[ccp4bb] Last day to apply: Scientific Coordinator Coronavirus Structural Task Force
Dear colleagues, We are looking for a scientific coordinator for the Coronavirus Structural Task Force (www.insidecorona.de). The position is 50% part-time, can mostly be done remotely, and requires German and English language skills as well as a Masters degree or comparable in a relevant subject. The salary is 50% TVL-13 with appropriate qualification. If you are - or know - someone who is interested, you can find more infos here: uhh.de/cst-coordinator Best wishes, Andrea. -- Dr. Andrea Thorn | group leader andrea.th...@uni-hamburg.de HARBOR (Institute for Nanostructure and Solid State Physics), Universität Hamburg Luruper Chaussee 149 / Bldg. 610 | 22761 Hamburg | Germany Tel. +49 (0)40 42838 3651 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/
Re: [ccp4bb] disinfecting keyboards
Hi Tim! 100% alcohol is less effective than 80%, and in order to completely be sure, the keyboard needs not only to be wiped. One can buy keyboards that can be disinfected because they are waterproof, such as the Cherry JK-1068DE-2 for about 50 €. We clean the keyboards in our lab occasionally anyway, and have used 70% alcohol on them without problem. Disinfectant wipes, a detergent cleaner (such as Viss Glass & Flächen) and cotton swabs also offer some help. We wipe our mobile phones with a disinfectant wipe after washing our hands when arriving home/at work. I would also be really interested in what could be done with a UV light, if someone knows? If the computer is used by one person during the shift, individual keyboards for each person could be a solution. If people sit down, the desk surface, which may be touched, should likely also be wiped at the beginning and end of the shift I would say. Stay save and best wishes, Andrea. Am 29/04/2020 um 21:04 schrieb Diana Tomchick: 100% ethanol or isopropanol work really well on the microscopes, I soak a Kimwipe and then clean the eyepieces and the knobs for changing magnification and focus, as well as the door handles, bench tops, etc. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) *From:* CCP4 bulletin board on behalf of Diana Tomchick *Sent:* Wednesday, April 29, 2020 2:00 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* Re: [ccp4bb] disinfecting keyboards EXTERNAL MAIL You could try doing what my technician does with her keyboard; she wraps it in a clear, thin food wrap that can be taped to the back of the keyboard. This is usually done to keep food and other things (liquids) from damaging the keyboard, but you could simply replace the wrap every time someone else uses it. Personally I like using a Kimwipe soaked with 100% isopropanol, I've never yet encountered a keyboard that suffered from having the writing removed with that or 100% ethanol. Both work and as long as they are 100% (no water), the keyboard and mouse have no issues. Diana ** Diana R. Tomchick Professor Departments of Biophysics and Biochemistry UT Southwestern Medical Center 5323 Harry Hines Blvd. Rm. ND10.214A Dallas, TX 75390-8816 diana.tomch...@utsouthwestern.edu (214) 645-6383 (phone) (214) 645-6353 (fax) *From:* CCP4 bulletin board on behalf of Tim Gruene *Sent:* Wednesday, April 29, 2020 1:53 PM *To:* CCP4BB@JISCMAIL.AC.UK *Subject:* [ccp4bb] disinfecting keyboards Dear all, can you make suggestions for how to disinfect computer keyboards, and instrument panels? Our facility is going to reboot next week, with shifts so that people don't meet. The main interface will be the computer keyboards, as well as the door of our X-ray diffractometer and the mounting of the crystals. The keyboard labels may not like alcohols (and the efficiency of injecting disinfecting through the USB cable is also under discussion, so I heard). One way would be to use individual keyboards, and wearing gloves for replugging, and to use gloves for mounting crystals. But maybe there are other ways that won't require gloves? Best regards, Tim -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 UTSouthwestern Medical Center The future of medicine, today. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 CAUTION: This email originated from outside UTSW. Please be cautious of links or attachments, and validate the sender's email address before replying. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- Dr. Andrea Thorn | group leader andrea.th...@uni-wuerzburg.de +49 931 31-83677 Rudolf Virchow Center, University of Wuerzburg Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/
[ccp4bb] Public resource for the structures, validation and re-modelling of Corona virus macromolecules
