August 2022 - phenixbb - phenix-online.org

RapiData at SSRL 2022 - application deadline extended by two weeks!
by Smith, Clyde 12 Jan '23

12 Jan '23

We have extended the deadline for applications for a place at the RapiData 2022 @ SSRL workshop to next Friday, February 4th 2022! There are still a few spots left, so get your application in! The workshop will be held virtually from May 4 - 14 2022. The course will comprise 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). There will also be several days of software tutorials (HKL3000,XDS, CCP4/DIALS, Phenix, AutoSharp/AutoProc, Shelx, Coot) and you will all get to connect remotely to the SSRL beamlines to collect both monochromatic and MAD/SAD data. There is also an opportunity to ship your own samples to SSRL prior to the workshop, and collect your own data. Please visit https://www-ssrl.slac.stanford.edu/rapidata/rapidata-2022/index.html and use the links on the "registration" page to apply for the course. Successful applicants will be notified later in February 2022 and invited to register at that time (there will be no fee for registration). Regards, Clyde Smith (csmith(a)slac.stanford.edu) and Silvia Russi (srussi(a)slac.stanford.edu) Workshop Organizers

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SSRL/LCLS User Meeting Registration is Open
by Mooers, Blaine H.M. (HSC) 29 Sep '22

29 Sep '22

Dear phenixbb: The SSRL/LCLS User's Meeting will be September 26-30, 2022. It will be virtual again due to COVID, but the of the sessions will be recorded live. Registration<https://urldefense.com/v3/__https://events.bizzabo.com/SLAC-UsersMeeting-20…> is free and open to all. We had about 1600 registrants last year. We will have 27 workshops, 3 poster sessions, and 3 plenary sessions. Distinguished plenary speakers include Drs. John Helliwell and Linda Young. Although the registered attendees will be able to view the videos at a later time, please do attend during the live sessions to participate in the question and answer periods. There will be several poster prizes. The BioXFEL prizes are not limited to work done at LCLS. The deadline<https://urldefense.com/v3/__https://events.bizzabo.com/SLAC-UsersMeeting-20…> for the submission of poster abstracts is September 9th. Best regards, Blaine Mooers on behalf of the SSRL/LCLS User's Meeting Organizing Committee and the SSRL User Executive Committee<https://urldefense.com/v3/__https://www-ssrl.slac.stanford.edu/content/abou…> and the LCLS User Executive Committee<https://urldefense.com/v3/__https://lcls.slac.stanford.edu/lcls-users-organ…>

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Question about occupancy and 2Fo-Fc and Fo-Fc maps
by Vatsal Purohit 20 Sep '22

20 Sep '22

Hi everyone, I had 2 questions regarding occupancy and maps generated in ligand-bound regions for various ligand models potentially present in the structure: 1. I’ve been working with some 2.0 angstrom structures and trying out refinements with 2 sets of bound ligands at varying occupancies (at the same active site) to get an approximate idea of their relative populations in the structure. For one set of ligands, I observe 2Fo-Fc density in regions uniquely occupied by them even when their occupancy is zero. Could there be a reason why this is the case? 2. Additionally, I observe red Fo-Fc density in the same region when the occupancy is set to 1.0. It disappears at lower occupancies of 0.7 indicating that a lower population of this ligand is present. However, when the occupancy is very low, we don’t see an equivalent green Fo-Fc density popping up in the same region. Could there be a reason for why the red Fo-Fc density at high occupancy doesn’t translate to green Fo-Fc for the same region at low occupancy? Any information or resources that could give me more insight into this question would be really helpful! Regards, Vatsal

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Reference model restraints
by Luca Pellegrini 01 Sep '22

01 Sep '22

Hello, Phenix.real_space_refine keeps pushing a residue out of density so I'd like to restrain it to its current position. Can you please let me know how to implement in the GUI the first example at point 14 at https://phenix-online.org/documentation/reference/real_space_refine.html#us… phenix.real_space_refine model.pdb map.mtz \ reference_coordinate_restraints.enabled=true \ reference_coordinate_restraints.selection="chain A and resseq 12:21" \ reference_coordinate_restraints.sigma=0.05 Best wishes, Luca Luca Pellegrini, PhD Department of Biochemistry University of Cambridge Cambridge CB2 1GA UK

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RNA structural biology position (Scientist-Sr.Scientist) at Arrakis Therapeutics
by Elena Menichelli 25 Aug '22

