- phenixbb - phenix-online.org

Validation_cryoEM Calculation the FSC model-map
by Marta Martinez 05 Feb '20

05 Feb '20

Dear all, we are wondering how the mask and unmasked values of the FSC model-map have been computed and how the mask is defined when the phenix tool phenix.validation_cryoem ("Comprenhensive Validation (cryo-EM)") is used. The motivation of this question comes from the results that we get when we have big maps (e.g. some viruses) and the atomic structure is determined only for the asymmetric subunit. We usually compute the validation considering both the whole map, and a fraction of the map that only contains the atomic structure of the asymmetric subunit (the atomic model is the same in both cases, the asymmetric subunit). We would expect the same results, as it happens for the validation statistics, but the FSC model-map values are different, especially when we talk about masked values. Recently we have checked that we have the same kind of results when we use small maps, so it doesn't seem to be due to the size of the map. Can you kindly explain the reason of these results and what we should expect in general. Is there any restriction when a fraction of the whole volume is selected? Thank you very much in advance. Regards, MARTA -- Marta Martinez Gonzalez Biocomputing Unit (Lab B13) National Center for Biotechnology-CSIC Darwin, 3. Campus de la Universidad Autonoma de Madrid 28049 Madrid. Spain Tel:+34 915854510 Fax:+34 913720112 E-mail: mmmtnez(a)cnb.csic.es

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Macromolecular Crystallography workshop in South America 2020
by Alejandro Buschiazzo 05 Feb '20

05 Feb '20

Dear colleagues, We are pleased to announce the 8th South American Macromolecular Crystallography School: Macromolecular Crystallography School 2020 "Structural Biology to enhance high impact research in health and disease” To be held at the Institut Pasteur de Montevideo (Uruguay) - September 9-19, 2020 http://pasteur.uy/novedades/mx2020/ The application deadline is July 9, 2020. For further inquiries : mx2020(a)pasteur.edu.uy <mailto:[email protected]> Main Topics: · data processing; · phasing and structure determination; · model refinement and validation; · introduction to crystallography + cryo-electron microscopy integration Confirmed speakers and tutors (so far... a few more will join the crew): Alejandro Buschiazzo (Institut Pasteur de Montevideo, Uruguay) Paul Emsley (Laboratory of Molecular Biology MRC, Cambridge, UK) Rafael Junqueira Borges (Instituto de Biociências UNESP, Botucatu, Brazil) Ronan Keegan (STFC Rutherford Appleton Lab - CCP4, Didcot, UK) Eugene Krissinel (STFC Rutherford Appleton Lab - CCP4, Didcot, UK) Joāo Muniz (Instituto de Fisica de São Carlos, Brazil) Garib Murshudov (Laboratory of Molecular Biology MRC, Cambridge, UK) Colin Palmer (STFC Rutherford Appleton Lab - CCP-EM, Didcot, UK) James Parkhurst (Diamond Light Source, Didcot, UK) Randy Read (University of Cambridge, UK) Kyle Stevenson (STFC Rutherford Appleton Lab - CCP4, Didcot, UK) Clemens Vonrhein (Global Phasing Ltd, Cambridge, UK) Please find the application form and further contact information at http://pasteur.uy/novedades/mx2020/ (this www site will be updated regularly, so stay tuned!) This Workshop is supported by the Collaborative Computational Project Nº4 (CCP4, UK) & Science and Technology Facilities Council (UK); the Centro de Biologia Estructural del Mercosur (CeBEM); and the Programa Iberoamericano de Ciencia y Tecnologia para el Desarrollo (CYTED) through de MICROBES consortium. Organizers: Alejandro Buschiazzo, PhD. Institut Pasteur de Montevideo, Uruguay Kyle Stevenson, DPhil. CCP4, STFC Rutherford Appleton Laboratory, United Kingdom Richard Garratt, PhD. Instituto de Fisica de Sao Carlos, USP, Brazil Applicants: 25 students will be selected, prioritizing advanced PhD, postdocs and young researchers. The Course will provide financial support covering registration fees, and for the case of those students coming from abroad, all local expenses (lodging, per diem and local transportation). Look in the www site for details on application procedures. The application deadline is July 9, 2020. Please address further inquiries to: mx2020(a)pasteur.edu.uy <mailto:[email protected]> Looking forward to hosting you in Montevideo!

