- phenixbb - phenix-online.org

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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isomorphous Fobs-Fobs maps
by Schulz, Eike-Christian 20 Jan '20

20 Jan '20

Dear all, we have recently tried to calculate isomorphous difference maps with phenix using the GUI. Unfortunately, we found that the results do _not_ seem to produce results that we would expect of a true difference map. Rather the resulting maps appear to show noise. We speculate that this is the result of _not_ scaling the datasets together. - Is this correct ? Applying the "multiscaling method" found in the advanced options changes the result, but it is still inconsistent with what we gain from e.g. the CCP4 procedures. Unfortunately, there is no online documentation to this tool. - Is there a way to scale the data to a reference before calculating the difference maps? - What is the proposed way of using this tool ? - Are there known bugs in the GUI version that are absent in the command line edition? With best regards, Eike

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Open scientist position at the EMBL-Grenoble - Project leader for ID30A/MASSIF-1 beamline upgrade
by Andrew MC CARTHY 13 Jan '20

13 Jan '20

Dear all, We have an open scientist position at the EMBL-Grenoble for a Project leader to oversee our contribution to the upgrade of the fully automated ID30A/MASSIF-1 macromolecular crystallography beamline at the ESRF. This is an exciting opportunity for an ambitious individual to join a team of scientists and engineers from the EMBL and ESRF in developing fully automated data collection protocols to maximise the scientific potential of the ESRF Extremely Brilliant Source upgrade. Closing date: Feb. 7th 2020. Interview date: March 6th, 2020 You can read more about the position and submit your application at: https://www.embl.de/jobs/searchjobs/index.php?ref=GR00139 Best regards, Andrew

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Postdoc position: Computational Algorithms combining Crystallography and WAXS for Drug Discovery
by Grant, Thomas 10 Jan '20

10 Jan '20

Dear PHENIX Community, Please share this notice with potential candidates. A post-doctoral position<https://www.ubjobs.buffalo.edu/postings/21288> is available immediately in the Grant Lab in the Department of Structural Biology at the University at Buffalo in Buffalo, NY, USA. Our group is currently seeking postdoctoral candidates to develop novel computational algorithms combining crystallography and solution scattering to aid in drug discovery. The successful completion of the project will impact many fields from drug discovery and development to basic biological processes. An excellent opportunity for creative, out-of-the-box thinkers who are self-motivated. Candidates will have the opportunity and support to present their research findings at national and international conferences and in high-impact scientific journals. The positions are for an initial term of two years with possibilities for renewal based on performance and available funding. Compensation will be commensurate with experience. Minimum Qualifications A PhD degree in structural or computational biology, chemistry, physics, mathematics, computer science or related fields. Preferred Qualifications Proficiency in computer programming, in particular Python. Excellent oral and written communication skills for presenting research at conferences and in scholarly journals. Background in physics or mathematics is a plus, in particular familiarity with concepts of Fourier transforms and diffraction. Experience with structural biology techniques such as crystallography and solution X-ray scattering is a plus. Apply Interested candidates can apply on the UBJobs website here: https://www.ubjobs.buffalo.edu/postings/21288 -- Thomas D. Grant, Ph.D. Research Assistant Professor Department of Structural Biology Jacobs School of Medicine and Biomedical Sciences<http://medicine.buffalo.edu/> University at Buffalo 955 Main Street, Room 5128 Buffalo, New York 14203 Email: tdgrant(a)buffalo.edu<mailto:[email protected]>

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3 years Postdoc positions Newcastle University, UK Prof. Nikolay Zenkin
by Arnaud Basle 06 Jan '20

06 Jan '20

Dear All, Please see the attached flyer and link below for 3-years postdoc position at Newcastle University. https://jobs.ncl.ac.uk/job/Newcastle-Research-Associate/577339301/ The positions are in Prof. Nikolay Zenkin's laboratory and informal enquiries should be directed to him (Nikolay.Zenkin(a)newcastle.ac.uk). Cheers, Arnaud -- Dr Arnaud Basle X-ray facilities manager Newcastle Structural Biology Laboratory Biosciences Institute Faculty of Medical Sciences Newcastle University Framlington place NE2 4HH Newcastle upon tyne Phone 0191 208 5482

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ISOLDE 1.0b4 released
by Tristan Croll 03 Jan '20

