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Low resolution refinement
by Ashu Sharma 06 Nov '18

06 Nov '18

Dear All, I am refining a ~7A single particle cryo-em structure of a protein. The protein has two domains and high-resolution crystal structures of individual domains are already known. I could fit these two crystal structures in the low resolution cryoem map of the full-length protein. I have two questions: 1) Is it acceptable to refine with side chains in this case? In most of the cases, with the guidane from crystal structures, side chains could be placed with reasonable confidence, particularly smaller ones. Should I restrict to poly-ala model or take the advantage of crystal structures and include side chains also? 2) When I tried to refine with side chains, longer side chains like K, R, Q, E which have weaker density tend to bend towards the backbone density. Is there a way to prevent this happening? Suggestions/comments from the community would be highly appreciated. Thanks ! Ashu

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Real-space correlation list for nucleotides?
by Boaz Shaanan 06 Nov '18

06 Nov '18

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(no subject)
by Matthew Bick 06 Nov '18

06 Nov '18

Dear Phenix BB administrator. Could you please post the following job opening to the mailing list? Thank you. Sincerely, Matthew Bick Senior Fellow Baker Laboratory for Computational Protein Design University of Washington The Institute for Protein Design, in the Department of Biochemistry at the University of Washington, currently has an outstanding opportunity for a full time X-ray Crystallographer Staff Scientist. The Institute for Protein Design is designing a new world of synthetic proteins for 21st-century challenges. PRIMARY RESPONSIBILITIES Collaborate with the Investigator and numerous researchers at the Institute for Protein Design on the X-ray crystal structure determination of de novo designed proteins. Manage the activities of research scientists and undergraduate research support with oversight of all protein-to-structure activities at the Institute for Protein Design. Design of new concepts, approaches and programs for structure determination of computationally designed proteins, of a diverse nature. Perform various specialized scientific investigative procedures in X-ray structure determination in collaborative support of numerous research projects with minimal input from Investigator. Use bio-informatics tools and pertinent laboratory and public databases, including the Protein Data Bank (PDB), and information resources to support gene-to-structure research, including deposition of atomic coordinates in the PDB for archival, sharing, and publication. Direct the activities of technical support staff in the Baker lab and at the Institute for Protein Design in collaboration with other research staff. Collaborate with other research staff, postdoctoral fellows and graduate students to select and maintain relevant protein research equipment to insure the lab meets required current and future needs. Direct the development of new protein crystallization and X-ray structure determination strategies, and ascertain if they effectively addresses needs. Manage complex multi-task projects directed at the design, production and structural characterization of numerous de novo designed proteins with higher order function. Train laboratory research staff, postdoctoral fellows and graduate students in protein X-ray crystallography, as well as wet lab equipment for protein production, structural elucidation, and biochemical characterization. Direct projects with undefined time lines and uncertain outcomes requiring analysis from multiple perspectives. Use expert knowledge and judgment to develop new methods and techniques for obtaining solutions. MINIMUM QUALIFICATIONS: Ph.D in Biochemistry, or related field, and X-ray Crystallography +5 or more years of related experience Technical proficiency, scientific creativity, collaborative ability, as well as independent thought. Advanced expertise in X-ray crystal structure determination, both computational and wet lab areas, with a full understanding of the underlying principles and concepts. May be recognized as a leader in their area of expertise. Recognized as a resource for others to use in dealing with complex protein structure determination, computational and wet lab methods, equipment, processes, or procedures. Anticipate future needs in technology support. In-depth understanding of organizational structure both within and outside the work unit, including the role of each position in the group and in other groups. Ability to develop innovative processes to achieve goals. Direct others to develop essential tasks. Review work activities to determine where new information could improve processes or move projects forward. DESIRED QUALIFICATIONS: Ph.D. degree in an appropriate field of science or technology or equivalent in education and experience AND total of six year’s research experience in protein biophysics, X-ray crystallography, computational biology and bioinformatics specifically in the X-ray crystal structure determination. Interested candidates should send a cover letter and CV to Matthew Bick at bickm(a)uw.edu.