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A tool to build ordered water into cryo-EM maps
by Pavel Afonine 31 Jan '20

31 Jan '20

Hi, a quick announcement.. Phenix versions dev-3765 and newer now have a new tool to build ordered water into cryo-EM maps, command line only for the moment. To get latest version: http://phenix-online.org/download/nightly_builds.cgi Use example: phenix.douse model.pdb map.mrc Some background: http://phenix-online.org/presentations/water.pdf This is still work in progress. Any feedback is very much appreciated! Happy Friday, Pavel

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Understanding Biology Through Structure, Santa Fe March 16-20
by Tom Terwilliger 28 Jan '20

28 Jan '20

Hi Structural Biology colleagues! Registration is still open for Understanding Biology through Structure 2020 (https://cvent.me/4kq9P March 16-20, 2020 in Santa Fe, NM). Poster abstracts can be submitted through Feb. 16. The conference is a forum where students, postdocs and established researchers can meet each other and discuss the latest methods and results. There will be an opportunity for all participants to present posters. Registration for the meeting is limited to 120. Speakers include Ilme Schlichting,Yvonne Jones, Hao Wu, Tom Terwilliger, Peijun Zhang, Christopher Russo, Claudio Ciferri, David Stuart, Blake Wiedenheft, Ci Ji Lim, Robert Stroud, Wayne Hendrickson, Bonnie Murphy, Anne Houdusse-Juille, Sonja Lonrenz, Chris Hill, Chun-wa Chung, Jian Payandeh, Amit Sharma, Marissa Matsumoto, Suzanne Scarlata, Osamu Nureki, Natalia Jura, Erica Ollmann Saphire, Eva Nogales, Andrej Sali, Anke Bill, Joanna Sulkowska, David Eisenberg, Marie Pancera, Karla Satchell, Jacques Philippe Colletier, Christopher Neale, and Tom Blundell. A Phenix crystallography/cryo-EM workshop will be held after the last day of the meeting (workshop is March 20). This is a great chance to ask questions about your own data. Sign up when you register for the meeting. All the best, 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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Error message when adding ions
by ahmed 23 Jan '20

23 Jan '20

Dear Phenix community, I was wondering whether you experienced previously this problem. I'm running the 1.17.1-3600 version under ubuntu 16. when I do refinment and try to add ions an error message appear : out = cStringIO.StringIO()NameError: global name 'cStringIO' is not definedCAUGHT EXCEPTION: (argument #559)ARGUMENT LEADING TO EXCEPTION: 6099Traceback (most recent cell last):File "usr/local/phenix-1.17.1-3600/modules/cctbx_project/libtbx/easy_mp.py", line 181, in_call_result = 0.func(arg)File "usr/local/phenix-1.17.1-3600/modules/cctbx_project/libtbx/ions/identify.py", line 1435, in_call_out = cStringIO.StringIO()NameError: global name 'cStringIO' is not defined Thanks for your help. RegardsAhmed

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Phenix Postdoc Position - Berkeley, California
by Paul Adams 22 Jan '20

