- phenixbb - phenix-online.org

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 27 Aug '19

27 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 22 Aug '19

22 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 19 Aug '19

19 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 18 Aug '19

18 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 15 Aug '19

15 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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