25 Aug '22

Dear all, We have an open position for an RNA structural biologist at Arrakis Therapeutics (Boston, MA area). The ideal candidate will have a background in structural characterization of RNA (X-ray crystallography, cryo-EM or atomic force microscopy) and a passion for developing small molecules that target RNA in a very collaborative environment. Please feel free to visit Arrakis’ website for a more detailed job description and to reach out to me for additional information and informal discussion. https://arrakistx.com/careers/current-openings/ With best regards, Elena ******* Elena Menichelli, PhD | Head of Structural Biology emenichelli(a)arrakistx.com<mailto:[email protected]> | www.arrakistx.com<http://www.arrakistx.com/>

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Launch of IUCrData Raw Data Letters: Editorial
by John R Helliwell 24 Aug '22

24 Aug '22

Dear Colleagues, I imagine you will be interested to know of the launch of IUCrData’s Raw Data Letters. The Main Editor is Dr Loes Kroon Batenburg. See https://forums.iucr.org/viewtopic.php?f=39&t=449&p=729#p729 Greetings, John Emeritus Professor John R Helliwell DSc Chair of IUCr CommDat

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phenix.refine command lane xyz restrains
by Błażej Bagiński 24 Aug '22

24 Aug '22

Dear Phenix community, lately I started toying with the terminal version of our favourite refinement software (on kubuntu linux). I'm refining a structure with a ligand that is not in the refmac database (.cif file needed), and I couldn't find anything on how to implement xyz coordinates restraints for the procedure. In other words, I have a ligand that I built into the polder map and I want to tell the software "do not change the positions in space of these atoms". How can I do that? Also, side question: why there are three different(?) versions of command line phenix.refine for every phenix installation? What is the difference between them? REMARK 6 I followed the online guide for "Refinement at high resolution" on my 1,2~1,3A structure and the results were surprisingly nice, I'd say potentially even better than usually used parameters in GUI (5 cycles both). Kind regards, Blazej

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Postdoctoral Research Associate in the Structural Biology of Supramolecular Protein Assemblies
by Owen Davies 19 Aug '22

19 Aug '22

Dear all, I would like to advertise a postdoctoral position that is currently available in my lab at the Wellcome Centre for Cell Biology, University of Edinburgh, UK (https://www.wcb.ed.ac.uk/research/owen-davies). This position is for an initial period of three years (with possibility to extend), to work on the integrative structural biology of the synaptonemal complex. The synaptonemal complex is a supramolecular protein structure that assembles during meiosis to facilitate homologous chromosome synapsis and crossover formation. Its immense structure, of many micrometers in length, is formed through the combination of at least three unique self-assembling protein systems, which individually form lattice-like arrays, para-crystalline filaments and 'intermediate filament'-like fibres. This position aims to determine the molecular structure of the human synaptonemal complex and its constituent complexes through their reconstitution from recombinant proteins. This will be achieved through a cutting-edge structural biology approach, involving cryo-EM single particle reconstruction and tomography, structure solution of components by X-ray crystallography, solution biophysics (including X-ray and light scattering, and single-molecule biophysics), and the integration of experimental findings by advanced computational modelling of structures and assembly dynamics. The post is funded by a Wellcome Senior Research Fellowship, and will be hosted in a well-equipped and well-funded lab, which includes the following: Extensive biochemical equipment (including numerous Akta Pure systems, SEC-MALS etc) Protein production and characterisation facility (https://www.ed.ac.uk/biology/research/facilities/edinburgh-protein-producti…) State-of-the-art biophysics equipment (including C-trap optical tweezers) In-house TEM, SEM and newly upgraded cryo-EM facility (https://www.ed.ac.uk/biology/research/facilities/electron-microscopy) Regular time on macromolecular crystallography and SAXS synchrotron beamlines at Diamond Light Source (https://www.diamond.ac.uk) Regular cryo-EM time on Titan-Krios microscopes at Diamond Light Source (https://www.diamond.ac.uk) and Jeol microscopes at the Scottish Centre for Macromolecular Imaging (https://www.gla.ac.uk/researchinstitutes/iii/cvr/facilities/scmi/) Local provision of high-performance GPU computation for cryo-EM, modelling and molecular dynamics This position provides a unique opportunity for a highly enthusiastic applicant to perform transformative research through an integrative approach that is directed towards the new era of structural biology that address protein assemblies at a cellular scale. The successful candidate will lead this project (including several PhD students), and will be fully supported in applying for postdoctoral research fellowships within the lab, and independent research positions at the end of the postdoc. In suitable cases, at least part of the project, or a new project to be started during the employment, could be taken by the successful candidate as the basis for their future research career. Please see the following manuscripts for examples of our previous work: https://www.nature.com/articles/s41594-021-00636-z https://www.nature.com/articles/s41594-018-0078-9 https://www.nature.com/articles/s41467-018-07794-7 https://www.science.org/doi/10.1126/sciadv.abb1660 https://elifesciences.org/articles/60175 Full publication list available at https://www.ed.ac.uk/profile/dr-owen-davies The advert for the position is available via the following link: https://www.jobs.ac.uk/job/CRX346/postdoctoral-research-associate-in-the-st… The application deadline is 6th September, and candidates should apply by following the 'apply' link on the above advert. Please feel free to contact me directly (Owen.Davies(a)ed.ac.uk<mailto:[email protected]>) for informal discussions and additional information. Best wishes, Owen. Dr Owen Davies Wellcome Senior Research Fellow Wellcome Centre for Cell Biology University of Edinburgh Michael Swann Building Max Born Crescent Edinburgh EH9 3BF United Kingdom The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336. Is e buidheann carthannais a th' ann an Oilthigh Dh?n ?ideann, cl?raichte an Alba, ?ireamh cl?raidh SC005336.

