- phenixbb - phenix-online.org

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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Real space refine of long side chains
by Luca Pellegrini 25 Nov '19

25 Nov '19

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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Software developer role at Diamond Light Source
by Hall, Dave (DLSLtd,RAL,LSCI) 25 Nov '19

25 Nov '19

Dear all We currently have a role for a software developer to work with the MX group at Diamond Light Source (www.diamond.ac.uk/mx<http://www.diamond.ac.uk/mx>). The successful candidate will work with scientific staff and software developers to enable experiments across the diverse suite of MX beamlines. For details of the role and how to apply see here https://vacancies.diamond.ac.uk/vacancy/data-acquisition-scientist-for-stru… Best regards Dave Hall MX Group Diamond Light Source -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Postdoc position in methods development at LBNL
by Dorothee Liebschner 22 Nov '19

22 Nov '19

Announcing a postdoc position on behalf of Dr. Kanupriya Pande: ======================================================================== Post-doc position in 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. Job description and how to apply: 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] weight optimization in refinement
by Alexei Gorelik 22 Nov '19

22 Nov '19

Thanks! What I meant is, phenix.refine seems to run a number of optimization threads (usually 10-14) independent of the number of cores specified (for example, 4 or 8). If i specify 8 cores, is there a way to force it to run 8 weight optimizations? On Nov 22, 2019 1:24 PM, Pavel Afonine <pafonine(a)lbl.gov> wrote: Hi Alexei, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? nproc parameter controls number of CPUs to be used in weight optimization. Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? No. There is some built-in logic, phenix.refine does it when these conditions are met and it can un-do the result if it is not an improvement. Is there particular need to do this in your context? Pavel

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problems running refinement of shaken model against half map
by L. Hielkema 22 Nov '19

22 Nov '19

Hi all, For the validation of my model to my map in phenix 1.17.1 I tried to refine my shaken model (0.5Å) against my half map in phenix real space refine. However, whatever I try I get a weird behaviour in the FSC(Model-map), see the image below. It seems not to be able to reach 0 in the correlation, but keeps getting stuck at 0.1. I tried various things to solve this, but unfortunately nothing helps: - Using the other half map - Cut of the heterogeneous part of my model and map and refine this - Used refined data without using a mask for the last iterations - Used different resolutions to refine against - Tried data from someone else in the lab (same microscope, same imaging conditions), to check if I am doing something wrong (this gave good results) When doing the same refinement in Refmac5 in ccpem 1.4 it does seem to work, however I would not like to switch programs, because this will mess up my final model. Best, Lisa

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weight optimization in refinement
by Alexei Gorelik 22 Nov '19

22 Nov '19

Hi, Is there a setting to control the number of parallel weight optimization threads in phenix.refine? Also, is there a way to force phenix.refine to perform global real-space refinement (rsrg)? Most of the time, when the "real-space" option is selected, it only carries out rotamer fitting (rsrl). I do know there's a separate real-space refinement program in Phenix. Thanks!

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Secondary structure restraints
by Luca Pellegrini 20 Nov '19

20 Nov '19

I have a protein-DNA complex and would like to apply SS restraints. What is the best way to apply the SS restraints to the protein only, using the GUI? I have tried the following: Select ‘Use secondary structure restraints’ in the ‘Refinement Settings’ tab ‘Select Atoms’ In the Selection Editor window, 'Find Secondary Structures' Removed manually all nucleic acid restraints in ‘Base Pairs’ and Stacking Pairs’ tabs Save and close. However, phenix refinement keeps switching SS restraints for nucleic acids to True. Kind regards, 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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Molybdenum cofactor refinement
by Cristiano Mota 20 Nov '19

20 Nov '19

Hi all, I'm using phenix.refine to refine a structure of a Molybo-protein at 1.9Å. The MGD cofactors (molybdopterin guanine dinucleotide) are being refined with a weird distorted geometry causing some clashes. The Fo-Fc maps show that something is going wrong in the aromatic rings interatomic distances. I'm using the readyset to pick up MGD and metal restraints. Am I using the right protocol? Best regards, Cristiano Mota -- *Cristiano de Sousa Mota* Postdoctoral Researcher, Macromolecular Crystallography Group UCIBIO / FCT - Universidade Nova de Lisboa 2829-516 Caparica, Portugal (00351 212948300, ext 10962) http://xtal.dq.fct.unl.pt/

