- phenixbb - phenix-online.org

IUCr Committee on Data Workshops at IUCr Congress Prague
by John R Helliwell 13 Feb '20

13 Feb '20

Dear Colleagues, The IUCr Committee on Data has two workshops, one in macromolecular & one in chemical crystallography, to be held at IUCr Congress Prague, each to be held August 22nd 2020. See https://forums.iucr.org/viewtopic.php?f=39&t=429 Best wishes, John Emeritus Professor John R Helliwell DSc Chairman of the IUCr Committee on Data

1 0

Phenix workshop at ACA 2020 (San Diego)
by Pavel Afonine 12 Feb '20

12 Feb '20

Dear Colleagues, please make a note of upcoming Phenix workshop focusing on crystallography and Cryo-EM tools for structure solution, August 2nd 2020 in San Diego, California. This is a day-long satellite workshop prior to ACA meeting. For schedule and registration see ACA 2020 web site: www.acameeting.com <https://www.acameeting.com/workshops> (Program -> Workshops). Looking forward to see you there! Pavel

1 0

Postbaccalaureate and postdoc position in membrane protein structure and function lab at the NIH
by Anirban Banerjee 09 Feb '20

09 Feb '20

Dear colleague, I have openings for the two following positions in my lab. I am also attaching a word document if you wouldn’t mind kindly posting it at an appropriate place in your Department *Postbac position* Postbac position in my lab for two years starting from the coming summer. The NIH Postbac IRTA program provides recent college graduates who are planning to apply to graduate or professional (medical/dental/pharmacy) school an opportunity to dofull-time research at the NIH. For this position I am looking for someone who has experience with protein purification, has good organizational skills and work ethics, and the right mindset to pay attention to nitty-gritty details that are essential for working with membrane proteins. The candidate should apply to the NIH Postbac Program (https://www.training.nih.gov/programs/postbac_irta) and get in touch with me as well. Postbac candidates have to be US citizens or permanent residents. *Postdoctoral position* There is an open postdoctoral position for a membrane protein structure-function project in my lab at the NIH. We are currently focusing on integral membrane enzymes (*Science. *2018, doi: 10.1126/science.aao6326) and transporters of transition metal ions (*J Biol Chem.* 2018, doi: 10.1074/jbc.M117.817478). Here is the formal announcement - *EUNICE KENNEDY SHRIVER NATIONAL INSTITUTE OF CHILD HEALTH AND HUMAN DEVELOPMENT, BETHESDA, MD AND SURROUNDING AREA* *Position Description: * The research group of Dr. Anirban Banerjee at the National Institutes of Health (NIH) is seeking candidates for postdoctoral fellows . The broad interests of the lab are in membrane protein structure and function. We combine structural techniques such as macromolecular crystallography and cryoEM together with biophysical and biochemical methods such as reconstitution based assays, high resolution microscopy and small molecule screening to investigate the structural bases of the mechanisms of a number of membrane proteins. The lab has state-of-the-art equipment and facilities. We have dedicated periodic access to the 22-ID beamline at the APS, for crystallographers at the NIH, as well as access to 23-ID and 24-ID beam lines at the APS. NICHD is now part of a consortium that has access to a Titan Krios on a regular basis. Our laboratory is part of the Cell Biology and Neurobiology Branch in the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD). *Qualifications:* The candidates should hold a Ph. D. degree (by the time of joining the lab), be author of at least one first author publication and have a strong background in biochemistry or structural biology. Experience with basic molecular biology, protein expression, purification and biochemical characterization are required. Prior experience in membrane protein biochemistry or mammalian expression system for protein purification will be added advantages. It is absolutely essential the candidate is motivated and prepared to put in the best efforts for fruition of the project goals. We are a small, friendly lab and ability to work as part of a cohesive group is important. Thanks very much in advance for any help and apologies for the bother. Warm regards, Anirban Anirban Banerjee Head, Unit on Structural and Chemical Biology of Membrane Proteins Neurosciences and Cellular and Structural Biology Division Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) National Institutes of Health (NIH) Building 35, Room 2F-127 35A Convent Drive MSC 3758 Bethesda, MD 20892-3758 Tel: 301-496-4855 Fax: 301-402-9319 anirban.banerjee(a)nih.gov https://science.nichd.nih.gov/confluence/display/banerjee/Home >

1 0

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

1 0

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!

1 0

A tool to build ordered water into cryo-EM maps
by Pavel Afonine 01 Feb '20

01 Feb '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

1 0

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

1 0

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

2 1

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 ] --

1 0

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

1 0

Re: [phenixbb] How critical is ncs operator for real space refinement
by BuddySphinx 22 Jan '20

22 Jan '20

4 4

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

2 3

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

21 Jan '20

3 3

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

2 1

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

1 0

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]>

1 0

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

1 0

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.

1 0

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.

2 1

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 ] --

1 0

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] ------------------------------

1 0

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

1 0

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

1 1

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

3 2

Re: [phenixbb] map to model fsc did not start from 1
by BuddySphinx 11 Dec '19

11 Dec '19

2 1