03 Jan '20

Happy new year to all my colleagues in the structural biology community! I'm delighted to announce the release of ISOLDE 1.0b4 to coincide with the stable release of ChimeraX 0.91. What is ISOLDE? ISOLDE is a plugin to UCSF ChimeraX, designed to ease the task of macromolecular model building into low-to-medium resolution maps derived from crystallographic or electron cryo-microscopy (cryoEM) experiments. Historically, this has been an extremely challenging task, since at low resolutions the maps alone are insufficient to precisely place individual atoms. ISOLDE aims to reduce this challenge in a number of ways: - Rebuilding is accomplished via GPU-accelerated interactive molecular dynamics (using OpenMM and the AMBER molecular dynamics forcefield) to make the task feel as close as possible to what it might be like to work with a real physical molecule. - Geometric validation of protein backbone and sidechain conformations is performed in real time, allowing you to see problem sites directly on the model as you work with it. - Remodelling can be performed by directly tugging on atoms, or via the interactive addition and removal of position, torsion and/or distance restraints - For crystallographic datasets, structure factors are constantly recalculated in the background as the model coordinates change - as the model improves, you see the map improve. For more details, see https://isolde.cimr.cam.ac.uk/. To install it for Linux, MacOS or Windows 10, go to http://preview.cgl.ucsf.edu/chimerax/download.html#release and install the **0.91** release build for your operating system. (IMPORTANT NOTES: this build of ISOLDE will **only** work with version 0.91 of ChimeraX. Additionally, Ubuntu users should use the "Generic Linux" ChimeraX build - the Ubuntu builds use compilers that are not compatible with ISOLDE). Start ChimeraX, go to Tools/More Tools... and follow the links to install ISOLDE. Equivalently, just type "toolshed install isolde" on the ChimeraX command line. You can then start ISOLDE via Tools/General/ISOLDE or the command "isolde start". If this is your first time using it I highly recommend running either or both of the first two tutorials found in the top left of the ISOLDE panel that will appear. A short list of what's new since 1.0b3: - source code for ISOLDE and its "sister" package ChimeraX-Clipper are now on GitHub at https://github.com/tristanic/isolde and https://github.com/tristanic/chimerax-clipper respectively. - integration with ChimeraX session save/restore framework. "save session.cxs" will save a snapshot of all models, maps and strucuture factors including all current ISOLDE restraints, and "load session.cxs" will return you to where you left off. - added new adaptive torsion restraint implementation (a periodic analogue to Geman-McClure distance restraints) to restrain protein torsions to their current geometry or to a reference model. For details, type "usage isolde restrain torsions" on the ChimeraX command line and click the link in the log. - documentation is now integrated with the ChimeraX documentation framework. In particular, "usage {command}" now provides a link to full documentation in the ChimeraX log window. - improved behaviour (speed and stability) of energy minimiser - significantly improved initial startup and simulation start times - clearer indication of simulation state (running/paused) - remote Python interface for communication with other packages - various improvements and bug-fixes to handling of crystallographic data. In particular: better handling of anisotropic datasets, and improved stability of bulk solvent and scaling calculations. - improved performance of live crystallographic map updates. - support for multiple independent sets of adaptive distance restraints (currently only available via the Python API). For example, one set may be used to maintain internal geometry, while another represents crosslinking/mass spec or evolutionary coupling restraints. - "Demo" button on ISOLDE GUI retired and replaced with a "Tutorials" drop-down menu. - added tugging support in ChimeraX VR (thanks to Tom Goddard). ChimeraX currently supports VR only in Windows.

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Adding a command line run job to the GUI job history
by Ahmad Khalifa 28 Dec '19

28 Dec '19

Hello, I ran a real space refinement job using the command line and an effective parameters file. Is it possible to link this job again to the Phenix GUI? How? Regards.

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Phenix Postdoc Position - Berkeley, California
by Paul Adams 23 Dec '19

23 Dec '19

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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NIH-Funded Post-Doctoral Position at the University of Illinois to Study the Ribosome Structure
by Yury Polikanov 18 Dec '19