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Deadline Extended to December 9th
by Nick DeHaan 20 Nov '19

20 Nov '19

Hi PhenixBB, Thanks for sharing information about the AIMS Awards with your colleagues! Many have told us they really appreciated it. We’ve had requests for more time - so we extended the deadline to December 9th! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development efforts, and get published. The program is open to investigators, postdocs, and graduate students worldwide. We encourage you to check out our flyer for more information: Flyer <http://bit.ly/37oIrS3> You can apply directly on the website: atomwise.com/aims. Please don't hesitate to reach out with any questions! Best, Nick Nick DeHaan, MsE *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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cryo-EM density modification
by Tom Terwilliger 19 Nov '19

19 Nov '19

Hi Phenix cryo-EM users, For those of you trying out density modification for cryo-EM (phenix.resolve_cryo_em), the automatic estimation of resolution in the current version uses unmasked resolution instead of masked, in some cases resulting in running density modification at too low a resolution. Consequently it is best with this version if you specify your nominal resolution. To run it you can type: phenix.resolve_cryo_em half_map_1.ccp4 half_map_2.ccp4 \ seq_file=seq.dat resolution=3.5 or something like that. It requires the current nightly build to run. You might also want to wait just a short while and a version that has this and a few other bugs fixed, a GUI, full documentation, and an example dataset will be out (hopefully this week). The full description of the method is at https://www.biorxiv.org/content/10.1101/845032v1 Let me know of any problems or suggestions! All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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Differences in refinement statistics
by Chancievan Thangaratnarajah 19 Nov '19

19 Nov '19

Hello, I have noticed differences in the refinement statistics between two different Phenix versions (see attachments) even though I am using the same cryo-EM map and model as input. The most notable difference are rotamer outliers, which were 0 % in Phenix 1.16-3549 and now 6 % in Phenix 1.17-3660. I was wondering whether anyone has noticed a similar behaviour? Or is there something that I have missed? Best, Chancie.

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Error in sequence assignment
by Tom Terwilliger 18 Nov '19

18 Nov '19

Hi Nicholas, I'm afraid there isn't a way to say which sequence goes with which chain. I would suggest using the tool phenix.replace_side_chains. Give it 1 chain and 1 sequence and if they have the same length it should just put it in. If it doesn't work, try phenix.sequence_from_map which can do the same thing. Let me know if that doesn't do it! All the best, Tom T Date: Sun, 17 Nov 2019 17:07:16 -0500 From: Nicholas Gao <dominion146(a)GMAIL.COM> Subject: Specify chain assignment in sequence file for rebuild-in-place of phenix.autobuild Dear CCP4, I currently have an MR solution that has the wrong sequence. The pdb file of the solution contains 3 chains, and I'd like to use the rebuild-in-place functionality within phenix.autobuild to correct the sequence of all 3 chains. Phenix allows me to supply a sequence file as input for this job, it's not clear to me how I tell the program which sequence should be assigned to which chain. Anyone know how to do this? Sincerely, Nicholas Gao -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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RapiData at SSRL 2020 - application deadline extended by one week!
by Smith, Clyde 15 Nov '19

15 Nov '19

Hi all, We have extended the deadline for applications for a place at the RapiData 2020 @ SSRL workshop to next Friday, November 22 2019! There are still a few spots left, so get your application in! The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu csmith(a)slac.stanford.edu jwierman(a)slac.stanford.edu

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General interest
by John R Helliwell 14 Nov '19

14 Nov '19

Dear Colleagues, I imagine the two articles that I describe in my posting at the IUCr’s Forum will be of interest to the MX community. See:- https://forums.iucr.org/viewtopic.php?f=39&t=427 All best wishes, John Emeritus Professor John R Helliwell DSc

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Scientist job position at AbbVie
by Longenecker, Kenton L 13 Nov '19

