (both written and oral) * Good basic understanding of cell biology and experience in infection biology and correl- ative microscopy methods are desirable * Willingness to share knowledge * Good team player * The ability to communicate effectively with a wide range of people * Very good organisational and interpersonal as well as negotiating skills (when dealing with industrial partners) The Free and Hanseatic City of Hamburg promotes equal opportunity. As women are currently under-represented at this salary level at Universität Hamburg according to the evaluation conducted under the Hamburg act on gender equality (Hamburgisches Gleichstellungsgesetz, HambGleiG), we encourage women to apply for this position. Equally qualified and suitable female applicants will receive preference. We explicitly encourage persons with an immigrant background to apply. Equally qualified severely disabled applicants or applicants with equivalent status will receive preference. For further information please contact Prof Dr Kay Grünewald by email on debora.l...@cssb-hamburg.de Please send your complete application including the reference number by 29 August 2019 to: Universität Hamburg Stellenausschreibungen Reference no. 602/8 Mittelweg 177 20148 Hamburg or via email: bewerbun...@verw.uni-hamburg.de Please do not submit original documents as we are not able to return them. Any documents submitted will be destroyed after the application process has concluded. This posting as PDF: https://www.uni-hamburg.de/en/uhh/stellenangebote/technisches-und-verwaltungspersonal/29-08-19-tvp-602-8-engl.pdf To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Two cryo-EM positions at CSSB in Hamburg, DE
Hi everyone, Two positions are available in the cryo-EM facility at the Centre for Structural Systems Biology (CSSB) in Hamburg. More information below. > We are seeking for support! We will recruit two scientists for > training and supporting many users in structural and systems biology > of infection ! We are looking for enthusiastic, cooperative, and > inspiring people with a good background in cryoEM! If you are > interested please check out the links below. Deadline is May 10th. https://www.uni-hamburg.de/en/uhh/stellenangebote/technisches-und-verwaltungspersonal/10-05-19-tvp-602-5-en-verl.pdf https://www.uni-hamburg.de/en/uhh/stellenangebote/technisches-und-verwaltungspersonal/10-05-19-tvp-602-4-en-verl.pdf To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Ultrafast X-ray Summer School (UXSS2019) in Hamburg: June 17-21
[second announcement - registration extended until 22 March 2019 - next week!] Dear All, The Ultrafast X-ray Summer School UXSS2019 will take place at the Center for Free Electron Laser Science (CFEL) in Hamburg, Germany, June 17-21, 2019. UXSS is an annual event jointly organized by the Center for Free-Electron Laser Science (CFEL) in Hamburg and the Stanford PULSE Institute. UXSS is intended to introduce students and postdocs to the latest science that is enabled by novel X-ray Free Electron Lasers. The program will be highly interdisciplinary, with topics ranging from materials physics to structural biology. The list of confirmed speakers can be found below. There will also be a coursework exercise involving a mock proposal for European XFEL, with the help of experienced mentors. The UXSS2019 website is now online with more information: https://conferences.cfel.de/uxss_2019 Registration is open: https://indico.desy.de/indico/event/22369. Registration will continue until March 22, with rolling acceptance. Financial support for UXSS2019 is very kindly provided by the Joachim Herz Stiftung and the Hamburg Centre for Ultrafast Imaging (CUI), meaning that participants will be asked to pay a registration fee of only 100 EUR. Limited participation scholarships to cover travel and lodging costs are available. You can specify on the registration website why you need a scholarship to participate. We hope to see you in Hamburg this summer! Michael Sentef (CFEL) and Thomas Wolf (PULSE) Co-chairs, UXSS2019 Lecturers: Henry Chapman (Hamburg University/DESY) Frank de Groot (Utrecht University) Arianna Gleason (SLAC) Giorgio Margaritondo (EPFL Lausanne) Brian Moritz (SLAC) Nina Rohringer (Hamburg University/DESY) Simon Wall (ICFO Barcelona) Oriol Vendrell (Heidelberg University) Junko Yano (LBL Berkeley) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