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Speeding direct summation ?
by Clement Degut 02 Nov '18

02 Nov '18

Hi, I have (very) high resolution data, for which direct summation method seems to give significantly better map than FFT (i.e. visible hydrogen vs not). My main problem is that refinement got from quite slow, to barely not really possible to handle slow. I have 2 question from that : Am I looking at an artifact ? Meaning should at this resolution (0.84A for CC1/2 at 30% and good overall statistics) see extreme difference between map quality with direct summation vs FFT ? And if yes, can I speed the process compiling phenix with openMP on our cluster ? Or shoul I just become patient ? Many thanks Clément

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Postdoctoral position in Indiana University School of Medicine
by Takagi, Yuichiro 02 Nov '18

02 Nov '18

Postdoctoral Fellow, Takagi Laboratory (https://medicine.iu.edu/research/faculty-labs/takagi/), Department of Biochemistry and Molecular Biology Indiana University School of Medicine We are looking for a highly motivated postdoctoral follow with a background in structural biology (X-ray crystallography, cryo-EM), to work on NIH-funded projects studying multi-protein complexes involved in eukaryotic transcription regulation. Who We Are: My laboratory is interested in understanding the mechanisms of assembly, structure and function of large multi-protein complexes -“molecular machines” - involved in eukaryotic gene regulation, utilizing both cryo-EM and X-ray crystallography. We are particularly interested in the Mediator complex in both yeast and humans. We believe that development and implementation of novel technologies is the key to unlocking the mysteries of how highly complex molecular machines (e.g. Mediator) function. Therefore, our overall research objective is two-fold: (i) development of novel technologies for studying multi-protein complexes, and (ii) application of these technologies to elucidate the structure and function of the Mediator complex. In addition, we have developed a novel technology for producing pure preparations of difficult-to-express proteins and protein complexes, which has enabled several exciting ongoing projects with outstanding collaborators, including work on: plant RNA polymerases, DNA helicases, DNA repair complexes, RNA editing complex, and insulator complex. What We Offer: State-of-the art protein and protein complex expression technologies (patent pending) enabling expression of difficult-to-express, problematic proteins and protein complexes Accessibility to crystallization drop-setting robots, home X-ray sources, Synchrotron data collection at the Advanced Photon Source (APS) at Argonne National Laboratory (within a 3 hour drive from our lab), as well as electron-microscopy (EM) facility: Titan Krios, Talos Artica, and JOEL-FS3200 A one-on-one mentoring opportunity by which a postdoctoral fellow can learn the craft of designing research strategy, preparing compelling grant proposals, and paper-writing and presentation skills The opportunity to work with multiple outstanding collaborators Who Should Apply: This position could be a great fit for you if: you have the expertise and experience in X-ray crystallography, and want to apply such skills toward structure determination of highly complex multi-protein complexes you are interested in learning and developing for the cutting-edge protein complex engineering and expression technologies you would like to extend your skill sets to cryo-EM you are self-confident and can communicate with the PI, other lab members, and collaborators with ease, and enjoy discussing research results and how to overcome technical challenges the specific research focus of our laboratory inspires you you love to gather information from the literatures and helps generate creative ideas and technical solutions you relish working on technically challenging problems, which often require an extended persistent effort to crack Job Description, Qualification, and Expectations: Primary activities in this position include, but are not limited to: Expression and purification of the protein complexes for biochemical and structural studies (cyo-EM, crystallization Structure determination of the protein complexes by cryo-EM or/and X-ray crystallography Biochemical assays to characterize the recombinant protein complexes Providing intellectual contributions to the projects including writing manuscripts, fellowship application and helping PI for grant applications Ph.D. in structural biology (X-ray crystallography, cryo-EM) is strongly preferred. If interested, please email a cover letter, CV, and two reference letters to ytakagi(a)iu.edu Applications will be screened until a suitable candidate is found. Indiana University is an equal opportunity/affirmative action employer.

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Submitting SLURM jobs through PHENIX GUI
by Thomas Cleveland 01 Nov '18

01 Nov '18

Hi all, Has anyone gotten SLURM job submission to work through the PHENIX GUI? Under Preferences/Processes, I set Queueing system to SLURM with queue submit comand "sbatch." The job does indeed submit to the queue, and I can see it in the listing using the "squeue" command. However, there is quickly an error, "OSError : [Errno 2] No such file or directory: '/home/clevelandt/data/MX/181016_P1_merge/phenix/.phenix/tmp/10.libtbx_info.LOCK'". I've attached the full error log. Basically the program is looking for a lock file that isn't there. I'm not sure why it's not there. All compute nodes should have access to this directory, and there is no caching of any kind, so any files placed there should immediately be accessible. I can manually submit e.g. phenix.refine jobs to the queue using the command line and everything works fine. It would be really nice to have it through the GUI though. Thanks for any help, Tom