Dear colleagues, we are methods developers in structural biology. During this time of crisis, we decided to put our brains to where our hearts are and have started a public resource for the structures from beta-coronavirus with a focus on SARS-CoV and SARS-CoV-2: https://github.com/thorn-lab/coronavirus_structural_task_force It can be used to download all relevant structures, look at structural validation information, diagnostic data for the quality of experimental data and available re-refinements. We will expand this resource in time, but as of today, it contains all deposited SARS-CoV and SARS-CoV-2 structures, sorted by protein and virus, PDB-REDO entries, diffraction data diagnostics from AUSPEX and PHENIX.XTRIAGE, WHATCHECK reports and Tristan Croll's fantastic manual ISOLDE re-refinements. We will soon add MOLPROBITY to lighten the traffic on the server at Duke, individual links to Global Phasing's efforts in re-processing and re-refinement of individual structures and HARUSPEX map annotations for the Cryo-EM structures. We may point out potential improvements in some structures in these data, but this is not meant as criticism of the achievements of the researchers who first elucidated these structures! It merely reflects on recent progress in methods development and the potential to push our methods to their limit in order to get every last bit of biological information from a given data set. We hope this can make a (small) difference for a cure of COVID-19. If you have any questions or would like to contribute, please let me know! Andrea Thorn. The collaborators, as of today, are: myself, Yunyun Gao, Kristopher Nolte, Ferdinand Kirsten, Sabrina Stäb (RVZ, University of Würzburg, Germany) Gianluca Santoni (European Synchrotron Facility, France) Tristan Croll (CIMR, University of Cambridge, UK) The Richardson Laboratory (Duke University, USA) We would also like to thank for their advice: Sameer Velankar, James Holton, Manfred Weiss, Gerard Bricogne, Clemens Vonrhein and Robbie Joosten. -- Dr. Andrea Thorn | group leader andrea.th...@uni-wuerzburg.de +49 931 31-83677 Rudolf Virchow Center, University of Wuerzburg Josef-Schneider-Str. 2 | 97080 Wuerzburg | Germany https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Two positions (PhD / Postdoc) in crystallographic methods development at Würzburg University, Germany
Dear Colleagues, for two projects in crystallographic methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The PhD project aims at a better understanding of macromolecular crystals and subsequent improvements in modelling and we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS). The postdoctoral project aims to establish new diagnostics and best practices in diffraction data collection and processing. We offer a 30-month full- or part-time position with a competitive salary as well as career and family support. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology or machine learning are also a bonus. Wuerzburg University offers very competitive employment conditions and an excellent scientific environment in the beautiful, wine-growing area of Franconia, Germany. For more details, send me an email or follow the link below: https://www.uni-wuerzburg.de/en/rvz/news/jobs-and-career/job-offers/ The closing date is January 31st, 2020 - end of this week! Best wishes, Andrea Thorn. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Two positions (PhD / Postdoc) in crystallographic methods development at Würzburg University, Germany
Dear Colleagues, for two projects in crystallographic methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The PhD project aims at a better understanding of macromolecular crystals and subsequent improvements in modelling and we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS). The postdoctoral project aims to establish new diagnostics and best practices in diffraction data collection and processing. We offer a 30-month full- or part-time position with a competitive salary as well as career and family support. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology or machine learning are also a bonus. Wuerzburg University offers very competitive employment conditions and an excellent scientific environment in the beautiful, wine-growing area of Franconia, Germany. For more details, send me an email or follow the link below: https://www.uni-wuerzburg.de/en/rvz/news/jobs-and-career/job-offers/ The closing date is January 31st, 2020. Best wishes, Andrea Thorn. To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] PhD and postdoc position - Structural Biology Methods development at Wuerzburg University