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Inability to connect the N and C terminal of peptide to form a peptid bond of a circular peptide structure
by Jiang Xu 14 Aug '22

14 Aug '22

Hello Guys, I have a circular peptide structure solved from Xtal. The peptide is actually a circular peptide that has the N terminal and C terminal joined together by a peptide bond. When refining the structure, I had a problem getting the C-N terminal (between G34 and S2) joined together by the peptide bond. I even made a link between the C terminal carbon atom and N terminal N atom in coot and used this model as the input model to do the refinement using Phenix.refine. It seemed that the program didn't consider the link made in coot as a valid bond and intentionally avoid forming a bond between the C atom and the N atom. So, how can I solve this problem? Thank you, Best regards, Jiang Lin Chen Lab University of Southern California P.S. coot manually made link between the C and N terminal [image: unnamed.jpg] After refinement [image: unnamed (1).jpg]

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Postdoc Opportunity - Multidataset X-ray Crystallography, Computational Structural Biology, & Protein Allostery - Upper Manhattan, New York City
by Keedy, Daniel 09 Aug '22

09 Aug '22

Hello Phenix community, The Keedy Lab at the CUNY Advanced Science Research Center in New York City has a funded Postdoctoral Scholar position available immediately. We seek applications from individuals with experience in computational biology, computer science, software development, biochemistry, biophysics, or a related area. Details of research projects and career training will be tailored to the goals of the successful applicant. Research: The Keedy Lab is interested in the interplay between protein sequence, conformational heterogeneity, and biological function. Using a unique combination of avant-garde computational and biophysical approaches, we aim to elucidate the conformational ensembles of proteins and to understand how they are shifted by perturbations, including temperature, pressure, mutations, ligands, protein:protein interactions, to control biological function. The successful applicant for this open position will join these efforts by developing and using new computational approaches to exploit families of related structures, extract hidden signatures of conformational heterogeneity, and explore how changes to amino acid sequence rewire protein allosteric networks. Location: The CUNY Advanced Science Research Center (https://asrc.gc.cuny.edu) is a cutting-edge research institution, perched atop a hill overlooking Harlem in New York City. Alongside its sister research building, the City College of New York’s Center for Discovery and Innovation, the ASRC sits in an oasis of green amidst upper Manhattan. The ASRC Structural Biology Initiative features eight tenure-track and research-track faculty members, pursuing diverse research problems using X-ray diffraction, mass spectrometry, cryo-EM, NMR, solution biophysics, and advanced microscopy. The ASRC is immediately adjacent to the New York Structural Biology Center, a consortium of CUNY and eight other New York academic institutions with world-class facilities, and is just 70 miles from Brookhaven National Laboratory, featuring the National Synchrotron Light Source II – the brightest synchrotron light source in the United States. You can read more about the Keedy lab here: https://keedylab.org Please officially apply for the position here: https://www.rfcuny.org/careers/postings?pvnID=RC-2207-004956 You may also email me directly to ask questions or discuss. I look forward to hearing from you! Best regards, Daniel Keedy — Daniel A. Keedy, PhD Assistant Professor Structural Biology Initiative, CUNY Advanced Science Research Center Department of Chemistry and Biochemistry, City College of New York Biochemistry, Biology, and Chemistry PhD Programs, CUNY Graduate Center dkeedy(a)gc.cuny.edu<mailto:[email protected]> | https://keedylab.org | 919-724-6064

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