- phenixbb - phenix-online.org

Molecular replacement of cyclic polypeptide with non-standard amino acid
by Ariela Samantha 10 Mar '22

10 Mar '22

Dear all, I have collected an XRD data from a crystal of cyclic polypeptide with non-standard amino acid (2,4-diaminobutyric acid). Is it possible to solve the structure by molecular replacement? Or does anyone have any suggestion for solving the structure? Thank you very much for your kind help. --- Best regards, Ariela Samantha PhD Candidate Department of Structural Biology School of Molecular Sciences The University of Western Australia Bayliss Building room 4.26 Phone +61 8 6488 ext. 3163

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Error message on minimization global
by Abhipsa Shatarupa 09 Mar '22

09 Mar '22

Hello, I am a beginner in phenix. Currently, I am running minimization global under real-space refinement. The input files for this job are a .pdb file generated from rigid-body refinement and a .ccp4 map. I end up receiving the following error message (image attached -Error file). The output log file gives me the description of the number of atoms and the atoms responsible for generating the error (image attached – atoms file). I ended up finding a couple of Q/A on a similar error message, but I am not sure how to generate the CIF file to overcome the problem using eLBOW? Could someone please help me resolve this issue? Thanks in advance, Abhipsa

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XChem access: Diamond AP32 Call for Proposals open until 30 March 2022
by Fearon, Daren (DLSLtd,RAL,LSCI) 08 Mar '22

