- phenixbb - phenix-online.org

Figure of merit from refinement
by Andre LB Ambrosio 01 Oct '19

01 Oct '19

Dear all, How is the FOM calculated for a given reflection specifically in the context of model refinement? How useful is it in assessing the phase quality, when not for initial experimental phases? Many thank in advance, -- Andre LB Ambrosio

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General interest
by John R Helliwell 30 Sep '19

30 Sep '19

Dear Colleagues, I draw your attention to my posting at the IUCr Committee on Data Public Forum ( https://forums.iucr.org/viewtopic.php?f=39&t=423 ) about the recent USA National Academies Report on Reproducibility and Replicability in Science. Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Final reminder: MicroED Workshop 2019
by Johan Hattne 30 Sep '19

30 Sep '19

Final reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice, and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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What OS do you use?
by Murpholino Peligro 22 Sep '19

22 Sep '19

I want to know what operating system you use. For that I made a poll, it is anonymous, quite simple and plus you get to see the results. (link https://forms.gle/7VT4pgbHQQmeAvpp8) I hope you contribute. Thanks

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Potential Berkeley Server Outage (September 23/24)
by Paul Adams 22 Sep '19

22 Sep '19

Dear Colleagues, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. They are predicting that Monday or Tuesday this coming week (September 23/24) might meet their criteria for a shutdown in the Bay Area. Hopefully this is just a worst case prediction and nothing will happen. However, there is a possibility that the Berkeley servers will be down for some time during that period (duration unknown). This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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XChem fragment screening - call for proposals - 2nd October 5pm
by Frank Von Delft 20 Sep '19

20 Sep '19

Dear all, This is a reminder that Diamond Light Source is accepting proposals for its XChem fragment screening facility, for the allocation period April to September 2020. The deadline is Wednesday 2nd October at 5pm (2 weeks from now). Details on how to apply are here - we're oversubscribed, so please follow the instructions! https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Applying-for-XC… XChem is a platform for high-throughput crystal-based fragment screening, operational since 2015. We provide fragment libraries (or you can bring your own) and the pipeline entails: rapid crystal soaking with an Echo acoustic liquid handler; high-throughput harvesting of hundreds of pre-soaked crystals using a Shifter; fully unattended data collection using dedicated beamtime on I04-1 beamline; and automated data integration along with tools for ligand detection (PanDDA) and streamlined model building (XChemExplorer). Since April 2019, we offer both standard and Block Allocation Group (BAG) access. Standard access accommodates both Tier 1 and Tier 2 proposals, for exploratory and ready-to-go projects respectively. Since this summer, the FragLites library from Newcastle university (J. Med. Chem.20196273741-3752) is also available for users. More information is on the XChem website: https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Methods-for-Fra…> https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Methods-for-Fra…<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Fragment-Librar…> https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Fragment-Librar… For more questions, please ask Alice (copied) or myself. We are looking forward to collaborating with you! The XChem team.

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Reminder: MicroED Workshop 2019
by Johan Hattne 19 Sep '19

19 Sep '19

Just a reminder: the application deadline for the 2019 MicroED workshop is October 1, 2019. From the initial announcement: The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice, and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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Re: [phenixbb] CCP4 Study Weekend 2020: registration now open!
by r.joosten＠nki.nl 11 Sep '19

11 Sep '19

Of course we want everyone to register immediately, but if you insist on seeing the programme first, please go to http://www.cvent.com/events/ccp4-study-weekend-2020/event-summary-001c74f5e… Cheers, Robbie, Jon, and Alan On 11 Sep 2019 13:37, "Robbie P. Joosten" <r.joosten(a)nki.nl> wrote: Dear colleagues, We are pleased to announce that the next CCP4 Study Weekend in its 2020 edition will be devoted to the single most synergic task in structural biology: model building. Aside from covering the latest advances in both automated and manual procedures, the meeting will offer sessions on related topics such as refinement, validation and representation, with a focus on helping you produce the best possible model from your experimental data. All sessions will have an integrative character, presenting methods and approaches that may be indistinctly used with X-ray crystallography, and electron cryo-microscopy or diffraction. This meeting will have a couple of innovations too - more announcements will follow in due course. The most important ones will be posted here (as always), but for more fluid news, speaker profiles and direct communication with the organisers, please use hashtag #CCP4SW on Twitter or give us a follow (vide infra). As in recent editions, the event will be held at the East Midlands Conference Centre in Nottingham, from the 7th to the 9th of January 2020. We are very much looking forward to welcoming you in Nottingham. And yes, there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh). Registration and programme details: https://tinyurl.com/ccp4sw2020 Best wishes, Robbie Joosten (@Robbie_Joosten), Alan Roseman (@AlanRoseman3), Jon Agirre (@glycojones), and the rest of CCP4 (@ccp4_mx) _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.org

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CCP4 Study Weekend 2020: registration now open!
by Robbie P. Joosten 11 Sep '19

11 Sep '19

Dear colleagues, We are pleased to announce that the next CCP4 Study Weekend in its 2020 edition will be devoted to the single most synergic task in structural biology: model building. Aside from covering the latest advances in both automated and manual procedures, the meeting will offer sessions on related topics such as refinement, validation and representation, with a focus on helping you produce the best possible model from your experimental data. All sessions will have an integrative character, presenting methods and approaches that may be indistinctly used with X-ray crystallography, and electron cryo-microscopy or diffraction. This meeting will have a couple of innovations too - more announcements will follow in due course. The most important ones will be posted here (as always), but for more fluid news, speaker profiles and direct communication with the organisers, please use hashtag #CCP4SW on Twitter or give us a follow (vide infra). As in recent editions, the event will be held at the East Midlands Conference Centre in Nottingham, from the 7th to the 9th of January 2020. We are very much looking forward to welcoming you in Nottingham. And yes, there will be a Cèilidh (https://en.wikipedia.org/wiki/Cèilidh). Registration and programme details: https://tinyurl.com/ccp4sw2020 Best wishes, Robbie Joosten (@Robbie_Joosten), Alan Roseman (@AlanRoseman3), Jon Agirre (@glycojones), and the rest of CCP4 (@ccp4_mx)

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Phenix user workshop just after Understanding Biology through Structure 2020
by Tom Terwilliger 10 Sep '19