[ccp4bb] Ultrafast X-ray Summer School (UXSS) 2019
Dear All, The Ultrafast X-ray Summer School UXSS2019 will take place at the Center for Free Electron Laser Science (CFEL) in Hamburg, Germany, June 17-21, 2019. UXSS is an annual event jointly organized by the Center for Free-Electron Laser Science (CFEL) in Hamburg and the Stanford PULSE Institute. UXSS is intended to introduce students and postdocs to the latest science that is enabled by novel X-ray Free Electron Lasers. The program will be highly interdisciplinary, with topics ranging from materials physics to structural biology. The list of confirmed speakers can be found below. There will also be a coursework exercise involving a mock proposal for European XFEL, with the help of experienced mentors. The UXSS2019 website is now online with more information: https://conferences.cfel.de/uxss_2019 Registration is open: https://indico.desy.de/indico/event/22369. Registration will continue until March 15, with rolling acceptance. Financial support for UXSS2019 is very kindly provided by the Joachim Herz Stiftung and the Hamburg Centre for Ultrafast Imaging (CUI), meaning that participants will be asked to pay a registration fee of only 100 EUR. Limited participation scholarships to cover travel and lodging costs are available. You can specify on the registration website why you need a scholarship to participate. We hope to see you in Hamburg this summer! Michael Sentef (CFEL) and Thomas Wolf (PULSE) Co-chairs, UXSS2019 Lecturers: Henry Chapman (Hamburg University/DESY) Frank de Groot (Utrecht University) Arianna Gleason (SLAC) Giorgio Margaritondo (EPFL Lausanne) Brian Moritz (SLAC) Nina Rohringer (Hamburg University/DESY) Simon Wall (ICFO Barcelona) Oriol Vendrell (Heidelberg University) Junko Yano (LBL Berkeley) To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] Open Access Repositories for Big Data?
Hi, > Is anyone aware of online repositories that will store huge sets of > raw data (>100 GB)? I’m aware of Zenodo and SBGrid, but Zenodo’s > limit is typically 50 GB and their absolute limit is 100 GB. SBGrid > has yet to respond to my emails. The Coherent X-ray Imaging Data Bank may be appropriate: http://cxidb.org The definition of "imaging" is taken quite widely, e.g. the data there includes many serial crystallography diffraction data sets. A lot of them are MUCH bigger than 100 GB. Tom -- Thomas White 4E1F C14D 0E0A A014 FE5D 3FC6 C628 75D1 D4CA 4C30 Direct telephone: +49 (0)40 8998-5786 To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB=1
Re: [ccp4bb] determining the point group and the space group
Hi Gihan, and anyone else who finds this interesting. Sorry for the late response: > how should one determine a point group and the space group of an > unknown crystal? > > I have a protein crystal with know unit-cell parameters. (these are > XFEL data so indexing wouldn't give the point and space groups). I > checked the PDB, but no luck the PDB structures have the different > space group assigned, no definitive answer hopefully, somebody can > point me in the right direction Space group determination using serial crystallography data is different to rotation crystallography because you have to start from the highest possible symmetry and work downwards by finding and resolving ambiguities, instead of merging in the lowest possible symmetry and working upwards by looking for possible symmetries. Just as with any data, the golden rule is that the space group is only a hypothesis until the structure is solved (and even then...). Here's a very brief step by step guide. Start by determining the cell parameters, which you've done already. Say the cell parameters look like a hexagonal P lattice. Proceed for a while on the assumption that it really is hexagonal P, but keep the golden rule in mind. In this case it might be, amongst others, monoclinic with two axes similar in length and an angle close to 120 degrees. Use your crystallographic knowledge to spot centering