18 Dec '19

*NIH-Funded Post-Doctoral Position in Structural Biology at the University of Illinois at Chicago (UIC) to Study the Structure and Function of the Ribosome* [image: Movie_S3_70S-mtRNA_320x240.gif] The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for a talented, skillful, and highly motivated researcher to fill the available *NIH-funded Post-Doctoral Scholar *position to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov research can be obtained from the most recent publications (*https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/50395623/public/?sort=date&direction=descending <https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…>*) or found on the web-page (https://bios.uic.edu/bios/people/faculty/yury- polikanov). The successful candidate will be involved in the determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography and potentially cryo-EM techniques. *Basic qualifications:* - PhD in chemistry, biochemistry , biophysics, or a related field; - Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); - Experience in structural biology (cryo-EM or X-ray crystallography); - Experience in RNA biology field is desired; *The successful candidate is also expected to:* - Act independently in terms of planning and executing the experiments; - Compile, analyze, and prepare data for publications; - Assist with training of graduate and undergraduate students. Review of applications will begin immediately and will continue until the position is filled. Interested candidates should send their CV, cover letter, and contact information for three references directly to Dr. Yury Polikanov at yuryp(a)uic.edu. *In the cover letter, the applicant should **describe how his/her previous research accomplishments and scientific interests fit with the scope of the research in the Polikanov research group.* -- ------------------------------ Yury Polikanov, Ph.D. Assistant Professor Department of Biological Sciences College of Liberal Arts and Sciences University of Illinois at Chicago 900 South Ashland Avenue, MBRB 4170 Chicago, IL 60607 Tel: 1-312-413-2408 (Office) Tel: 1-312-355-0463 (Laboratory) Fax: 1-312-413-2691 E-mail: yuryp(a)uic.edu Web-Page: *http://bios.uic.edu/bios/people/faculty/yury-polikanov <http://bios.uic.edu/bios/people/faculty/yury-polikanov>* [image: Image result for uic logo] ------------------------------

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PhD / PostDoc positions @NKI Amsterdam
by a.perrakis＠nki.nl 17 Dec '19

17 Dec '19

Dear all, We are looking for enthusiastic, motivated PhD students and Post-Docsto join the Division of Biochemistry in the Netherlands Cancer Institute (https://www.nki.nl) in the groups of Tassos Perrakis and Titia Sixma. If you have a keen interest in the general field of integrative structural cell biology, and previous experience in cryo-EM, X-ray crystallography, cell biology, biochemistry, or biophysics … well, read on! The project in the laboratory of Titia Sixma (https://www.nki.nl/divisions/biochemistry/sixma-t-group/ ) is in the area of DNA repair. The projects in Anastassis (Tassos) Perrakis group (https://www.nki.nl/divisions/biochemistry/perrakis-a-group/) are in the general field of controlling the progress of cell division and microtubule interacting proteins, in lysolipids signaling focusing on Autotaxin and its interactions, and together with Robbie Joosten in PDB-REDO . The Netherlands Cancer Institute is an international center of excellence with a high standard of biological research and outstanding research facilities, and has an interactive atmosphere. It is located in Amsterdam, with all its cultural amenities, close to the Schiphol airport. The two groups share a common research infrastructure in the Department of Biochemistry, and have an interest in structural studies coupled to functional analysis. Facilities include the ability to produce and purify proteins in bacterial, insect, and mammalian cells, and a well-equipped macromolecular biophysics laboratory that are sites in the Instruct Centre NL (https://instruct-eric.eu/centre/protein-facility---nki/). Equipment for structural analysis is spearheaded by a brand-new cryo-EM (Jeol F2 200kV with a K2 detector) and high-throughput crystallisation robotics; these local facilities are coupled with regular access to Krios cryo-EM at NeCEN (https://www.necen.nl , https://instruct-eric.eu/centre/necen---lu/) and to the ESRF, SLS and DLS synchrotrons, and access possibilities for NMR experiments (https://instruct-eric.eu/centre/bijvoet-center---uu/). Dedicated computing facilities include privileged access to both CPU and GPU clusters. Both groups participate in various European and National collaborative projects and are members of the Oncode Institute (https://www.oncode.nl). We are looking flexibly for either highly motivated PhD students (strong master-level placements in reputable laboratories and familiarity with some of the methods we outline would be strong plus) or post-docs (experience in cryo-EM would be highly desirable for most positions; candidates with a strong background and track record in X-ray crystallography, protein purification, cell biology, would be taken seriously under considerations depending on the project). For the PDB-REDO project a background in bioinformatics and some experience in computerprogramming would be necessary. Applicants should write an email, stating their specific interests and attaching a CV and names of three references to t.sixma.AT.nki.nl or a.perrakis.AT.nki.nl; feel free to also make informal inquiries. We expect applications to be sent in by Monday 13th January and all positions are available asap. PhD candidate positions are for four years; post-doc positions can be for 1-4 years depending on qualifications and experience; the CAO salary levels apply according to the NKI collective agreement. Anastassis Perrakis and Titia K. Sixma