08 Mar '22

Hi all, Friendly reminder that the Diamond AP32 call for proposals (which includes XChem access between October 2022 and March 2023) is open until Wednesday 30th March at 17:00hrs UTC/GMT+1. Please check our webpage<https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/XChem-Applicati…> for more details and if you have any questions about applying then do get in touch. Cheers, Daren Dr Daren Fearon (he/him) Senior Beamline Scientist (XChem) Diamond Light Source Ltd Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE Tel: 01235 778936 Mobile: 07425638147 Email: daren.fearon(a)diamond.ac.uk<mailto:[email protected]> Web: www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html<http://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening.html> [https://gallery.mailchimp.com/3de94671e0e91f373e1995d94/images/557065e4-53a…] Reminder: Diamond – AP32 Call for Proposals Dear Colleague, This is a gentle reminder that our call for proposals for AP32 is open and the deadline for this call is Wednesday 30th March at 17:00hrs UTC/GMT+1. The period will cover October 2022 to March 2023. Please note that as this is in working hours the call will be closed at this time. A table of instrument access is given here<https://www.diamond.ac.uk/Users/Apply-for-Beamtime.html>. Users from the EU: Submitting proposals and visiting Diamond post-Brexit Users from European organisations continue to be welcome to submit proposals to Diamond. The same funding policy and procedure for expenses continue to be in place for any visit to Diamond as was in place before Brexit. You can find our expenses procedure here.<https://www.diamond.ac.uk/Home/Legal-and-Compliance/Procedures/Financial-Su…> Proposal Information The science case and reporting templates have been updated. You are strongly encouraged to use the most up-to-date template available for download in the User Administration System. Experiments that can be completed remotely or by mail-in should be highlighted. Please refer to the relevant information that each of the beamlines have published. You will find relevant information under each instrument’s specific information here.<https://www.diamond.ac.uk/Instruments.html> Do discuss your planned work with our instrument scientists and submit all proposals to UAS<https://uas.diamond.ac.uk/>. In addition, please ensure that any outstanding reports are submitted, and that your publications related to your previous beamtimes are in our database<http://publications.diamond.ac.uk/> as the peer review panel will take these into consideration during the review. A number of additional instruments will be taking submissions for proposals: I06<https://www.diamond.ac.uk/Instruments/Magnetic-Materials/I06.html> - Laser-PEEM/LEEM Facility for Multidisciplinary Nanoscience Imaging: A new multidisciplinary nanoscience imaging facility, using PhotoEmission Electron Microscopy (PEEM) and Low-Energy Electron Microscopy (LEEM), will be available for peer-reviewed access starting in AP32 (from October 2022). PEEM gives nanoscale insights into the magnetic properties of materials whilst LEEM provides detailed nanoscale structural insights through full-field imaging combined with spatially resolved Low-Energy Electron Diffraction (micro-LEED). The facility combines PEEM/LEEM with a continuous wave (CW) laser (Laser-PEEM/LEEM) providing high spatial resolution with probing depths ranging from less than a nanometre to tens of nanometres. To submit a proposal please select I06 in submission process. Further details are available from Dr. Sarnjeet Dhesi (dhesi(a)diamond.ac.uk<mailto:[email protected]>). The multidisciplinary Laser-PEEM/LEEM facility is funded by Diamond Light Source and the Engineering and Physical Sciences Research Council (EPSRC Grant: EP/V029258/1) and is being developed in collaboration with the Central Laser Facility, the University of Oxford, the University of Cambridge, the University of Nottingham and University College London. ________________________________ Diamond's new Active Materials Laboratory<https://www.diamond.ac.uk/Science/Integrated-facilities/active-materials-la…> (AMLab) is in the process of being fitted out and is now ready for use. Users who want to use this facility in their proposals will be able to select it as an instrument in UAS<https://uas.diamond.ac.uk/>. ________________________________ DL-SAXS<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> - The Offline SAXS instrument, Xeuss 3.0<https://www.xenocs.com/saxs-products/saxs-equipment-xeuss/>, from Xenocs<https://www.xenocs.com/>, has been delivered with both Excillium Gallium MetalJet and Molybdenum Microsource options. The instrument has a set of sample holders<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> available for use. Please discuss any ideas for Sample Environment driven experiments with a member of the team<https://www.diamond.ac.uk/Instruments/Soft-Condensed-Matter/small-angle/Off…> before submitting. ________________________________ B07<https://www.diamond.ac.uk/Instruments/Structures-and-Surfaces/B07.html> – When submitting proposals for B07 the award will be assigned by the beamline staff<https://www.diamond.ac.uk/Instruments/Structures-and-Surfaces/B07/Staff.html> to the branch line (B07-B or B07-C) which is optimal for a given experiment. Please select B07 when you submit your proposal with a view to beamline staff determining which of the two branch lines, B07-B and B07-C, will be the optimal choice. Applicants are encouraged to discuss the options with the beamline staff before submission and will be able to express their preference in the “beamline questionnaire” part of the proposal form. ________________________________ DIAD<https://www.diamond.ac.uk/Instruments/Imaging-and-Microscopy/DIAD.html> - The Dual Imaging and Diffraction (DIAD) beamline is a dual beam X-ray instrument for imaging, diffraction and scatterin g, which operates at energies of 7-38 keV. Information and questions to consider when writing the proposal can be found on the DIAD web-pages. ________________________________ I08<https://www.diamond.ac.uk/Instruments/Imaging-and-Microscopy/I08.html> has extended its portfolio with a new instrument for soft X-ray ptychography (I08-1). When submitting proposals for I08 the award will be given for that instrument with a view to beamline staff determining which of the two instruments will be the optimal choice for a given experiment. Please contact Burkhard Kaulich<mailto:[email protected]> (I08 PBS) for further information. Best wishes, Diamond User Office [Diamond Light Source Logo]<https://www.diamond.ac.uk/> Diamond Light Source is the UK's national synchrotron science facility, located at the Harwell Science and Innovation Campus in Oxfordshire. [Follow Us on Twitter]<http://www.twitter.com/DiamondLightSou> [Website]<https://www.diamond.ac.uk/> Copyright © 2022 Diamond Light Source, All rights reserved. Our mailing address is: Diamond Light Source Diamond House Harwell Science & Innovation Campus Didcot, Oxfordshire OX11 0DE United Kingdom Add us to your address book<https://diamond.us20.list-manage.com/vcard?u=3de94671e0e91f373e1995d94&id=7…> You are receiving this email because you are registered in our User Administration System (https://uas.diamond.ac.uk). If you would like to opt out of future bulk emails, please click unsubscribe<https://diamond.us20.list-manage.com/unsubscribe?u=3de94671e0e91f373e1995d9…>. Please note that unsubscribing from this mailing list will not stop you from receiving operational emails related to your upcoming visits or essential information related to your account. If you wish to update your personal information, please do so directly in the User Administration System (https://uas.diamond.ac.uk<https://uas.diamond.ac.uk/>). For more information about our privacy policy, please visit www.diamond.ac.uk/Legal<http://www.diamond.ac.uk/Legal.html>. -- 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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Online Workshop Series on Structural and Crystallographic Databases -- Registration Open
by Mitchell D. Miller 04 Mar '22