10 Sep '19

Hi Structural biologists, particularly students and postdocs! A Phenix crystallography/cryo-EM workshop will be held after the last day of Understanding Biology through Structure 2020 (https://cvent.me/4kq9P, the meeting is March 16-19, 2020 in Santa Fe,NM; the workshop is March 20 and the workshop program is also at https://cvent.me/4kq9P). You can learn how to use the latest X-ray and cryo-EM tools in Phenix this way. Also student/postdoc fellowships are available for Understanding Biology through Structure 2020 (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). The fellowships cover registration and hotel (you still have to get there) and are being awarded after registration on a competitive rolling basis based on a publication you upload. You can register now at https://cvent.me/4kq9P ! Best regards, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Submissions to the Computational Crystallography Newsletter – 15 NOV 19
by Nigel Moriarty 10 Sep '19

10 Sep '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 202-0 issue is 15 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. As a reminder, the last issue is detailed here. July 2019 <http://phenix-online.org/newsletter/CCN_2019_07.pdf> Articles - Processing serial crystallographic data from XFELs or synchrotrons using the cctbx.xfel GUI <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=11> Short Communications - Automatic β-peptide linking in Phenix <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=5> - phenix.hbond: a new tool for annotation hydrogen bonds <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=7> - Bytes and Bobs : Accelerating python code with Numba <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=8> Fitting tips #18 – A subversive kind of misfit “water” <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=2> FAQ - Can I submit my X-ray model to the Protein Data Bank in PDB format? <http://phenix-online.org/newsletter/CCN_2019_07.pdf#page=4> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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General interest
by John R Helliwell 09 Sep '19

09 Sep '19

Dear Colleagues, The recent IUCr Committee on Data Satellite Workshop at ECM32 Vienna on “Data science skills in publishing” speaker presentations, overall report and photos from the day are now available via the IUCr CommDat Public Forum weblink:- https://forums.iucr.org/viewtopic.php?f=39&t=422&sid=f14add194ce5e9c146b51b… Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of IUCr Committee on Data

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Post-doctoral position for structure determination of large RNAs and RNP
by Sunandan Mukherjee 09 Sep '19

09 Sep '19

Hi everyone, Laboratory of Bioinformatics and Protein Engineering (LBPE) at the International Institute of Molecular and Cell Biology (IIMCB), Warsaw, Poland, headed by Prof. Janusz M. Bujnicki, is looking for a Postdoctoral Researcher for experimental structure determination of large RNAs (in particular lncRNAs and viral RNAs) and their complexes with proteins (RNPs). LBPE is an interdisciplinary and international team, focused on developing new approaches to determine RNA and RNP structures with the combined use of experimental methods and computational modeling. This position is ideal for you if you have solid experience (documented in publications) in at least one of the following techniques: 1) X-ray crystallography, 2) SAXS 3) cryo-EM, 4) AFM, and if you wish to learn new techniques of integrative structural biology, including computational modeling methods. You are expected to have a strong publication record, which includes at least one first-author publication in a very good international peer-reviewed journal. You are expected to take a lead and apply for fellowship/grant funding within the first year of your employment, with a project that combines the initial research area (structural analyses of large RNAs) with your own ideas. We are particularly interested in candidates interested in the gradual development towards scientific independence (next stage: junior group leader elsewhere) or growing towards a position of a senior scientist within our organization (long-term cooperation, involvement in multiple projects, supervision of junior scientists). The Postdoctoral Researcher will be selected from candidates in an open competition, according to the procedure complying with the rules of the European Charter for Researchers and the Code of Conduct for the Recruitment of Researchers as a part of HR Excellence in Research strategy https://www.iimcb.gov.pl/en/institute/hr-excellence . Application deadline: September 14th, 2019. For more details, please visit http://genesilico.pl/employment . With regards, Sunandan

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Selenium Nucleic Acids
by SeNA Research Institute 07 Sep '19

07 Sep '19

Dear Chemical and/or Structural Biologists, To serve our community, we have developed the selenium-atom specific derivatization of nucleic acids for crystallographic studies. We have discovered that virtually without any perturbations, the incorporated Se-atoms on nucleic acids can (I) rationally solve the phasing problem and (II) significantly facilitate nucleic acid crystallization (even with higher resolution and much larger crystals) in many cases, including protein-nucleic acid complexes. Currently, we are looking for collaborators and would be happy to offer free samples of Se-DNAs and Se-RNAs for your structure-and-function investigations. If you are interested, please contact us at SeNA(a)senaresearch.org Thanks, Mike SeNA Research Institute Email: SeNA(a)senaresearch.org Web: www.SeNAresearch.org http://www.senaresearch.org/

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Postdoctoral position
by Tobias Beck 05 Sep '19

05 Sep '19

Dear all, The Beck group is moving to Hamburg, where we will have labs well-equipped for chemistry, biochemistry and molecular biology. Moreover, state-of-the-art facilities for structural characterizations such as PETRA III are close by. We are looking for a postdoctoral fellow, funded by the Boehringer Ingelheim Foundation, for a project involving protein redesign, protein production and functionalization, and application in imaging and therapy. You should have a PhD degree in chemistry, biochemistry or biology and some experience with protein production and purification. Skills in structural biology / computational design are a plus. The post is available from January 01 2020. Full details of the post and the applications process are available here: https://www.uni-hamburg.de/uhh/stellenangebote/wissenschaftliches-personal/… The group homepage can be found here: https://www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck.html https://www.ac.rwth-aachen.de/extern/beck/ The deadline for applications is Oct 06 2019. Please contact me for further information or informal inquiries: tobias.beck(a)chemie.uni-hamburg.de Best, Tobias. -- ___________________________________________ Dr. Tobias Beck - independent group leader - RWTH Aachen University Institute of Inorganic Chemistry Landoltweg 1, office: 304N 52056 Aachen, Germany phone: +49-241-80-90057 fax: +49-241-80-99003 web: http://www.ac.rwth-aachen.de/extern/beck/ ___________________________________________ >From October 01: ____________________________________________________________ Prof. Dr. Tobias Beck University of Hamburg Department of Chemistry Institute of Physical Chemistry Grindelallee 117 D-20146 Hamburg Germany email: tobias.beck(a)chemie.uni-hamburg.de web: www.chemie.uni-hamburg.de/institute/pc/arbeitsgruppen/beck/ ____________________________________________________________

