- phenixbb - phenix-online.org

Alternative to AlphaFold2?
by Chip Lesburg 22 Sep '22

22 Sep '22

Hi PHENIX users, At this past summer's Diffraction Methods GRC meeting<https://www.grc.org/diffraction-methods-in-structural-biology-conference/20…>, Tom Terwilliger presented the utility of incorporating AlphaFold2 predictions during structure fitting and rebuilding. I wonder if anyone has experience using that or an alternative such as OmegaFold<https://www.biorxiv.org/content/10.1101/2022.07.21.500999v1> or OpenFold<https://github.com/aqlaboratory/openfold>? Are any of these easier or harder to get set up? Chip [cid:153156_edd5022b-de61-48a6-bf68-1a41de35ba89.png] Charles Lesburg Vice President, Structural Biology M 908-265-2064 301 Binney Street, Cambridge, MA 02142 odysseytx.com This message is for the named person's use only. It may contain confidential, proprietary or legally privileged information. If you receive this message in error, please immediately delete it and all copies of it from your system, destroy any hard copies of it and notify the sender. ODYSSEY THERAPEUTICS, INC. ("ODYSSEY THERAPEUTICS") reserves the right to monitor all e-mail communications through its networks. ODYSSEY THERAPEUTICS cannot be committed by this e-mail or warrant the accuracy or validity of any information presented. Any views expressed in this message are those of the individual sender.

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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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General interest article
by John R Helliwell 09 Sep '22

09 Sep '22

Dear Colleagues, I imagine you will find the article “The 4Rs and crystal structure analysis: reliability, reproducibility, replicability and reusability” of interest. The weblink is https://journals.iucr.org/j/issues/2022/05/00/dv5002/index.html The article is open access. It is a Teaching and Education article in J Appl Cryst. Best wishes, John Emeritus Professor John R Helliwell DSc

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Runtime error : Bond distance
by Luca Pellegrini 06 Sep '22

06 Sep '22

Phenix real space refine (dev 4704) crashes with: RuntimeError : Bond distance > max_reasonable_bond_distance: 67.4676 > 50: I’ve found various reports of this error in the bb but no (to me) clear solution, only one suggestion to increase the max_reasonable_bond_distance (Nov 2017). I tried setting excessive_bond_distance_limit (I guess is the same) to 999 but with no success as Phenix stops with the same error. Any help on how to fix this gratefully received. Best wishes, Luca

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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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Phenix website downtime
by Billy Poon 01 Sep '22

01 Sep '22

Hi everyone, There was some networking issue which caused the Phenix website to be down for several hours. The site should be back to normal, but please let us know if you have 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 Fax: (510) 486-5909 Web: https://phenix-online.org

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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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