possibilities, for example a cubic F lattice might look rhombohedral with angles of 60 degrees (however, the indexing program should spot these for you). Merge the snapshots according to the highest point symmetry permissible by the lattice. You can look this up in many places including the symmetry chart distributed with CrystFEL: https://www.desy.de/~twhite/crystfel/twin-calculator.pdf It's always the point group with a grey background in the bottom left corner of the individual table for the lattice type. For the example hexagonal P lattice, it's point group 622. Do the standard tests on the data, particularly twinning tests including an L-test. Whenever you see apparently twinned data with serial crystallography, either the crystals are physically twinned or the true symmetry is lower and you need to resolve an indexing ambiguity and merge again. You will need to try rounds of ambiguity resolution until the tests are clean and the structure can be solved. The difficult part is finding your way through the maze of possible symmetries. You can attempt a resolution into any subgroup of the current symmetry, provided that the "ambiguity operator" is just a rotation (no reflections/inversions). The CrystFEL table shows the most obvious subgroups (the ones with the same lattice type). The comprehensive map of possibilities can be found in International Tables A, Fig 10.1.3.2 (in 5th edition). There are many special cases, and the find_ambi tool from the CrystFEL extra programs repository can help you find cases of "accidental" ambiguities due to the particular values of the lattice parameters: https://www.desy.de/~twhite/crystfel/programs.html If there are signs of twinning, try resolving the ambiguity into each of the subgroups. If the ambiguity resolves nicely (one way to tell is by the correlation coefficient graph, which should separate nicely: http://journals.iucr.org/j/issues/2016/02/00/zd5001/zd5001fig3.html), try merging the reindexed patterns in the lower symmetry point group, and check the twinning tests again. Once you have a merged set of reflections with no apparent twinning, things are the same as rotation crystallography. Examine the systematic absences to see if they suggest any screw axes. Try molecular replacement in all the possible space groups. Consider revisiting the earlier steps if there are problems. It's not easy, but it's also not that difficult, just different to usual. I would almost go as far as saying it's fun, like cracking a secret code. This kind of situation is my personal favourite part of crystallography (!) This recent paper embodies a similar workflow in a nice algorithm: https://journals.iucr.org/d/issues/2018/05/00/rr5155/ Hope that helps, Tom -- Thomas White <thomas.wh...@desy.de> <t...@physics.org> 4E1F C14D 0E0A A014 FE5D 3FC6 C628 75D1 D4CA 4C30 Direct telephone: +49 (0)40 8998-5786
[ccp4bb] Ultrafast X-ray Summer Seminar (UXSS) 2018
Hi everyone, The early registration deadline and travel scholarship deadline for UXSS 2018 is approaching - see below. Please direct all questions to the UXSS chairs, address at the very bottom. Tom The Ultrafast X-ray Summer Seminar (UXSS) 2018 will take place at SLAC National Accelerator Laboratory, in Menlo Park, California, 24-28 June 2018. UXSS is an annual event jointly organized by the Stanford PULSE Institute at SLAC and the Center for Free-Electron Laser Science (CFEL) at DESY. UXSS is intended to introduce students and postdocs to the latest science that is enabled by novel X-ray Free Electron Lasers. The program will be highly interdisciplinary, with topics ranging from materials physics to structural biology. The list of confirmed speakers can be found below. There will also be a coursework exercise involving a mock proposal for the LCLS, with the help of experienced mentors. The UXSS 2018 website is now online with more information: https://app.certain.com/profile/web/1008141 Registration is open! Early registration will continue until April 30, and registration will close on June 4. Limited travel scholarships are available in the amounts of $500 (domestic) or $1000 (foreign) to help cover the cost of travel and lodging. Students will have the opportunity to apply for travel scholarships upon registration until April 20. Lecturers: Frank Abild-Pederson (SLAC) Phil Bucksbaum (SLAC, Stanford University) Claudia Draxl (University of Berlin) Nils Huse (University of Hamburg) So Iwata (Kyoto University) Hae Ja Lee (SLAC) Giorgio Margaritondo (EPFL) Ian McNulty (Argonne National Laboratory) Mariano Trigo (SLAC) We hope to see you at SLAC this Summer! Amy Cordones-Hahn (PULSE) and Michael Sentef (CFEL) Co-chairs, UXSS 2018 uxss.pu...@gmail.com