Dear colleagues, for two projects in structural biology methods development, we are looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) The Thorn Laboratory the Rudolf Virchow Center at the University of Wuerzburg develops new methods for macromolecular X-ray crystallography and Cryo-EM. In these exciting projects you will improve how well we understand, measure and model macromolecular crystal structures using practical experiments and big data analyses. We are looking for candidates with skills in data analysis and programming. Any previous experiences in crystallography, molecular biology, machine learning, image or statistical analysis are also a bonus. You should be a good communicator. For the PhD project, we offer a 36-month full- or part-time position, embedded in the Würzburg Graduate School for Life Sciences (GSLS); for the postdoctoral position, we offer a 30-month full- or part-time position with a competitive salary as well as career and family support. Women are particularly encouraged to apply. For more details, see: https://www.uni-wuerzburg.de/fileadmin/4302/2019/Stellenanzeige_PhD_Thorn_September_2019_final_Auslage.pdf https://www.uni-wuerzburg.de/fileadmin/4302/2019/Stellenanzeige_PostdocThorn_Sep_2019_final_Auslage.pdf If you have any questions, please email me: andrea.th...@uni-wuerzburg.de. Best wishes, Andrea Thorn. _ Dr. Andrea Thorn group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.th...@uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] PhD position - Crystallographic Methods development at Würzburg University
For a project in crystallographic methods development, the Thorn Laboratory at the University of Würzburg, Germany, is recruiting a PHD CANDIDATE (m/f/d) Our lab develops new methods for macromolecular X-ray crystallography and Cryo-EM. In this exciting PhD project you will improve how well we understand, measure and model macromolecular crystal structures using practical experiments and big data analyses. We are looking for a good communicator with skills in crystallography and programming. Any previous experiences in machine learning, biochemistry, image or statistical data analysis are a bonus. We offer a 36-month full- or part-time position with a competitive salary, embedded in the Würzburg Graduate School for Life Sciences (GSLS). For more details, see: https://www.uni-wuerzburg.de/fileadmin/4302/2019/PhD_Thorn_August_2019_Anzeige.pdf If you have any questions, please email me: andrea.th...@uni-wuerzburg.de. _ Dr. Andrea Thorn group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.th...@uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] Postdoctoral position in crystallographic methods and software development at Wuerzburg University, Germany
Dear colleagues, we are a young and active research group at the University of Wuerzburg, the birthplace of X-rays, and are looking for a POST-DOCTORAL RESEARCHER in the field of crystallographic methods development He or she will uncover problems and pitfalls in the measurement and processing of XFEL, neutron and conventional X-ray diffraction data from single crystals and develop new diagnostics in AUSPEX (www.auspex.de) using machine learning, practical experiments and statistical data analysis as well as establish new best practices in collaboration with major European diffraction facilities. We are looking for someone with a good working knowledge of statistical analysis, Python and C++ who is an excellent communicator and likes to travel. Previous experience in crystallography and machine learning is a bonus. We offer a position at the Rudolf-Virchow Center in Wuerzburg, Germany, with a competitive salary, benefit package, career development and training courses. For a full description, see https://www.uni-wuerzburg.de/en/rvz/news/jobs-and-career/job-offers/ (Click on "Post-doctoral researcher") If you have any questions, please email: andrea.th...@uni-wuerzburg.de. -- Dr. Andrea Thorn Group leader Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany andrea.th...@uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/thorn-group/ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] AUSPEX - now also as web server!
Since January, the diagnostic software AUSPEX for diffraction data has been available in CCP4 (in GUI2 and from the command line), and is now also available as a web service at www.auspex.de AUSPEX can help you to quickly recognize ice rings as well as other pathologies (have a look at www.auspex.de/pathol ) using an MTZ file or even only a PDB code. The main reference is http://journals.iucr.org/d/issues/2017/09/00/hi5647 If encounter any problems, or want to request a new feature, please let us know: aus...@uni-wuerzburg.de - we aim to extend AUSPEX functionality in the near future. I would also like to thank Philipp Mostosi and Hermann Schindelin and the University of Würzburg for their help regarding the web server. Andrea Thorn. -- Dr. Andrea Thorn Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] AUSPEX - now also as web server!