13 Nov '19

Hi - I'd like to draw attention of interested candidates to the following job opportunity with full description to apply at: http://abbvie.referrals.selectminds.com/jobs/senior-scientist-i-ii-protein-… Company overview: AbbVie (NYSE:ABBV) is a global, research-driven biopharmaceutical company committed to developing innovative advanced therapies for some of the world's most complex and critical conditions. The company's mission is to use its expertise, dedicated people and unique approach to innovation to markedly improve treatments across four primary therapeutic areas: immunology, oncology, virology and neuroscience. In more than 75 countries, AbbVie employees are working every day to advance health solutions for people around the world. Job Description: The Structural Biology Group at AbbVie Headquarters in Lake County, Illinois, USA is seeking a highly motivated scientist to join our Structure-Based Drug Discovery team. The ideal candidate should have extensive hands-on experience in modern structural biology techniques and computational methods of molecular structure analysis. As part of multidisciplinary teams, the Senior Scientist will utilize X-ray crystallography techniques to identify ligands and provide insight to advance drug discovery targets through structure-based design. The successful candidate will contribute to drug discovery projects across the portfolio of AbbVie interests that also include therapeutic antibodies and novel biologics. ________________________________ Kenton Longenecker, Ph.D. Sr. Principal Research Scientist AbbVie R&D Discovery, DDST Structural Biology 1 N. Waukegan Road, AP10-LL North Chicago, IL 60064 OFFICE 847-938-1428 EMAIL kenton.longenecker(a)abbvie.com<mailto:%[email protected]> abbvie.com<http://www.abbvie.com> This communication may contain information that is proprietary, confidential, or exempt from disclosure. If you are not the intended recipient, please note that any other dissemination, distribution, use or copying of this communication is strictly prohibited. Anyone who receives this message in error should notify the sender immediately by telephone or by return e-mail and delete it from his or her computer. ________________________________

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Submissions to the Computational Crystallography Newsletter – 30 NOV 19
by Nigel Moriarty 12 Nov '19

12 Nov '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the January 2020 issue is 30 November 2019. The Computational Crystallography Newsletter (CCN) is an electronic newsletter for structural biologists, and is published online every 6 months. Feature articles, meeting announcements and reports can be submitted to me at any time for consideration. Submission of text by email or word-processing files using the CCN templates is requested. Past newsletters and a Microsoft Word template are available at www.phenix-online.org/newsletter <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory Berkeley, CA 94720-8235 Phone : 510-486-5709 Email : NWMoriarty(a)LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov

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Postdoc Position in Berkeley
by Petrus Zwart 08 Nov '19

08 Nov '19

Dear All, We have two postdoc positions open in LBNL's Center for Advanced Mathematics in Energy Research Applications (CAMERA; https://www.camera.lbl.gov/) to work on a diverse set of problems in managing, cleaning and interpreting biophysical data ranging from microscopy to crystallography. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88805 https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Feel free to contact me for more information. Regards Peter Zwart -- ------------------------------------------------------------------------ P.H. Zwart Staff Scientist Molecular Biophysics and Integrated Bioimaging & Center for Advanced Mathematics for Energy Research Applications Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 PHENIX: http://www.phenix-online.org CAMERA: http://camera.lbl.gov/ -------------------------------------------------------------------------

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RapiData at SSRL 2020 reminder - just over a week left to apply!
by Smith, Clyde 04 Nov '19

04 Nov '19

Hi all, A reminder that there is only a week left to apply for a place at the RapiData 2020 @ SSRL workshop. Applications close the middle of this month, November 15 2019. The workshop will be held from March 30 - April 4 2020 on the SLAC campus in Menlo Park, California. The course will comprise hands-on experiments at the SSRL beamlines, software tutorials, and lectures on the following topics: Specimen preparation, data collection strategies, X-ray light sources, X-ray detectors, data reduction, structure solution by MAD, SAD and molecular replacement, complementary methods (spectroscopy, small angle scattering and cryoEM). Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2020/ and use the links on the "registration" page to apply for the course. Successful applicants will be notified early in December 2019 and invited to register at that time. A limited amount of travel support funding may be available. We look forward to seeing you all out in sunny California in March 2020! Silvia Russi, Clyde Smith and Jeney Wierman (Organizers) srussi(a)slac.stanford.edu jwierman(a)slac.stanford.edu csmith(a)slac.stanford.edu

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Phenix version 1.17 released
by Paul Adams 04 Nov '19