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Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK
by David Barford 31 Oct '18

31 Oct '18

Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein Crystallography Facility Manager. The LMB is one of the birthplaces of structural biology and remains at the forefront of methods development as protein crystallography is a critical technique for understanding the mechanisms of macromolecular complexes, one of the major goals of the LMB. The post-holder will provide support to researchers from all Divisions of the LMB in the collection of X-ray diffraction data using both synchrotrons and in-house X-ray facilities, will maintain and develop the in-house facilities, will provide expert advice and support during subsequent structure determinations, and will act as the coordinator for LMB's synchrotron access. It is expected that there will be the opportunity for collaboration on structural projects with research groups at the LMB. The successful applicant will have several years of post-doctoral experience in the field of protein crystallography including data collection at synchrotrons and all aspects of structure determination. Excellent communication and inter-personal skills are required because the post will involve interacting with a diverse range of scientists with different levels of expertise. Closing date for applications: 28th November 2018 For further details and information on how to apply please visit: Jobs.ac: https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-… <https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-…> Nature: https://www.nature.com/naturecareers/job?id=661643 <https://www.nature.com/naturecareers/job?id=661643> Informal enquires should be addressed to Dr. David Barford. E.mail: dbarford(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>

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Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK
by David Barford 31 Oct '18

31 Oct '18

Protein Crystallography Facility Manager, MRC Laboratory of Molecular Biology, Cambridge, UK The MRC Laboratory of Molecular Biology (LMB) seeks to appoint a Protein Crystallography Facility Manager. The LMB is one of the birthplaces of structural biology and remains at the forefront of methods development as protein crystallography is a critical technique for understanding the mechanisms of macromolecular complexes, one of the major goals of the LMB. The post-holder will provide support to researchers from all Divisions of the LMB in the collection of X-ray diffraction data using both synchrotrons and in-house X-ray facilities, will maintain and develop the in-house facilities, will provide expert advice and support during subsequent structure determinations, and will act as the coordinator for LMB's synchrotron access. It is expected that there will be the opportunity for collaboration on structural projects with research groups at the LMB. The successful applicant will have several years of post-doctoral experience in the field of protein crystallography including data collection at synchrotrons and all aspects of structure determination. Excellent communication and inter-personal skills are required because the post will involve interacting with a diverse range of scientists with different levels of expertise. Closing date for applications: 28th November 2018 For further details and information on how to apply please visit: Jobs.ac: https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-… <https://www.jobs.ac.uk/job/BNU298/protein-crystallography-facility-manager-…> Nature: https://www.nature.com/naturecareers/job?id=661643 <https://www.nature.com/naturecareers/job?id=661643> Informal enquires should be addressed to Dr. David Barford. E.mail: dbarford(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>

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RNA starting with triphosphate
by Phoebe A. Rice 25 Oct '18

25 Oct '18

A question from my collaborators: what is the best way to get phenix to handle a GTP as nt #1 of an RNA chain? That is, what is the best way to specify a covalent bond with the proper geometry between the 3’ O of GTP1 and the 5’ P of nt #2? Thanks in advance, Phoebe ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Phoebe A. Rice Dept. of Biochem & Mol. Biol. and Committee on Microbiology https://voices.uchicago.edu/phoebericelab/

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RapiData 2019 applications open!
by Smith, Clyde 24 Oct '18

24 Oct '18

Dear all, Applications are now open for the 2019 edition of RapiData at SSRL. RapiData is a practical course in macromolecular X-ray diffraction data collection, data processing and structure solution. The aim of the RapiData course is to educate and train young scientists in data collection and processing methods at synchrotron beamlines, using state-of-the-art software and instrumentation. The course will be held at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from May 5-10 2019. Course organizers for 2019 are Silvia Russi, Clyde Smith and Jeney Wierman. 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 and small angle scattering) Please visit http://smb.slac.stanford.edu/news/rapidata/rapidata-2019/ and use the links on the "registration" page to apply for the course. The application deadline is December 31 2018. Successful applicants will be notified early in January 2019 and invited to register and book accommodation at the SLAC Guesthouse at that time. A limited amount of travel support funding may be available. Please direct questions to Silvia Russi (srussi(a)slac.stanford.edu), Jeney Wierman (jwierman(a)slac.stanford.edu) or Clyde Smith (csmith(a)slac.stanford.edu).

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