22 Jan '20

Postdoctoral Researcher Lawrence Berkeley Laboratory Job ID: 89267 Division: Molecular Biophysics & Integrated Bioimaging (Computational Crystallography Initiative) Date Opened: 12/23/2019 Summary: Berkeley Lab’s Molecular Biophysics and Integrated Bioimaging Division has an opening for a Postdoctoral Researcher. In this role you will develop new computational methods for the structure determination and refinement of protein structures using the PHENIX software system. Primary duties and responsibilities will include development and implementation of numerical methods and new computational protocols, including the application of machine learning methods. The Phenix software is used worldwide for the determination of atomic structures using X-ray and neutron crystallography and cryo-electron microscopy. The software is developed as part of an international collaboration supported by the National Institutes of Health and the Phenix Industrial Consortium. To apply visit - https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=89267 Duties: • Development and implementation of computational algorithms for structure determination using crystallography and cryo-electron microscopy including: improved methods for the optimization of models and automated detection of model heterogeneity. • Application of machine learning methods to problems in crystallography and cryo-electron microscopy. • Develop and test new components of the PHENIX software system in collaboration with others • Document software developments. • Collaborate with other researchers in the PHENIX program. • Interact with P.I.s, other postdocs, scientists and external collaborators involved in the PHENIX project. • Publication of research results in scientific journals and presentation of results at scientific meetings. Additional Responsibilities as needed: • Participate in workshop and tutorials to educate researchers in the use of Phenix • Actively participate in writing progress reports What is Required: • Ph.D. in computational crystallography, computational cryo-electron microscopy, computational biology, bioinformatics, computational chemistry or a related field • Demonstrated experience in developing computational algorithms for solving problems • Demonstrated experience with computational methods development • Publications in macromolecular crystallography, cryo-electron microscopy or closely related fields • Familiarity with Python, C++ and other software development tools • Good programming and mathematical skills • Strong interpersonal skills and the ability to work in a team environment Additional Desired Qualifications: • Familiarity with macromolecular structure or computational chemistry. • Experience with the practical aspects of crystallography and/or cryo-electron microscopy. The posting shall remain open until the position is filled. Notes: • This is a full time, 2 year postdoctoral appointment with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. You must have less than 3 years paid postdoctoral experience. Salary for Postdoctoral positions depends on years of experience post-degree. • Full-time, M-F, exempt (monthly paid) from overtime pay. • This position is represented by a union for collective bargaining purposes. • Salary will be predetermined based on postdoctoral step rates. • This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment. • Work will be primarily performed at: Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA. Learn About Berkeley Lab: Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science. Working at Berkeley Lab has many rewards including a competitive compensation program, excellent health and welfare programs, a retirement program that is second to none, and outstanding development opportunities. To view information about the many rewards that are offered at Berkeley Lab- Click Here. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4. Click here to view the poster and supplement: "Equal Employment Opportunity is the Law. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source (https://als.lbl.gov) 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: Ashley Dawn [ ashleydawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Postdoc position in methods development at LBNL
by Dorothee Liebschner 22 Jan '20

22 Jan '20

Announcing a postdoc position on behalf of Dr. Kanupriya Pande: ======================================================================== Post-doc position in computational methods development in the Molecular Biophysics and Integrated Bioimaging division at LBL. The overall objectives of the project are to develop theory and computation to extract conformational heterogeneity and disorder from diffraction and imaging data. The position is available immediately with an initial appointment for 2 years with the possibility of renewal based upon satisfactory job performance, continuing availability of funds and ongoing operational needs. Qualified candidates must have a PhD in Biophysics, Physics, Mathematics, Chemistry, or related fields. https://lbl.referrals.selectminds.com/jobs/computational-biologist-postdoc-… ======================================================================== -- 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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Re: [phenixbb] How critical is ncs operator for real space refinement
by BuddySphinx 22 Jan '20

22 Jan '20

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How critical is ncs operator for real space refinement
by Yangqi Gu 21 Jan '20

21 Jan '20

Dear PHENIX developers, I have a question about NCS operator. Since I have a cryo-EM map and I want to refine my filament coordinates within the map. I generated the coordinate map manually in Chimera by building multiple chains with rigid body refinement. Since I did not generate the NCS operator file (I tried by doing map symmetry, it did not give me the right helical symmetry), I did not refine with ncs restraints. I am wondering in this case, how critical it is to refine a model with helical symmetry applied. Is it a must or can I go with the way I did? Hope to hear from you soon! Best, Yangqi

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Re: [phenixbb] How critical is ncs operator for real space refinement
by BuddySphinx 21 Jan '20

21 Jan '20

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