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77th Annual Pittsburgh Diffraction Conference
by Leighton Coates 04 Sep '19

04 Sep '19

Dear Colleagues You are invited to the 77th Annual Pittsburgh Diffraction Conference which will be hosted onsite at Oak Ridge National Laboratory in Oak Ridge, Tennessee, USA Start Date: 24th Oct 2019 End Date: 26th Oct 2019 URL: https://conference.sns.gov/event/78/ The conference will take place over three days, and feature sessions focused on all areas of diffraction, from powders to protein crystals. Topics will include Biological Diffraction, Total Scattering, Magnetic scattering, and small molecule Diffraction. The Chung Soo Yoo Award, established by the Pittsburgh Diffraction Society to honor Dr. Yoo’s memory, and a $400 cash prize will be given to the graduate student having the best poster presentation at the conference. Registration for the conference is only $100 and will close on September 20th, and we are still accepting abstracts for posters until that date. Confirmed Speakers are Jahuan Azadmanesh, (University of Nebraska) Emil S. Bozin (Brookhaven National Laboratory) Theodore Betley, (Harvard University) Chris Davies, (Medical University of South Carolina) Bob Von Dreele, (Argonne National Lab) Fred Dyda, (National Institutes of Health, NIDDK) Martin Egli, (Vanderbilt University) Jaime Fernandez-Baca, (Oak Ridge National Laboratory) Dustin Gilbert, (University of Tennessee) Margarida Henriques, (CAS Institute of Physics) Ken Herwig, (Oak Ridge National Laboratory) Patrick Holland, (Yale University) Robert Koch (Brookhaven National Laboratory) Joeseph Kolis, (Clemson University) Cora Lind Kovacs, (University of Toledo) Patricia Langan, (Lentigen Technologies) Jeremy Lohman, (Purdue University) Rebecca McAuliffe (Oak Ridge National Laboratory) Leonard Mueller, (University of California, Riverside) Tim Mueser, (University of Toledo) Robert Philips, (University of Georgia) Raktim Roy, (The Scripps Research Institute) Ella Mara Schmidt, (Friedrich-Alexander Universität Erlangen-Nürnberg) David J. Schuller, (Cornell University) Michael Shatruk, (Florida State University) Timothy Stachowski, (Hauptman Woodward Institute) Corey Thompson, (Purdue University) B.C. Wang, (University of Georgia) Weiwei Xie, (Louisiana State University) Haidong Zhou, (University of Tennessee) Best Wishes Leighton Coates

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Post-doctoral position in membrane protein structural biology
by Hasan, Syed Saif 31 Aug '19

31 Aug '19

A post-doctoral research position is high-resolution structural biology of membrane protein complexes is available in my laboratory at the Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. The post-doctoral researcher will have a choice of multiple structure-focused projects in cancer biology and viral pathogenesis using single particle cryoEM and crystallography. The researcher will have independence to guide the direction of their research and to pursue novel ideas should (s)he find an interesting scientific question related to the general research focus of my laboratory. IBBR is run jointly by the University of Maryland and the National Institute of Standards and Technology (NIST). We are home to a large community of structural biologists and have extensive interactions with national laboratories and private companies located in the DC-Maryland area. Our new cryoEM facility houses a 200 keV Thermo Fisher Talos Arctica microscope equipped with a Falcon 3 direct electron detector. Our facilities will soon be expanded to include a new 200 keV Thermo Fisher Glacios microscope, a Gatan K3 direct electron detector and a Volta phase plate. My lab works in close collaboration with research groups in IBBR that specialize in mass-spectrometry, computational biology, NMR spectroscopy, and small angle X-ray scattering. Applicants should have experience in insect or mammalian cell culture for protein production. Experience in handling membrane proteins will be helpful. Prior training in single particle cryoEM and/or crystallography is desirable but not essential. If you are a membrane protein biochemist, especially with experience in G-proteins, and you want to explore questions in structural biology, this is the position for you. Applicants who have received their PhD or MD/PhD degree should email me (sshasan(a)som.umaryland.edu) a single PDF file containing a short cover letter (no more than one page), a detailed curriculum vitae, contact information for three references, and upto 3 reprints of representative first authorship publication(s). The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. Saif S. Saif Hasan, PhD Fellow, Institute for Bioscience and Biotechnology Research (IBBR), 9600 Gudelsky Drive, Rockville, MD 20850 Assistant Professor, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, 108 N. Greene St., Baltimore, MD 21201 AND Center for Biomolecular Therapeutics (CBT), 9600 Gudelsky Drive, Rockville, MD 20850 Phone: 240-314-6396 Fax: 240-314-6225 https://www.ibbr.umd.edu/profiles/s-saif-hasan

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Re: [phenixbb] [bruker-axs] cbf to sfrm
by Tim Gruene 29 Aug '19