04 Nov '19

The Phenix developers are pleased to announce that version 1.17 of Phenix is now available (build 1.17.1-3660). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Please note that there is a new publication that describes recent Phenix developments for structure determination with X-rays, neutrons and electrons: https://doi.org/10.1107/S2059798319011471 Highlights for the 1.17 version of Phenix: 1.17.1 Changes - Fix bug on Windows where xtriage results would fail to display - Other bug fixes 1.17 Changes - Improved handling of SHELX data in phenix.reflection_file_converter - eLBOW can output files for Amber and supports the Orca QM package - dials.image_viewer is used for viewing diffraction images - Updated map smoothing - Fix inconsistency in clashscore values in phenix.validation_cryoem when hydrogens are in the model For a full list of changes see: http://www.phenix-online.org/documentation/CHANGES Please note that this new publication should be used to cite the use of Phenix: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix. Liebschner D, Afonine PV, Baker ML, Bunkóczi G, Chen VB, Croll TI, Hintze B, Hung LW, Jain S, McCoy AJ, Moriarty NW, Oeffner RD, Poon BK, Prisant MG, Read RJ, Richardson JS, Richardson DC, Sammito MD, Sobolev OV, Stockwell DH, Terwilliger TC, Urzhumtsev AG, Videau LL, Williams CJ, Adams PD: Acta Cryst. (2019). D75, 861-877. Full documentation is available here: http://www.phenix-online.org/documentation/ There is a Phenix bulletin board: http://www.phenix-online.org/mailman/listinfo/phenixbb/ Please consult the installer README file or online documentation for installation instructions. Direct questions and problem reports to the bulletin board or: help(a)phenix-online.org and bugs(a)phenix-online.org Commercial users interested in obtaining access to Phenix should visit the Phenix website for information about the Phenix Industrial Consortium. The development of Phenix is principally funded by the National Institute of General Medical Sciences (NIH) under grant P01-GM063210. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (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: Nikki Humphreys [ nhumphreys(a)lbl.gov ][ 1-510-486-4610 ] --

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Postdoc position available in LBNL
by Peter Zwart 31 Oct '19

31 Oct '19

Dear All, We have a postdoc position available at LBNL to work on the development of computational approaches for twinned crystallographic data. This is an exciting opportunity to address a relatively common phenomenon in crystallographic data analysis for which there are currently limited twinning-aware approaches. The aim is to develop tools that impact substructure solution, molecular replacement, density modification and structure refinement. Click the link below for more info or contact me directly. https://lbl.taleo.net/careersection/2/jobdetail.ftl?job=88480 Regards Peter Zwart -- ----------------------------------------------------------------- P.H. Zwart Research Scientist Berkeley Center for Structural Biology Lawrence Berkeley National Laboratories 1 Cyclotron Road, Berkeley, CA-94703, USA Cell: 510 289 9246 BCSB: http://bcsb.als.lbl.gov PHENIX: http://www.phenix-online.org SASTBX: http://sastbx.als.lbl.gov -----------------------------------------------------------------

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Understanding Biology through Structure 16-20 March 2020
by Tom Terwilliger 30 Oct '19

30 Oct '19

Hi Colleagues, particularly students and postdocs, I would like to encourage you to sign up for "Understanding Biology through Structure 2020" (https://cvent.me/4kq9P, March 16-20, 2020 in Santa Fe,NM). Student and postdoc fellowships covering registration and hotel are available (awarded competitively after registration on a rolling basis). The conference is a forum where students and postdocs can meet established researchers and discuss the latest methods and results. For a one-line review and info on the last one see https://bit.ly/2Gfkm4t and https://bit.ly/2Gg39rm. Confirmed speakers are Ilme Schlichting, Yvonne Jones, Hao Wu, 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, Tom Terwilliger, Christopher Neale, and Tom Blundell. All the talks will be followed by 10-15 minutes of discussion with participation by students and postdocs especially encouraged. After the main conference there will be an optional Phenix workshop with lectures and hands-on sessions on using Phenix for crystallography and cryo-EM. Registration is first-come first served, with a limit of 120. All the best, Tom T -- Thomas C Terwilliger Laboratory Fellow, Los Alamos National Laboratory Senior Scientist, New Mexico Consortium 100 Entrada Dr, Los Alamos, NM 87544 Email: tterwilliger(a)newmexicoconsortium.org Tel: 505-431-0010

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GUI reorders file data type in EM validation task
by Ashley Pike 30 Oct '19

30 Oct '19

Hi, I am having problems convincing the GUI which EM map is which for halfmap validation. Version is 1.17-3644 Here is input: [cid:[email protected]] and what is written to Summary tab: [cid:[email protected]] Any tricks to getting this to work? Editing the .eff file written by the gui is an option but running phenix.validation_cryoem on the command line doesn't seem to produce much viewable output. Cheers, Ashley -- Dr. Ashley Pike Membrane Protein Crystallography | Structural Genomics Consortium | University of Oxford Phone: +44 (0)1865 617576 | FAX: +44 (0)1865 617575 | ashley.pike(a)sgc.ox.ac.uk<mailto:[email protected]> | www.thesgc.org<http://www.thesgc.org/> Address: Structural Genomics Consortium, Old Road Campus Research Building, Headington, Oxford OX3 7DQ, UK