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First CCP4 Study Weekend illustration competition
by Jon Agirre 16 Dec '19

16 Dec '19

Dear colleagues, We are pleased to announce the opening of the first CCP4 Study Weekend illustration competition, made possible by CCP4’s long standing collaboration with IUCr Journals. Getting your science out to the public requires more than good research. You need to make it memorable! And what better way to do it than with excellent figures? We invite you to make a figure that tells a structural biology story in a creative and informative way. The submitted figures will be showcased during the Study Weekend at several locations at the conference venue. *Prize* The creator of the winning illustration gets to design the cover illustration of the Study Weekend’s proceedings to be published early 2021. Apart from this commission there may be another (sur)prize. *Format* Illustrations, along with a short description of content and methods used, are to be sent to jon.agirre(a)york.ac.uk before December 15th 2019. Images must have a resolution of 1920x1080 (16:9) in order to fit the format of the screens and main room projector. Any combination of graphics and (if any) post-processing software may be used, as long as details are given with the submission. The format of the illustration should be PNG. *Judges* As you may know, Dr Jeroen Claus (founder of Phospho Biomedical Animation) will give the closing talk at the 2020 edition of the CCP4 Study Weekend. He, along with Louise Jones (managing editor of Acta Crystallographica sections D & F) will judge the submitted figures based on their graphical quality as well as their ability to convey a complex structural message clearly. *Decision* The winner will be announced on January 8th at the dinner - before the céilidh. Up to date information and registration: http://www.cvent.com/d/fyq0g9/4K?cpc=FCNF5V7H4B4 Looking forward to receiving your images! Jon Agirre, Alan Roseman, Robbie Joosten and Karen McIntyre -- Dr Jon Agirre Royal Society University Research Fellow York Structural Biology Laboratory / Department of Chemistry University of York, Heslington, YO10 5DD, York, UK http://www.york.ac.uk/chemistry/research/ysbl/people/staff/jagirre/ Office: /B/K/065 Phone: +44 (0) 1904 32 8252 Twitter: @glycojones

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Emergency power test at Berkeley this weekend (12/13-12/16)
by Billy Poon 13 Dec '19

13 Dec '19

Hi everyone, To mitigate disruptions from future power shut offs due to wildfire concerns, we are performing an emergency power test for our web servers. This will affect the phenix-online.org and cci.lbl.gov servers. The websites, mailing lists, and repositories will remain available, but the servers will be running on emergency power instead. The servers will be switched to emergency power at around 2 pm Pacific time on Friday (12/13) and switched back to main power around 10 am Pacific time on Monday (12/16). Please let me know if you experience 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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Re: [phenixbb] map to model fsc did not start from 1
by BuddySphinx 11 Dec '19

11 Dec '19

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map to model fsc did not start from 1
by Yangqi Gu 11 Dec '19

11 Dec '19

Dear Phenix developer, I have a question regarding the map to model fsc. I have a filament map and a model with arbitrary copy of the protomer ( I built them in Chimera), then I used the filament model to refine against my map. But I encountered an issue is that the reported FSC (map to model) did not start from 1 but rather 0.8. I am wondering if there is anyway to fix it. Also, in the case of a filament, how do I use NCS operator to refine rather than manual building the filament model? I tried specifying NCS with helical symmetry, but it did not work. Best, Yangqi

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Re: [phenixbb] problems running refinement of shaken model against half map
by L. Hielkema 06 Dec '19