[ccp4bb] Ultrafast X-ray Summer School in Hamburg: 12-15 June 2017
Hi all, The Ultrafast X-ray Summer School (UXSS) 2017 will take place at DESY in Hamburg, Germany, 12-15 June 2017. UXSS is an annual event jointly organized by the Center for Free-Electron Laser Science (CFEL) at DESY and the PULSE institute at SLAC National Accelerator Laboratory. As you can see from the list of speakers below, the program will be highly interdisciplinary, with topics ranging from accelerator physics to molecular biology. There will also be a coursework exercise involving a mock proposal for the European XFEL, with the help of experienced mentors. The UXSS 2017 website is now online with more information: https://conferences.cfel.de/uxss2017/ Registration will open on the 31st January 2017 (tomorrow!). Please note that the number of summer school participants will be limited. In order to facilitate the selection of participants, we ask applicants to provide a short description of their educational and scientific background and their motivation for applying for participation in UXSS 2017. The registration deadline will be the 31 March 2017. Financial support for UXSS 2017 is very kindly provided by the Joachim Herz Stiftung, meaning that participants will be asked to pay a registration fee of only 100 EUR. Accepted applicants will receive a financial contribution towards travel and accommodation expenses. We hope to see many of you in Hamburg this Summer! Thomas White, CFEL, DESY Amy Cordones-Hahn, PULSE Co-chairs, UXSS 2017 List of lecturers: Rasmus Ischebeck (PSI), FEL diagnostics Hae Ja Lee (SLAC), matter in extreme conditions Filipe Maia (Uppsala University), coherent diffractive imaging Giorgio Margaritondo (EPFL), fundamentals of X-ray sources Arwen Pearson (CUI & University of Hamburg), structural biology Robin Santra (DESY, University of Hamburg), x-ray - matter interactions Joachim Stohr (SLAC, Stanford University), condensed matter and magnetism Simone Techert (DESY & Göttingen Campus), structural dynamics Linda Young (Argonne/UChicago), atomic and molecular physics
[ccp4bb] Mildred Dresselhaus Guest Professorship 2014
We are calling for applications for the Mildred Dresselhaus Guest Professorship 2014. The award has been established by The Hamburg Centre for Ultrafast Imaging (CUI), the new cluster of excellence at the Universität Hamburg, Germany, to promote outstanding female scientists. The CUI aims to observe and understand molecular processes at the atomic length and time scales, and includes the development of structure determination using ultrafast electron pulses and X-ray free-electron laser pulses. In 2014 the guest professorship will be awarded for the second time to a successful senior scientist and a younger scientist with high potential. The awardees are invited to work in Hamburg within CUI for a period of up to six months in 2014. We provide excellent research conditions to attract world-leading researchers to Hamburg with the aim of starting new and intensifying existing collaborations. Our current awardees are: Prof. Dr. Tamar Seideman, Northwestern University, USA and Prof. Dr. Rosario Gonzalez-Ferez, Universidad de Granada, Spain. Please feel invited to submit your nomination of a suitable candidate or your own application (letter of motivation, scientific CV including the five most important publications, list of invited talks, teaching experience as well as research interests as one single PDF file) to wiebke.kirchei...@cui.uni-hamburg.de by April 15, 2014. For more details, see also http://www.cui.uni-hamburg.de/en/opportunities/mildred- dresselhaus-guest-professorship-programme/ or contact Ms. Kircheisen directly.