29 Aug '19

Dear Holger, thanks a lot for the prompt reaction! This will be very useful, in particular in case of proper twins. I look forward to the update, Tim On Thursday, August 29, 2019 11:32:00 AM CEST bruker-axs(a)lists.wisc.edu wrote: > Dear Tim, > > > > Thanks for having brought the bug to our attention. It got fixed in the > PROTEUM3/APEX3 2019.1 version which will be available for download next > week. > > > > Cheers, > Holger > > > Dr. Holger Ott > Global Application Coordinator SC-XRD & Senior Application Scientist > Chemical Crystallography > > Bruker AXS GmbH > Oestliche Rheinbrueckenstr. 49 > 76187 Karlsruhe, Germany > > Phone: +49 721 50997-5628 > Fax: +49 721 50997-45628 > > Holger.Ott@bruker<mailto:Holger.Ott@bruker>.com > www.bruker.com<http://www.bruker.com/> > > ________________________________ > > > > Sitz der Gesellschaft/Registered Office: Karlsruhe, HRB 107524 Amtsgericht > Mannheim, Umsatzsteuer-Ident.Nr. DE812037551, Geschäftsführer/Managing > Directors: - Dr. Frank Burgäzy, Dr. Klaus Gohlke > > Diese E-Mail einschließlich etwaiger Anlagen kann vertrauliche Informationen > enthalten. Sie ist daher vom Adressaten vertraulich zu behandeln und darf > nicht veröffentlicht werden. This email, including possible attachments, > may contain confidential information. It should therefore be treated as > confidential by the addressee and may not be published. > > > > > > -----Ursprüngliche Nachricht----- > Von: bruker-axs(a)lists.wisc.edu [mailto:[email protected]] > Gesendet: Sonntag, 28. Juli 2019 18:25 > An: bruker-axs(a)lists.wisc.edu; ccp4bb(a)jiscmail.ac.uk; > phenixbb(a)phenix-online.org Betreff: [bruker-axs] cbf to sfrm > > > > Dear all, > > > > recently the conversion from CBF to SFRM frame format with APEX was > discussed on the Bruker mailing list ("Synchrotron data with Bruker > Software"), including a potential bug that parameters in the frames other > than the first frame are not set correctly. The workaround to re-convert > from SFRM to SFRM a second time did not help in my case. > > > > I therefore updated my program sfrmtools, available at https:// > homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/ > > > > With the option '-u',you can provide the first frame of the run, and via > '-p' > > a parameter file that contains the critical parameters (see documentation at > above URL) to update the header for all frames in this run. In case you > have twinned data and want to benefit from SAINT, this should be possible > with this feature. > > > > Both 64bit Linux binary and the source code are available. The program has > no dependencies and should compile under any platform. > > > > I did not debug this new feature very thoroughly, but it worked for me so > far. > > Any bug reports are welcome to this address > tim.gruene(a)univie.ac.at<mailto:[email protected]> > > > > I hope this is helpful for one or two users. > > > > I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM > header format. > > > > Kind regards, > > Tim > > > > cc Bruker mailing list, CCP4BB, phenixBB > > -- > > -- > > 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 -- -- 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

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Job posting - CryoEM Research Group Leader in Australia
by Peter Czabotar 29 Aug '19

29 Aug '19

Dear colleagues, I’d like to bring to your attention a job opening for a Research Group Leader specialising in CryoEM at the The Walter and Eliza Hall Institute of Medical Research in Melbourne Australia. For details see - https://www.wehi.edu.au/cryoem-laboratory-head This is a 7-year appointment in the first instance with opportunities for further renewal. WEHI is a highly collaborative world-class institution that has been in operation for more than 100 years and was recently ranked in Nature’s Top 20 non-profit/non-governmental biomedical research institutes globally. The link above contains all necessary information for enquiries and applications. Many thanks and kind regards, Regards Peter Czabotar Associate Professor Peter Czabotar Joint Division Head of Structural Biology The Walter and Eliza Hall Institute of Medical Research 1G Royal Parade Parkville VIC 3052 Australia Phone: +61 (0)3 9345 2311 | Email: czabotar(a)wehi.edu.au _______________________________________________ The information in this email is confidential and intended solely for the addressee. You must not disclose, forward, print or use it without the permission of the sender. The Walter and Eliza Hall Institute acknowledges the Wurundjeri people of the Kulin Nation as the traditional owners of the land where our campuses are located and the continuing connection to country and community. _______________________________________________

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rosetta installation problem
by Almudena Ponce Salvatierra 28 Aug '19

28 Aug '19

Dear all, yesterday I spent quite some time trying to install Rosetta, so that I can use all it's modules within Phenix. However, when I am running the tests, rosetta stops and I get the following message (see below). Any help would be much appreciated. Thank you Almudena ======================= ROSETTA/PHENIX X-ray refinement ======================= Traceback (most recent call last): File "/Applications/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 307, in <module> run(sys.argv[1:], create_dir=True) File "/Applications/phenix-1.14-3260/build/../modules/phenix/phenix/command_line/rosetta_refine.py", line 159, in run default_directory_number=params.output.directory_number) File "/Applications/phenix-1.14-3260/modules/cctbx_project/libtbx/utils.py", line 1925, in create_run_directory os.makedirs(dir_name) File "/Applications/phenix-1.14-3260/base/Python.framework/Versions/2.7/Resources/Python.app/Contents/MacOS/../../../../../../../Python.framework/Versions/2.7/lib/python2.7/os.py", line 157, in makedirs mkdir(name, mode) OSError: [Errno 13] Permission denied: 'rosetta_1' Almudenas-MacBook-Pro:bin almudenaponce$

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Student/postdoc fellowships for Understanding Biology through Structure, March 16-20, 2020
by Tom Terwilliger 28 Aug '19

28 Aug '19

Hi Structural biologists, particularly students and postdocs! Student/postdoc fellowships still available for Understanding Biology through Structure 2020 (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). The fellowships cover registration and hotel (you still have to get there) and are being awarded after registration on a competitive rolling basis based on a publication you upload. Speakers at the symposium will be encouraged to present sufficient background and experimental detail so that students can understand the significance, promise, and limitations of their work. Each talk will have a full 10 minutes of discussion (15 minutes for Keynote talks). Moderators for each session will help include students and postdocs in the discussion. Students and postdocs will have many opportunities to talk with more senior researchers at conference breaks, meals, receptions and poster sessions. The last conference was a huge success (see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm) and this one is looking great (see https://cvent.me/4kq9P) We have a super group of speakers (keynote speakers are Ilme Schlichting, David Stuart, Erica Ollmann Saphire, Robert Stroud, Suzanne Scarlata, David Eisenberg, Wayne Hendrickson, Yvonne Jones, Eva Nogales, and Tom Blundell) After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. You can register now at https://cvent.me/4kq9P ! Best regards, Tom T Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Phenix refine on queueing server
by Johannes Cramer 23 Aug '19

23 Aug '19

Dear phenix developers/community, could anyone please point me to a tutorial on how to set up phenix for a job queueing system (preferably PBS). I am interested to use the gui on several systems, but to do the calculations on another. Is this possible? Cheers, Johannes

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6th International Symposium on Diffraction Structural Biology
by Leighton Coates 22 Aug '19