06 Dec '19

Dear Pavel, Thanks again for your answer. I understand that you have some concerns with regard to the validation we use. Now this makes me really curious how the rest of the EM community feels about this. > "widely used" does not always mean "makes sense". As it often happens, some may just blindly follow the crowd. And how "widely" it is used, in fact? I stated my arguments as to why this does not make sense (to me at least). I'm yet to hear any strong counter-arguments. > So you stated the following before: "First off, I think this way of validation is quite faulty conceptually... How you know 0.5A is the best number and say not 0.7 or 0.3? By shaking the model, you validate the shaken (perturbed) model, which is not the model you are publishing and reporting statistics for. If you shake the model twice with same shake doze, you will get two different models with the same amount of perturbation, which means numbers you derive from such models can (and likely will) be different.” Is there anyone that would have any strong counter arguments? Or thinks along the same way? Because we would really like to know if we should change anything in our approach. Or would then the approach that Pavel suggest with the phenix tool Comprehensive validation be a good solution to this issue? > The paper you refer to indeed describes the protocol they followed but it does not answer concerns that I raised before. > > History knows plenty of examples of something being almost a standard for a while and then discarded later. Such as cutting off low-resolution diffraction data (because at the time there was no good bulk-solvent models invented) or cutting data by 2 or 3 "sigma" criteria (because maximum-likelihood target functions were not in use yet), etc etc etc. Or not adding H atoms to atomic models... > > Cryo-EM isn't as mature as protein crystallography where most procedures and protocols are pretty much standard. Cross validation for cryo-EM is yet to settle to some more meaningful method. There is indeed a number of attempts made so far but none of them seem to be as good as Brunger's free-R approach! Sure many things have to be still established, but it would be nice to know what is the generally accepted method at the moment according to the community. > >> As far as I could see the phenix tool Comprehensive validation did not provide the validation against the half maps, that one needs to obtain FSCwork and FSCfree, which is described in the attached papers. > > This is correct, it doesn't for reasons I mentioned before. Best, Lisa > On 5 Dec 2019, at 21:02, Pavel Afonine <pafonine(a)lbl.gov> wrote: > > Hi Lisa, > >> Thanks for your answer. Though I am a bit confused, as far as I and my group understand this method is widely used for several years (see attached papers for first introduction and since then you see many performing this type of validation). > > "widely used" does not always mean "makes sense". As it often happens, some may just blindly follow the crowd. And how "widely" it is used, in fact? I stated my arguments as to why this does not make sense (to me at least). I'm yet to hear any strong counter-arguments. > > The paper you refer to indeed describes the protocol they followed but it does not answer concerns that I raised before. > > History knows plenty of examples of something being almost a standard for a while and then discarded later. Such as cutting off low-resolution diffraction data (because at the time there was no good bulk-solvent models invented) or cutting data by 2 or 3 "sigma" criteria (because maximum-likelihood target functions were not in use yet), etc etc etc. Or not adding H atoms to atomic models... > > Cryo-EM isn't as mature as protein crystallography where most procedures and protocols are pretty much standard. Cross validation for cryo-EM is yet to settle to some more meaningful method. There is indeed a number of attempts made so far but none of them seem to be as good as Brunger's free-R approach! > >> As far as I could see the phenix tool Comprehensive validation did not provide the validation against the half maps, that one needs to obtain FSCwork and FSCfree, which is described in the attached papers. > > This is correct, it doesn't for reasons I mentioned before. > > All the best, > Pavel >

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Submission deadline on Monday
by Nick DeHaan 05 Dec '19

05 Dec '19

Hi PhenixBB, The extended deadline for the AIMS Awards program is less than a week away! If any PIs, postdocs, or grad students you know are interested in submitting a proposal, please remind them to apply on the website by Monday, December 9th. Website: www.atomwise.com/aims <http://bit.ly/2PkkOlB> Best regards, Nick Nick DeHaan *Partnering Executive* *Atomwise* <http://www.atomwise.com/> | *Better Medicines Faster* ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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15 PhD scholarships in Braunschweig, Germany
by Blankenfeldt, Wulf 29 Nov '19

29 Nov '19

Dear colleagues & prospective Ph.D. students, The Technische Universität Braunschweig in collaboration with Helmholtz Centre for Infection Research and Ostfalia University of Applied Sciences currently initiate the doctoral program "Drug Discovery and Cheminformatics for New Anti-Infectives (iCA)" which is granted by the Ministry of Science and Culture of Lower Saxony. The program aims at studying fundamental principles of drug discovery by combining life sciences and digital sciences. The iCA consortium is offering 15 Georg-Christoph-Lichtenberg scholarships (duration: 3 years). The program of the iCA consortium offers an ambitious, structured and interdisciplinary training based on top-level fundamental research. This joint program provides an internationally competitive research environment with state-of-the-art facilities. The participating groups use a variety of different methods, including experimental, digital, and theoretical approaches. More information about specific projects and participating groups can be found at: https://www.tu-braunschweig.de/en/pharmchem/translate-to-english-promotions… The graduate program starts in the period from February to July 2020. For details and individual project descriptions please refer to the scholarship announcement attached. If you have any questions, please contact pvz-apply(a)tu-braunschweig.de<mailto:[email protected]>. The program is open for applications now. Applications should include letter of motivation, curriculum vitae, certificates, etc. combined in a single PDF file (max. 15 MB). Please send your application to pvz-apply(a)tu-braunschweig.de<mailto:[email protected]> until 31 December, 2019. Please forward these information to interested colleagues. Kind regards, Wulf Blankenfeldt ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Position at Diamond: XChem Beamline Scientist
by Frank Von Delft 29 Nov '19