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Potential Berkeley Server Outage (October 25)
by Billy Poon 29 Oct '19

29 Oct '19

Hi everyone, As a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will probably be shut down today and will return next week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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Berkeley Server Outage (Starting October 26th)
by Paul Adams 25 Oct '19

25 Oct '19

Dear Colleagues, yet again, as a result of the increased frequency of wildfires in California the power company is taking steps to reduce risk under certain weather conditions. This entails shutting down electricity to regions that are experiencing dry windy conditions. We have been informed that the weather this weekend meets their criteria for a shutdown in our part of the Bay Area. Therefore several of the Berkeley servers will be shut down this weekend and will return later the following week. This will affect: - The Phenix web site (http://phenix-online.org/) - The DIALS West web site (http://dials.lbl.gov/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Berkeley Lab (http://biosciences.lbl.gov/divisions/mbib) Division Deputy for Biosciences, Advanced Light Source, Berkeley Lab (https://als.lbl.gov) Principal Investigator, ALS-ENABLE, Advanced Light Source, Berkeley Lab (http://als-enable.lbl.gov) Group Leader, Computational Crystallography Initiative, Berkeley Lab (http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Laboratory Research Manager, ENIGMA Science Focus Area (http://enigma.lbl.gov) Adjunct Professor, Department of Bioengineering, U.C. Berkeley (http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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real space refine and nonbonded_weight
by Cheung, Alan 25 Oct '19

25 Oct '19

Dear Developers A structure we refined back in 2017, using phenix.real_space_refine on a cryoEM map @ 3.7A (version 1.11.1–2575) produces a clashscore of ~8 but the exact same refinement run with the latest phenix (version 1.17.1) generates a clashscore of ~22. Our refinements with the latest version on other EM structures tend to generate pretty high clashscores too. I think i've tracked this down to the nonbonded_weight parameter, which defaults to 1000 in the older version, and to 100 in the latest version. At which version did the default change, and is there a reason for it? I couldn't find it in the changelog. Alan

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rosetta.run_tests crash
by wtempel 25 Oct '19

25 Oct '19

Hi, has anyone tried the combination of phenix-1.17 and rosetta-2019.40? Crashes in my hands, crash log attached. I may have modified the phenix installation by phenix.python -m pip install readline, in case it matters. Any suggestions appreciated. Many thanks in advance. Wolfram Tempel

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Yeast microtubule model
by Sebastiano Pasqualato 24 Oct '19

24 Oct '19

Dear all, I’m addressing to people working in the microtubule field. Has someone created, or knows where I could find, a pdb file of the yeast microtubule, or a portion of it? I’m interested in studying the contacts between subunits within the lattice. I know one could generate that using yeast tubulin dimers, but I don’t know exactly how. If someone has already done that and is willing to share it, that would be extremely helpful. Thanks a lot in advance, ciao, S PS: sorry for the cross posting to members of both bulletin boards. -- Sebastiano Pasqualato, PhD Biochemistry and Structural Biology Unit Department of Experimental Oncology European Institute of Oncology IFOM-IEO Campus via Adamello, 16 20139 - Milano Italy tel +39 02 9437 5167 fax +39 02 9437 5990

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Phenix-RSR model fit issue in CS-Map
by pramod kumar 23 Oct '19

23 Oct '19

Dear Experts, I have a map generated through cryosparc (ab initio-reconstr and homo-refine at 3.7A* FSC and sharpened in Scipion and separately in EMAN2). I have build the initial pdb through BALBES which has perfect validation parameters and nice fitting in the map (with the mtz output) but the co-ordinates are shifted from the true origin of CS-map. I used phenix-RSR to fit and refine, but validation results remained too far to accept the model as good solution and also a small region entered in wrong nearyby densities. So far following independent and downstream approaches I have taken:- In phenix; dock in map, map to model, rigid body refine followed by real space refine (with both .map and converted .mtz), using only chain A-map boxing and model generation through NCS. I have tried chimera fit for entire assembly and also only one chain in boxed map and full map but still the validation remained far from acceptable values and a small region in wrong neighboring density. Please help. -- Best regards, Promod

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