22 Aug '19

Dear Colleague You are invited to the 6th International Symposium on Diffraction Structural Biology which will take place at the University of Osaka in Japan. The early bird registration and abstract submission deadline of 31st August 2019 is rapidly approaching. Start Date: 17th Oct 2019 End Date: 20th Oct 2019 URL: https://isdsb2019.symposium-hp.jp/ The 6th International Symposium on Diffraction Structural Biology (ISDSB2019) is an international symposium organized by the Japan Society for the Promotion of Science, University-Industry Research Cooperative Research Committee, 169th Committee on Structural Biology using Diffraction Techniques. This symposium is positioned as an interface between academic researchers and industry researchers, as well as an interface between diffraction techniques and other related techniques in the field of structural biology. Symposium topics will include Macromolecular crystallography, CryoEM, software and databases and drug discovery, registration and abstract submission for the symposium is now open and costs 25,000 Japanese yen for academics. Confirmed Speakers are Nobel Lecture Joachim Frank, Columbia University, USA (Nobel Prize in Chemistry 2017) Plenary Lectures Stephen K. Burley, RCSB Protein Data Bank, Rutgers University and UC San Diego, USA Yoshinori Fujiyoshi, Tokyo Medical and Dental University, Japan Ian Wilson, The Scripps Research Institute, USA Invited Speakers Shinichi Adachi, Institute of Materials Structure Science (IMSS), KEK, Japan Terese Bergfors, Uppsala University, Sweden Caterina Biscari, ALBA Synchrotron, Spain Gérard Bricogne, Global Phasing Limited, UK Jacqui Gulbis, Walter and Eliza Hall Institute of Medical Research Vadim Cherezov, University of Southern California, USA Leighton Coates, Oak Ridge National Laboratory, USA Michael Henning, LeadXpro, Switzerland Roderick E. Hubbard, York University, UK Tamir Gonen, UCLA, USA Jie-Oh Lee, KAIST, Korea Mei Li, Institute of Biophysics, Chinese Academy of Science, P.R.China Jose A. Márquez, EMBL, France Yukihiko Sugita, Institute for Protein Research, Osaka University Marjolein Thunnissen, Max IV, Lund University, Sweden Leann Tilley, University of Melbourne, Australia Contact: Atsushi Nakagawa (Osaka University) Email: isdsb2019(a)gmail.com URL: https://isdsb2019.symposium-hp.jp/

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PhD and Postdoc position - Structural biology methods development at Würzburg University, Germany
by Andrea Thorn 22 Aug '19

22 Aug '19

Dear colleagues, for two projects in structural biology methods development, the Thorn Laboratory the Rudolf Virchow Center at the University of Würzburg is looking for a PHD CANDIDATE (m/f/d) and a POSTDOCTORAL RESEARCHER (m/f/d) Our lab 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. For more details, see: https://www.uni-wuerzburg.de/fileadmin/43020000/2019/PhD_Thorn_August_2019_… https://www.uni-wuerzburg.de/fileadmin/43020000/2019/Postdoc_Thorn_July_201… https://www.uni-wuerzburg.de/rvz/forschung/assoziierte-forschungsgruppen/ag… If you have any questions, please email me: andrea.thorn(a)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.thorn(a)uni-wuerzburg.de https://www.uni-wuerzburg.de/en/rvz/research/associated-research-groups/tho…

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Error very small nonbonded interaction distances.
by Ahmad Khalifa 21 Aug '19

21 Aug '19

Hello, I attached the log file below. Best regards.

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CCTBX documentation questionnaire
by Dorothee Liebschner 20 Aug '19

20 Aug '19

Hi everyone, During this year's ECM computing school, it came up that the CCTBX does not have a lot of documentation. This seems to be a major reason why people don't use it, even if they would like to employ the libraries. We would like to find out which parts of the CCTBX are the most interesting for users. We certainly cannot provide extensive documentation for the entire toolbox, but we can see what we can do once we know the main areas of interest. So if you were in the situation of wanting to use the CCTBX but decided to stay away from it because the documentation was non-existent or obscure, please let us know by filling out the questionnaire below (it's anonymous): questionnaire CCTBX documentation <https://forms.gle/9RawJFfHyEvhCVVP7> Best wishes, Dorothee -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Berkeley Server Downtime (8/16 - 8/18)
by Billy Poon 19 Aug '19

19 Aug '19

Dear all, On Friday, August 16, our servers will be shut down starting at 4:00 pm Pacific for scheduled maintenance in our building. We expect that the servers will be available by 10:00 am Pacific on Sunday (8/18) at the latest. This will affect, - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Re: [phenixbb] [cctbxbb] CCTBX documentation questionnaire
by Dorothee Liebschner 16 Aug '19

16 Aug '19

Hi Ben, Yes there is a reason: Checkbox option (multiple answers) does not support redirecting the answer (I wanted that feature). Your options: - You can choose "other" and list the libraries in question and describe what is problematic for each. - You can fill out the questionnaire several times (choose a different module each time) - You can write us (or me) an email and tell us details Cheers, Dorothee On Fri, Aug 16, 2019 at 12:21 AM ben.williams(a)diamond.ac.uk < ben.williams(a)diamond.ac.uk> wrote: > Dear Dorothee, > > Is there a reason for only allowing a single choice of library in the > questionnaire? I've wanted to use several components from across the CCTBX > project and would like my response to reflect that. I'm sure there are > probably others in the same boat. > > Many thanks, > Ben > > — > Ben Williams > Post-doctoral research associate > Scientific Software > Diamond Light Source > > On 15 Aug 2019 20:05, Dorothee Liebschner <dcliebschner(a)lbl.gov> wrote: > Hi everyone, > > During this year's ECM computing school, it came up that the CCTBX does > not have a lot of documentation. This seems to be a major reason why people > don't use it, even if they would like to employ the libraries. > We would like to find out which parts of the CCTBX are the most > interesting for users. We certainly cannot provide extensive documentation > for the entire toolbox, but we can see what we can do once we know the main > areas of interest. > So if you were in the situation of wanting to use the CCTBX but decided to > stay away from it because the documentation was non-existent or obscure, > please let us know by filling out the questionnaire below (it's anonymous): > > questionnaire CCTBX documentation<https://forms.gle/9RawJFfHyEvhCVVP7> > > Best wishes, > > Dorothee > > -- > Project Scientist, Molecular Biophysics and Integrated Bioimaging > Lawrence Berkeley National Laboratory > 1 Cyclotron Road, M/S 33R0345 > Berkeley, CA 94720 > Tel: (510) 486-5709 > Fax: (510) 486-5909 > Web: https://phenix-online.org<https://phenix-online.org/> > > > -- > This e-mail and any attachments may contain confidential, copyright and or > privileged material, and are for the use of the intended addressee only. If > you are not the intended addressee or an authorised recipient of the > addressee please notify us of receipt by returning the e-mail and do not > use, copy, retain, distribute or disclose the information in or attached to > the e-mail. > Any opinions expressed within this e-mail are those of the individual and > not necessarily of Diamond Light Source Ltd. > Diamond Light Source Ltd. cannot guarantee that this e-mail or any > attachments are free from viruses and we cannot accept liability for any > damage which you may sustain as a result of software viruses which may be > transmitted in or with the message. > Diamond Light Source Limited (company no. 4375679). Registered in England > and Wales with its registered office at Diamond House, Harwell Science and > Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom > > _______________________________________________ > cctbxbb mailing list > cctbxbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/cctbxbb > -- Project Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Postdoctoral Research Assistant (Structural biology) at University of Dundee (Alessio Ciulli)
by KH Chan 16 Aug '19