[ccp4bb] Position available at DESY: Protein Nanocrystallography
DESY, Hamburg location, is seeking a Scientist for Protein Nanocrystallography (f/m) DESY is one of the world’s leading centres for the investigation of the structure of matter. DESY develops, runs and uses accelerators and detectors for photon science and particle physics. The Center for Free-Electron Laser Science (CFEL) is a jointly operated research cooperation between DESY, the Max Planck Society and the University of Hamburg. DESY supports three CFEL divisions with leaders jointly appointed with the University of Hamburg. The Coherent Imaging Division of CFEL is developing novel methods in macromolecular structure determination, using intense X-ray laser pulses to out-run radiation damage and thereby removing the biggest bottleneck in structural biology: the need to grow large well-diffracting crystals. The Division is leading a consortium to deploy serial femtosecond crystallography at the European XFEL. For this we are seeking a scientist. The position * Lead the design, development and construction of the Serial Femtosecond Crystallography (SFX) instrument at the European XFEL. * Develop beamline equipment, diagnostics, and analysis methods for serial crystallography, and to critically evaluate new concepts for the instrument. * Pursue independent and collaborative research in serial crystallography. * Communicate developments within the consortium and the broad community. Requirements * A PhD in experimental physics or a related field * An ability for teamwork in a group of scientists and engineers * Expert knowledge in crystallographic theory and methods and X-ray physics * Strong background in development of instrumentation * Excellent English For further information please contact Prof. Henry Chapman, +49 40 8998 4155, henry.chap...@cfel.de The position is limited to 3 years. Salary and benefits are commensurate with those of public service organisations in Germany. Classification is based upon qualifications and assigned duties. DESY operates flexible work schemes. Handicapped persons will be given preference to other equally qualified applicants. DESY is an equal opportunity, affirmative action employer and encourages applications from women. There is an bilingual kindergarten on the DESY site. The deadline for applications is 28 February 2013. Please send your application, quoting reference code EM242/2012, by post or e-mail as follows: Deutsches Elektronen-Synchrotron DESY Human Resources Department Notkestraße 85 22607 Hamburg Germany E-Mail: recruitm...@desy.de PDF version of these details: http://www.desy.de/v2/docs/1354184737-e.pdf Phone: +49 40 8998-3392 www.desy.de
Re: [ccp4bb] P321 space group reindex problem
On Wed, 30 May 2012 13:16:12 +0100 Ian Tickle ianj...@gmail.com wrote: From the point of view of deciding which are the alternate settings I don't think it's helpful to consider polar directions anyway. What matters is which symmetry axes of the lattice are not present in the point group. Possibly relevant here is a set of tables I put together for our free-electron laser experiments, where tens or even hundreds of thousands of patterns have to be indexed independently: https://www.desy.de/~twhite/crystfel/twin-calculator.pdf Underlying these tables is the same underlying information as everything else mentioned on this thread, but these ones tell you what the apparent symmetry would be if the intensities were mixed up according to all the available indexing ambiguities. So far, no-one has been able to reliably resolve these ambiguities in our case: the intensities are just obscured by too much noise, partiality, a spiky X-ray spectrum and so on. That's why we have to have so many patterns. For the time being, we just merge according to the higher symmetry, accept that the data may be (perfectly) twinned, and handle it at the later stages. Later on when we've hopefully solved this problem, these tables will serve as a menu of options for doing the whole thing backwards. I agree that polarity isn't the right criterion. Point group 2 is polar but does not exhibit any indexing ambiguity. Point group 4/m, which is most definitely not polar, does. This paper, Le Page et al., has some similar tables but lists the actual ambiguity operators: http://scripts.iucr.org/cgi-bin/paper?S0108767384001392 Of course, all of this only covers merohedral ambiguities, not pseudo-merohedral ones which might arise by accident in special cases. Comments on and corrections to the tables are welcome! Tom
[ccp4bb] CrystFEL: Software for FEL crystallography
Hi all,
This is just to draw the attention, of anyone who might find it
interesting, to the availability of the first public version of
CrystFEL: a new software suite for analysis of serial femtosecond
crystallography data acquired using free-electron laser sources such
as the Linac Coherent Light Source (LCLS). Early versions of CrystFEL
powered much of the analysis for the first demonstration of this
technique on small crystals of photosystem I which was published (and
discussed here) back in February last year. I described some aspects
of CrystFEL and its algorithms in my talk at the CCP4 study weekend a
couple of months ago.
CrystFEL comprises programs for indexing and integrating diffraction
patterns, scaling and merging intensities, simulating patterns,
calculating figures of merit for the data and visualising the results.
Supporting scripts are provided to help at all stages, including
importing data into CCP4 for further processing. The underlying shared
library ('libcrystfel') means that you can use CrystFEL's features in
your own programs or even incorporate them into other frameworks.
If you're interested, you can read more on the CrystFEL website (link
below) and in an article in Journal of Applied Crystallography which
will be published very soon (hopefully tomorrow).
http://www.desy.de/~twhite/crystfel/index.html
Questions, comments and bug reports/fixes to this address.