Since January, the diagnostic software AUSPEX for diffraction data has been available in CCP4 (in GUI2 and from the command line), and is now also available as a web service at www.auspex.de AUSPEX can help you to quickly recognize ice rings as well as other pathologies (have a look at www.auspex.de/pathol ) using an MTZ file or even only a PDB code. The main reference is http://journals.iucr.org/d/issues/2017/09/00/hi5647 If encounter any problems, or want to request a new feature, please let us know: aus...@uni-wuerzburg.de - we aim to extend AUSPEX functionality in the near future. I would also like to thank Philipp Mostosi and Hermann Schindelin and the University of Würzburg for their help regarding the web server. Andrea Thorn. -- Dr. Andrea Thorn Rudolf Virchow Center for Experimental Biomedicine University of Wuerzburg Josef-Schneider-Str. 2 97080 Wuerzburg Germany To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
[ccp4bb] [Meeting Announcement] European Crystallographic Computing Forum 2018 in Mieres, Spain
Dear all, Registration for the European Crystallographic Computing Forum is open: https://www.mrc-lmb.cam.ac.uk/harry/ecacomsig/mieres.html A poster for print can be downloaded here: https://we.tl/CyPFzYvorG Spread the word! The Forum will be held in Mieres, Spain, 18th - 22nd August 2018 (preceding the ECM). We invite both beginners (from graduate level) and experienced software developers from all crystallographic disciplines. Participants can bring their own software development project to work on it in teams, interspersed with tutorials and lectures. There will be opportunity to exchange and connect with other crystallographic software developers. The registration fee (360 €) includes: accommodation (4 nights), full board and refreshments and transfer to the ECM. We offer childcare and family rooms. Bursaries are available. We hope to see you there! The Organisers Andrea Thorn, Harry Powell, Laura Roces Fernandez We would like to thank our kind sponsors! - CCP4 - Dectris - Rigaku - Bruker - -- Dr. Andrea Thorn Secretary ECA Special Interest Group 9 (Crystallographic Computing) University of Wuerzburg http://shelx.uni-ac.gwdg.de/~athorn
Re: [ccp4bb] Strange Ancient Diffraction Pattern...
These diffraction patterns, called "matzo" (Hebrew: מַצָּה) have been observed already by the ancient jews, and it is thought that the invention of the millstone (see http://galleryhip.com/millstone.html) is a consequence of early detector technology to produce these images. Andrea. On 01/04/2015 12:03, Keller, Jacob wrote: Can anyone index this? It's got mostly split spots and a strange diffuse scattering background JPK *** Jacob Pearson Keller, PhD Looger Lab/HHMI Janelia Research Campus 19700 Helix Dr, Ashburn, VA 20147 email: kell...@janelia.hhmi.org *** -- Dr Andrea Thorn MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge Biomedical Campus Cambridge CB2 0QH, U.K. andrea.th...@web.de http://shelx.uni-ac.gwdg.de/~athorn
[ccp4bb] European Crystallographic Computing School 20-22/8/2015 in Croatia
We would like to announce the European Crystallographic Computing School: Advanced Software Development for Crystallographers from the 20th to 22nd August 2015 in Duga Uvala, Croatia. Location: Hotel Croatia at the beach location Duga Uvala, Croatia, 40 kms from Rovinj Cost: 100 € including full board, excluding accommodation. (Bursaries are available.) More infos and registration: http://sig9.ecanews.org/rovinj.html This School for active and future software developers will cover advanced topics in the design of crystallographic programs. We will focus on tutorials in small groups, with plenary lectures covering aspects relevant to all crystallographic disciplines. We will also provide opportunity for one-on-one problem solving sessions as well as networking, integrating new developers into the crystallographic software community. Participants are invited to contribute tutorials. The School is organized by the Crystallographic Computing Special Interest Group (ECACOMSIG) as a satellite meeting to the European Crystallographic Meeting (ECM29) in Rovinj. All queries should be sent to Harry Powell (ha...