29 Nov '19

Dear all, We are recruiting as permanent position a Beamline Scientist on the XChem fragment screening facility at Diamond. This role is to join the XChem team to support academic and industrial users with experiments and service work, co-manage the XChem lab, develop new fragment-related methodologies, and over next few years, work on expanding the XChem offering beyond hit identification. If you are a technically-minded crystallographer that enjoys teaching or training people, like an organised life, thrive on collaboration and like to see how you're making others productive, you will enjoy this job. Besides, Diamond is incredibly collegial and has a terrific user community. The ad is here: https://vacancies.diamond.ac.uk/vacancy/xchem-beamline-scientist-404499.html (for some reason you may need to click twice on the link to make it work). The application deadline is the 15th Dec 2019, and we wil linterview on 17th Dec (i.e. before Xmas). If you have questions, contact me or Alice Douangamath <Alice.Douangamath(a)diamond.ac.uk><mailto:[email protected]>, who heads the facility. Frank -- Frank von Delft Professor for Structural Chemical Biology Principal Beamline Scientist: I04-1 Diamond Light Source +44 1235 778997 (office: M,T,T) +44 7471 026103 (mobile) Principal Investigator: Protein Crystallography Structural Genomics Consortium Oxford University +44 1865 617583 (office: W,F)

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Re: [phenixbb] Real space refine of long side chains
by Leonid Sazanov 27 Nov '19

27 Nov '19

Hi, We have addressed exactly this problem by writing a script, in which B-factors are refined first and only then real-space refinement happens. This allows disordered side-chains to acquire high B-factors and so they are not pulled into backbone anymore. This cycle is repeated twice to achieve convergence. Parameters for B-factor refinement (ADP restrains) were optimized to account for consistent lack of density for acidic side chains in cryoEM. It is described in: https://www.ncbi.nlm.nih.gov/pubmed/31492636 If needed, I can send a script. Best Leonid -- Prof. Leonid Sazanov FRS IST Austria Am Campus 1 A-3400 Klosterneuburg Austria Phone: +43 2243 9000 3026 E-mail: sazanov(a)ist.ac.at Date: Mon, 25 Nov 2019 19:11:16 +0000 From: Luca Pellegrini <lp212(a)cam.ac.uk> To: PHENIX user mailing list <phenixbb(a)phenix-online.org> Subject: [phenixbb] Real space refine of long side chains Message-ID: <37F0D7B2-3C9E-4FE1-B0BF-6B23F0D8925B(a)cam.ac.uk> Content-Type: text/plain; charset=us-ascii I have noticed that real-space refinement in cryoEM maps has a tendency to pull long disordered side chains (Lys, Glu etc) back towards main chain density, resulting in unrealistic hairpin-like bent conformations. Is there a way to counter or moderate this behaviour? It would save me from having to manually straighten them all out again afterwards... 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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Group ADP refinement restraints
by Taylor Stevens 26 Nov '19

26 Nov '19

Hello, I am currently refining a low-ish resolution structure (through the phenix.refine GUI) with phenix version 1.14 and had some questions about the use of restraints in group ADP refinement. In the phenix.refine documentation (https://www.phenix-online.org/documentation/reference/refinement.html#refin… <https://www.phenix-online.org/documentation/reference/refinement.html#refin…>) it is stated that “Group isotropic ADP or TLS refinement do not use any restraints”, however, this does not seem to be the case. If I look in the log file I can see the following lines of text which I believe indicate that the restraints are being applied: |-group b-factor refinement (macro cycle = 0; iterations = 0)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = None | |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 1; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 2; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| |-group b-factor refinement (macro cycle = 3; iterations = 22)————————| | r_work = 0.3331 r_free = 0.3717 target = 5.823062 restraints weight = 821.871| |——————————————————————————————————————| If I manually set the wu parameter to 0 under “Refinement target weights" nothing changes, however, if I navigate to "All parameters > ADP settings > Group B-Factors" in the GUI there is a “Use restraints” box that is checked by default. If I uncheck this box, there are no longer any restraints being applied according to the log file, and in the case of the structure I am refining, there is a substantial drop in the rfree/rwork. Is this an issue with the program or documentation? Or am I misunderstanding how the program is supposed to work? Is it generally a good idea to use group ADP refinement without restraints? Thanks, Taylor

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