Thanks for reading!
Tom
[ccp4bb] Position available: X-ray FEL Crystallography
http://www.desy.de/v2/docs/1310651114-e.pdf DESY, Hamburg location, is seeking a Senior Scientist or Postdoc (m/f) to conduct research in the area of X-ray FEL Crystallography. DESY is one of the world's leading centres for the investigation of the structure of matter. DESY develops,runs and uses accelerators and detectors for photon science and particle physics. The Center for Free-Electron Laser Science (CFEL) is a jointly operated research cooperation between DESY, Max Planck Society and the University of Hamburg. DESY supports three CFEL divisions with leaders jointly appointed with the University of Hamburg. For a joint EU Project with the European XFEL, the Coherent Imaging Division offers the following position. The European X-Ray Free Electron Laser Facility (XFEL) is a multi-national non-profit company. It will make available X-rays of unique quality for studies in physics, chemistry, life sciences, materials research and others. Located in the Hamburg area, Germany, it will comprise scientific instruments for a wide range of experimental techniques. Construction of the European XFEL is underway, its commissioning is scheduled for 2015. The position * Join a team from CFEL and XFEL to design and implement specific algorithms for diffraction analysis and image processing * Development of methods and software to analyse the large amounts of data generated by XFELs * Develop new algorithms for parameterized profile fitting; integrate, optimise and test code on parallel computers and GPUs; and develop advanced user interfaces Requirements * Ph. D. in Physics * Good knowledge of crystallographic theory and programming background * Demonstrated experience with large datasets, broad collaborations, and programming on distributed systems * Experience in the theory of matter/X-ray interactions is desirable * Ability to work in teams and sound communication For further information please contact Henry Chapman, +4940 8998-4155, henry.chap...@cfel.de or Adrian Mancuso, +4940 8998-2512, adrian.manc...@xfel.eu The position is limited to 1.5 years for DESY and with prolongation to 1.5 years within the XFEL GmbH Salary and benefits are commensurate with those of public service organisations in Germany. DESY operates flexible work schemes. Handicapped persons will be given preference to other equally qualified applicants. DESY is an equal opportunity, affirmative action employer and encourages applications from women. There is an English-speaking Kindergarten on the DESY site. Please send your application quoting the reference code 119/2011, by post or e-mail to: Deutsches Elektronen-Synchrotron DESY Human Resources Department | Reference code: 119/2011 Notkestraße 85 | 22607 Hamburg | Germany Phone: +49 40 8998-1589 E-Mail: personal.abteil...@desy.de Deadline for applications: 31. August 2011 www.desy.de
Re: [ccp4bb] Intensity-Weighted Reciprocal Lattice
On Thu, 21 Jul 2011 18:36:59 -0700 (PDT) Michael Thompson mi...@chem.ucla.edu wrote: I would like to view the intensity-weighted reciprocal lattice for several data sets that I have collected. (The data have been indexed, integrated and scaled with Denzo and Scalepack.) I was wondering if anyone could offer some advice on what might be the best and/or most practical way to do this? For the Hollywood graphics shown in various talks about the LCLS X-ray laser nanocrystal work, I generated something very similar to what you want. To do it, I wrote a program which ate a list of reflections and wrote a script for Persistence of Vision (raytracer), then invoked the raytracer in animation mode to make individual frames of animation before using a video encoding program (mencoder or Final Cut Pro) to stich them together. It was all a bit hacky, and it's a terrible way to visualise results for anything other than impressing audiences, but it did work. The code to do it is in our FEL crystallography suite which will be released publicly quite soon. Customising the animation is done by editing the source code, and isn't easy. For something a few years ago, I wrote a different program which, amongst many other things, showed a 3D reciprocal lattice weighted exactly how you describe and allowed you to roll it around and zoom in and out. If it sounds useful, I could resurrect that old code and tidy it up a bit to make it useful - there's not much to it. It could be useful for my own work, so I could prioritise it a little higher if it could be useful to other people...? Tom