16 Aug '19

Posting on behalf of Prof. Alessio Ciulli: Professor Alessio Ciulli’s laboratory is seeking a postdoctoral researcher to undertake research in collaboration with one of the leading pharmaceutical companies supporting the Division of Signal Transduction Therapy (DSTT). The DSTT facilitates collaborations between some of the world’s major pharmaceutical companies (Boehringer Ingelheim, GlaxoSmithKline, and Merck-Serono) and leading Dundee-based researchers with a proven track record of achievement in understanding and exploiting the fundamental molecular causes of human disease in the fields of cancer, immune-regulation, neurodegeneration and hypertension resulting from disruptions in protein ubiquitylation, phosphorylation and other signalling networks. The successful applicant will be based within the Ciulli lab in Dundee ( http://www.lifesci.dundee.ac.uk/groups/alessio-ciulli). The laboratory is pioneering novel chemical structural biology approaches to target E3 ubiquitin ligases with small molecules. The applicant will employ state of the art structural biology, cell biology and biophysical approaches to conduct molecular and structural studies on disease-relevant human E3 ubiquitin ligases. The Ciulli lab has close collaborations and access to facilities available within both the MRC Protein Phosphorylation Unit ( http://www.ppu.mrc.ac.uk/) and more widely within the School of Life Sciences. This set-up will ensure the successful candidate will have access to whatever technologies required to conduct the projects that they are working on, including molecular, biochemical, mass spec proteomics, pharmacological and genetic methodologies including CRISPR/CAS9 knock-out and knock-in technologies. There will be regular opportunity for interaction and to discuss data within the group and with the collaborating pharma company. Job Title: Postdoctoral Research Assistant (Structural Cell Biology of E3 Ubiquitin Ligases) Grade Grade 7 (£32,236 - £39,609) Closing Date 25 August 2019 Details: https://www.jobs.dundee.ac.uk/fe/tpl_uod01.asp?s=4A515F4E5A565B1A&jobid=103…

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cut out density
by xiaowp82＠hotmail.com 14 Aug '19

14 Aug '19

Hello everyone I want to use a EM map as a model for molecular replacement. When I run "cut_out_density" in PHENIX_GUI, an error message was appeared: "Resolve error message: Could not run resolve with size 547". Does anyone meet the same problem and know how to sovle it? Thanks a lot! Sincerely yours Pan ________________________________ xiaowp82(a)hotmail.com

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MicroED Workshop 2019
by Johan Hattne 14 Aug '19

14 Aug '19

The Gonen Laboratory will hold the 5th MicroED Workshop in 2019. The workshop will be held at the MicroED Imaging Center at the UCLA David Geffen School of Medicine during December 9-12, 2019 and is open to both academia and industry. Space is limited and historically, the workshop is typically oversubscribed. Topics covered: * MicroED conception, practice and future opportunities * Electron optics for MicroED * Microscope alignment and calibration for MicroED * Sample preparation: protein and organic/inorganic materials, small molecules * Data collection for both protein and small molecules * Data analysis software, structure solution, and refinement * Choice of electron microscope hardware and cameras * MicroED publication standards: what statistics to include and when is your structure publication-ready? Further application information is available from https://cryoem.ucla.edu/pages/Workshop The application deadline is October 1, 2019. // Best wishes; Johan, on behalf of the organizers Research Specialist @ Gonen Lab ____________________________________________________ UCLA * 615 Charles E. Young Drive South BSRB #347 * Los Angeles, CA 90095

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Clipper updates for C++11
by Billy Poon 13 Aug '19

13 Aug '19

Hi everyone, As part of making CCTBX-based software compile with C++11, it looks like we need to update our checkout of clipper to the latest version. http://www.ysbl.york.ac.uk/~cowtan/clipper/clipper.html As a side note, is this a feature that is widely used? If not, we can disable the downloading of the clipper source files. Also, in addition to this post on the bulletin board, I have started an issue on Github (https://github.com/cctbx/cctbx_project/issues/379). Feel free to comment on any of these forums. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Setting master for finding NCS operators from PDB
by Ahmad Khalifa 13 Aug '19

13 Aug '19

Hello, I have a macro-molecular structure that I want to find the NCS rotation/translation for. Does the program automatically set the first alphabetical letter chains as master's?! Is there a way to specify which chains I want as master? Regards.

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Lectureship Positions University of Kent
by Gary Thompson 07 Aug '19

07 Aug '19

We have two Jobs advertised at the University of Kent that may be of interest to structural biologists with expertise in macro molecular crystallography. https://jobs.kent.ac.uk/Vacancy.aspx?ref=STM-032-19 The School of Biosciences has a long and continuing interest in structural biology with several groups exploiting NMR and Macromolecular Crystallography to study a wide range of problems. These include infection and drug resistance, cancer and age-related diseases, cellular architecture and dynamics and reproduction, evolution and genomics and industrial biotechnology. The School of Biosciences consistently has time as a BAG at Diamond and has recently invested in a new Mosquito LCP System with humidity control for crystallisation drop set up. Other facilities available for structural biologists include a well equipped Biomolecular Science Facility (electrospray and MALDI-TOF mass spectrometers, peptide synthesisers, CD etc) an in house X-Ray source in the School of Physical Sciences (Rigaku Oxford Diffraction Supernova) and a dedicated Biological NMR Facility with BAG access at the UK national NMR facilities at the Crick and Birmingham. Applications close 23.59 hours BST 19th August. See Job Description for further details. regards gary ------------------------------------------- Dr Gary S Thompson School of Biosciences, University of Kent, Canterbury, Kent, England, CT2 7NZ tel: 01227 82 7117 e-mail: g.s.thompson(a)kent.ac.uk<mailto:[email protected]> orchid: orcid.org/0000-0001-9399-7636<http://orcid.org/0000-0001-9399-7636> -------------------------------------------