@mrc-lmb.cam.ac.uk) or Andrea Thorn (ath...@mrc-lmb.cam.ac.uk). Confirmed speakers include: •Luc Bourhis, Paris, France •Kay Diederichs, Konstanz, Germany •Eleanor Dodson, York, UK •Vincent Favre-Nicolin, Grenoble, France •Christian Jelsch, France •Anders Madsen, Copenhagen, Denmark •Santosh Panjikar, Melbourne, Australia •Harry Powell, Cambridge, UK •Andrea Thorn, Cambridge, UK •George Sheldrick, Goettingen, Germany The school is kindly sponsored by CCP4, Dectris, Agilent Technologies and Bruker AXS. -- Dr. Andrea Thorn Secretary of ECA SIG9 (Crystallographic Computing)
Re: [ccp4bb] how to deal 3 twin-related domains
Dear Fulvio, what did your L-Test with the unmerged (P1) data look like? In order to use twin refinement you should be sure that the structure is twinned. Did you try all possible subgroups of R3? Generally, a triplet can be treated as any other pseudo-merohedral twin, given it really is a triplet - meaning integration and scaling in the lower (real) space group, MR and twin refinement. What is the indication that MR worked? The random R value (meaning an unsolved structure) goes down from 58.5 to 50% if your structure is (pseudo-)merohedrally twinned, and you are not very much under this value. Best wishes Andrea. Am 07.05.2013 14:47, schrieb Fulvio Saccoccia: Dear ccp4 users, I have a reflections file obtained from a crystal initially scaled in H3. All the attempts to phase by Molecular Replacement were not successful and I succeeded only in P1. Based on previously solved structures from the same protein, I suspected that twinning affected crystals; so I used Twin refinement in Refmac. The program gave indication of 3 domains: Twin operator: H, K, L: Fraction = 0.335 Twin operator: H, L, -H-K-L: Fraction = 0.332 Twin operator: H, -H-K-L, K: Fraction = 0.333 With P1 and twin refinement I obtained a reasonable initial value of FOM (0.50) but R/Rfree still remain at very large values (0.46/0.49). I am not sure about twinning and data handling in presence of 3 twin domains and I will appreciate a lot if someone will suggest me how to deal out with these data. Thanks Fulvio -- Dr. Andrea Thorn Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Wellcome Trust/MRC Building Hills Road Cambridge CB2 0XY, U.K. andrea.th...@web.de http://shelx.uni-ac.gwdg.de/~athorn Tel: + 44 1223 763234
Re: [ccp4bb] Crystal twinning
Dear Theresa, all types of twinning - merohedral, pseudo-merohedral and non-merohedral ones - can be solved given somewhat favorable conditions. In small molecule crystallography, it's quite common, especially for (pseudo) merohedral twins, it becomes increasingly popular for macromolecules as well. However, if your crystal is a split one with many domains, you should possibly look for a better crystal. You need to treat your data correctly: - In cases of (pseudo) merohedral twinning: Integrate in the lower - correct - space group. Not all methods of structure solution work well with twins, especially S-SAD - which is very sensitive towards data errors - and those methods that require several crystals. For refinement, the free R set has to contain also reflections related by twinning, and the random R value will go down, so don't be fooled. - In case of a non-merohedral twin, particular attention should be paid to overlapping reflections, they should be left out at first for indexing and treated special in integration. Scaling is also more difficult. While non-merohedral twins can be dealt with, it is not (yet?) common practice for macromolecules. Best wishes Andrea. Am 22.02.2012 19:56, schrieb Theresa H. Hsu: Hi all. I have a 'learning' question based on recent thread where crystal twinning is mentioned. With the current computational methods, what types of twinnig can and cannot be solved with computers? Thank you. Theresa ath...@shelx.uni-ac.gwdg.de http://shelx.uni-ac.gwdg.de/~athorn