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Phenix downloads are now available
by Billy Poon 07 Aug '19

07 Aug '19

Hi everyone, We fixed the issue with our server, so downloads are now available. We apologize for the inconvenience and please let us know if you encounter any issues. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Phenix downloads are currently unavailable
by Billy Poon 07 Aug '19

07 Aug '19

Hi everyone, There is currently an issue with the server hosting the Phenix downloads. We are looking into it and we will post and update when the issue is resolved. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Ligand build in coot
by Pham, Hang 02 Aug '19

02 Aug '19

Hello, I have an alpha-lactose as ligand in my model. It is possible that the glucose ring of alpha-lactose is opened since I do not see the whole density of ring and there are an extend density after C2’ of the glucose molecule. Does anyone know how to cleave the covalent between O’ and C1’ to form linear glucose in coot or should I build a new ligand from beginning (beta-galactose cyclic forming beta-1-4 glycosidic linkage with a linear glucose) in coot ? Thank you in advance Hang Pham ------------------------------------------------------ Hang Pham, Ph.D Student, The Doucet Lab Centre Armand-Frappier Santé Biotechnologie Institut National de la Recherche Scientifique (INRS) Université du Québec Réseau International des Instituts Pasteur 531 Boulevard des Prairies Laval (Québec) H7V 1B7 CANADA Téléphone : (450) 687-5010, poste 4210 Site web: http://www.profs.inrs.ca/ndoucet/

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General interest
by John R Helliwell 01 Aug '19

01 Aug '19

Dear Colleagues, The details, including all abstracts, for the IUCr Satellite at ECM32 Vienna on Data Science Skills in Publishing for Editors, Authors and Referees can be found here:- https://forums.iucr.org/viewtopic.php?f=39&t=419 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

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Phenix, MolProbity, and Amber
by Eric Williams 31 Jul '19

31 Jul '19

Greetings, all I'm trying to run the MolProbity programs (reduce, ramalyze, etc) in Phenix 1.16-3649, and I get the following warning: "Could not import the compiled Python-sander interface. Make sure you have the Python development libraries installed and that you have sourced amber.sh or amber.csh" I do not recall seeing that in earlier versions. Do I need to worry about it? If so, how do I fix it? Thanks. :) Eric

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General interest
by John R Helliwell 31 Jul '19

31 Jul '19

Dear Colleagues, For your general interest, you can find the lecture slides that I presented at ACA 2019 in the Transactions Symposium on Data via the weblink here:- https://forums.iucr.org/viewtopic.php?f=39&t=421 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of IUCr CommDat

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ISOLDE dev builds now available
by Tristan Croll 30 Jul '19

30 Jul '19

Hi all, Since the release of ISOLDE 1.0b3 I've begun releasing regular (weekly~fortnightly) development builds of ISOLDE. These are built against the ChimeraX daily build at the time of release - if you download a ChimeraX-daily build and install ISOLDE in the usual way via Tools/More Tools... this is what you'll get. In case you're worried, the dev and official 1.0b3 builds install into different directories, so it's quite straightforward to have both versions running independently on the same machine. The dev builds are *not* compatible with the ChimeraX 0.9 stable release. Some important changes since 1.0b3/ChimeraX 0.9: - the ChimeraX team have fixed some bugs affecting PDB and mmCIF I/O (primarily involving the handling of "imperfect" files) - fixed a bug causing the simulation to crash if the minimiser didn't converge in the first round - added status messages during simulation startup, and clear indications of when a simulation is running/paused - improved simulation startup time, and handling of custom ligands (preparing ligand definition files is a work in progress and will currently need you to do some work outside ISOLDE - feel free to contact me if you have an urgent case) Best regards, Tristan

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modify.remove option in phenix.refine
by wtempel 30 Jul '19

30 Jul '19

Hi, for calculation of an omit map, with the atoms in question fully removed from the model, I experimented with the modify_start_model.modify.remove option and got: ====================== Modifying start model if requested ===================== Size before: 505 size after: 491 Traceback (most recent call last): File "/home/user1/phenix-1.16-3549/build/../modules/phenix/phenix/command_line/refine.py", line 11, in command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/command_line.py", line 106, in run log=log) File "/home/user1/phenix-1.16-3549/modules/phenix/phenix/refinement/driver.py", line 271, in __init__ self.model.set_xray_structure(modify_model_obj.xray_structure) File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py", line 693, in set_xray_structure self.set_sites_cart_from_xrs() File "/home/user1/phenix-1.16-3549/modules/cctbx_project/mmtbx/model/model.py", line 1722, in set_sites_cart_from_xrs self._pdb_hierarchy.adopt_xray_structure(self._xray_structure) File "/home/user1/phenix-1.16-3549/modules/cctbx_project/iotbx/pdb/hierarchy.py", line 688, in adopt_xray_structure raise RuntimeError("Incompatible size of hierarchy and scatterers array.") RuntimeError: Incompatible size of hierarchy and scatterers array. I verified that my intended selection indeed comprises 14 atoms. Has anyone used the remove option inside phenix.refine successfully. Thanks. Wolfram Tempel

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cbf to sfrm
by Tim Gruene 29 Jul '19

29 Jul '19

Dear all, recently the conversion from CBF to SFRM frame format with APEX was discussed on the Bruker mailing list ("Synchrotron data with Bruker Software"), including a potential bug that parameters in the frames other than the first frame are not set correctly. The workaround to re-convert from SFRM to SFRM a second time did not help in my case. I therefore updated my program sfrmtools, available at https:// homepage.univie.ac.at/tim.gruene/research/programs/conv/sfrmtools/ With the option '-u',you can provide the first frame of the run, and via '-p' a parameter file that contains the critical parameters (see documentation at above URL) to update the header for all frames in this run. In case you have twinned data and want to benefit from SAINT, this should be possible with this feature. Both 64bit Linux binary and the source code are available. The program has no dependencies and should compile under any platform. I did not debug this new feature very thoroughly, but it worked for me so far. Any bug reports are welcome to this address tim.gruene(a)univie.ac.at I hope this is helpful for one or two users. I acknowledge the thorough documentation of XDS, of SAINT, and of the SFRM header format. Kind regards, Tim cc Bruker mailing list, CCP4BB, phenixBB -- -- 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

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Unwanted LINK records
by Luca Pellegrini 27 Jul '19

27 Jul '19

Hello, Phenix.real_space_refine generates a few spurious covalent bonds between protein and ligand in my structure, which distort the local structure, and then adds the corresponding LINK records in the output file. Is there a way to avoid this? I am aware of the anti-link option previously mentioned in the phenixbb: http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html, but I was wondering if there was another way of preventing this from happening. I am using Phenix 1.15.2-3472. Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA United Kingdom lp212(a)cam.ac.uk tel.: 0044 1223 760469 https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group @PellegriniLab

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Symmetry of map vs Symmetry of model
by pramod kumar 27 Jul '19

27 Jul '19

Dear all, I have a query related to symmetry imposition and corresponding tweaking of model. If symmetry (say, C4) was imposed during the reconstruction of a 3D volume, does symmetry also need to be imposed when building the atomic model (say, in Phenix)? Or could this constrain be relaxed? Do we need to tweak the model in Coot for other chains or since it is build on symmetrical partners therefore should only be made in one chain and copied for all without any fitting? Pramod Jaykar, Ph.D.

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Re: [phenixbb] Unwanted LINK records
by Dale Kreitler 27 Jul '19

27 Jul '19

Hi Luca, Try running with the parameter: refinement.pdb_interpretation.automatic_linking.link_ligands=False Check if automatic linking is enabled with the All parameters button in the GUI. Looks like the default might be True? -D On Fri, Jul 26, 2019 at 11:21 AM Luca Pellegrini <lp212(a)cam.ac.uk> wrote: > Hello, > > Phenix.real_space_refine generates a few spurious covalent bonds between > protein and ligand in my structure, which distort the local structure, and > then adds the corresponding LINK records in the output file. Is there a way > to avoid this? > > I am aware of the anti-link option previously mentioned in the phenixbb: > http://www.phenix-online.org/pipermail/phenixbb/2018-January/023677.html, > but I was wondering if there was another way of preventing this from > happening. I am using Phenix 1.15.2-3472. > > Best wishes, > Luca > > Luca Pellegrini, PhD > Department of Biochemistry > University of Cambridge > Cambridge CB2 1GA > United Kingdom > > lp212(a)cam.ac.uk > tel.: 0044 1223 760469 > https://www.bioc.cam.ac.uk/pellegrini-group/pellegrini-group > @PellegriniLab > > > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > -- Dale Kreitler Graduate Research Assistant Gellman Lab Department of Chemistry University of Wisconsin-Madison

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Symmetry of map Vs Symmetry of model
by pramod kumar 26 Jul '19

26 Jul '19

Dear all, I have a query related to symmetry imposition and corresponding tweaking of model. If symmetry (say, C4) was imposed during the reconstruction of a 3D volume, does symmetry also need to be imposed when building the atomic model (say, in Phenix)? Or could this constrain be relaxed? Do we need to tweak the model in Coot for other chains or since it is build on symmetrical partners therefore should only be made in one chain and copied for all without any fitting? Pramod Jaykar, Ph.D.

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CryoEM specialist positions open at CSIR-CCMB, India
by Rukmini Raju 23 Jul '19

23 Jul '19

Dear All, This is to bring to your kind attention two vacancies for Structural Biologists with CryoEM expertise at the CCMB, Hyderabad, India. CSIR-Centre for Cellular and Molecular Biology, Hyderabad (CSIR-CCMB) is a Premier Research Laboratory under the Council of Scientific & Industrial Research (CSIR), involved in multidisciplinary R&D programmes of both basic and applied nature across scientific disciplines of biological sciences. The link for the application is given below: http://www.ccmb.res.in/index.php?view=notifications&mid=0&id=71&nid=268 Best regards, Sankar -- ****************************************************************************** Dr. Rajan Sankaranarayanan Chief Scientist, Structural Biology Laboratory CSIR-Centre for Cellular and Molecular Biology (CCMB) Uppal Road Hyderabad - 500 007 India. Ph: +91-(0)40 2719 2832 to 2835 (Lab) +91-(0)40 2719 2500 (CCMB Reception) Fax: +91-(0)40 2716 0252, 2716 0591 e-mail: sankar(a)ccmb.res.in sankarfr(a)yahoo.com Web: http://e-portal.ccmb.res.in/e-space/sankar/index.html ******************************************************************************** -- ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ R. Rukmini Principal Technical Officer Structural Biology, R-100, R&D Building CSIR-Centre for Cellular and Molecular Biology Uppal Road, Hyderabad - 500 007 India Phone# +91-40-27192953(callto:+91-40-27192953) (R-100) +91-40-27192835(callto:+91-40-27192835) (Lab, Main Building) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Real space refinment keeps messing up my taxol conformation
by Ahmad Khalifa 21 Jul '19

21 Jul '19

I used elbow to generate restraints for taxol using chemical componenet and sdf file. I posted before to the list and Oleg was kind enough to provide restraints generated by readyset. No matter what restraints I use, the taxol is messed up! The other thing is, the refinement keeps breaking the peptide bond at a specific location! I would like to send some files to someone privately to investigate! Please let me know. Regards.

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phenix.pdbtools
by Raja Dey 19 Jul '19

19 Jul '19

Dear Members, I like to regularize the geometry of selected residues' side chains using phenix.pdbtools? I couldn't find the syntax. I used the following command line syntax, but didn't work. Can someone help correcting this command? phenix.pdbtools myprotein.pdb geometry-regularization=true selection="((chain A and ((resseq 236:237 not backbone) or (resseq 240:241 not backbone) or (resseq 244 not backbone) or (resseq 254 not backbone) or (resseq 258 not backbone) or (resseq 261:262 not backbone) or (resseq 412:413 not backbone) or (resseq 416:417 not backbone) or (resseq 419 not backbone))) or (chain X and ((resseq 104 not backbone) or (resseq 107:108 not backbone) or (resseq 111 not backbone) or (resseq 113 not backbone)))) Best regards, Raja

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