04 Mar '22

On behalf of The U.S. National Committee for Crystallography (USNC/Cr) of the National Academies of Sciences, Engineering, and Medicine, I am happy to announce that registration is now open for "EXPLORING STRUCTURAL DATABASE USE IN CRYSTALLOGRAPHY: WORKSHOP SERIES". The topics will focus on using, developing, and maintaining crystallographic and structural databases- encompassing macromolecular, small molecule, and powder diffraction. We will open the series with a keynote delivered by John Helliwell (IUCr Chair of the Committee on Data) on March 21, 2022 followed by 10 one-day and two-day workshops focused on 8 different structural and crystallographic data resources. An overview of the program can be found in the attached PDF. Graduate students, postdoctoral fellows, faculty members and researchers in any of the crystallographic, diffraction, and imaging sciences affiliated with the International Union of Crystallography (IUCr) are encouraged to register and participate in the training sessions that interest them. Registration for this online series is free. To read more about each session and to register, please visit: https://www.nationalacademies.org/our-work/exploring-structural-database-us… The details about each session can be found by clicking the event pages along with a registration link allows one to register for any combination of the 1 and 2 day sessions (each meeting for 2-4 hrs/day). The workshop series is sponsored by the National Institute of Standards and Technology (NIST). For more information, please contact Ana Ferreras, Telephone: (202) 334-1697 Email: aferreras(a)nas.edu[1] Sincerely, Mitch Links: ------ [1]

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Coot opening problem
by Afshan Begum 03 Mar '22

03 Mar '22

Hi Expert, I am refinening my strcuture on phenix , Could you kindly suggest me why after refinement in phenix (version i used 1.9-1692, Mac operation system) COOT does not open up by clicking on COOT button.Its seems open but only black screen (or blank window) come up without out any data, As previously always its open very smoothly , so now i have to open all files manually every time. Best Regards =============================== Afshan Begum

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Output MTZ file from Phenix Refine
by Mark Saper 03 Mar '22

03 Mar '22

Thanks to Tom the issue is resolved. If I examine the MTZ file with phenix.mtz.dump the angles are in degrees as they should be. For some reason CCP4 ViewHKL program shows them in radians although they are stored internally as degrees. > The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? > > -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Output MTZ file from Phenix Refine
by Mark Saper 03 Mar '22

03 Mar '22

The output MTZ from Phenix refinement contains F-model and PHIF-model. I wanted to use the PHIF-model term in CCP4 but I discovered that PHIF-model in a Phenix mtz is in radians while CCP4 expects degrees. Why the discrepancy? -Mark _____________________ Mark A. Saper, Ph.D. Associate Professor Emeritus of Biological Chemistry University of Michigan Medical School saper(a)umich.edu | +1 734 276 6505 Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Call for Topical review articles for Acta Cryst F Structural Biology Communications
by John R Helliwell 26 Feb '22

26 Feb '22

Dear Colleagues, We draw your attention to our call for Topical review articles for Acta Cryst F Structural Biology Communications described here:- https://journals.iucr.org/f/issues/2021/11/00/me6156/index.html We welcome your proposals. Best wishes, John, Mark and Janet John Helliwell, Mark van Raaj and Janet Newman Emeritus Professor John R Helliwell DSc

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General interest
by John R Helliwell 03 Feb '22

03 Feb '22

Dear Colleagues, I imagine you would be interested in the book “Collecting Experiments. Making Big Data Biology” which I have reviewed here:- https://journals.iucr.org/j/issues/2022/01/00/xo0187/index.html My book review is open access. I have dedicated my book review to John Westbrook. Best wishes, John Emeritus Professor John R Helliwell DSc

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PhD fellowship at NC State & Oak Ridge National Laboratory
by Meilleur, Flora 25 Jan '22

25 Jan '22

Thank you for sharing the following PhD opportunity with interested students! Best wishes, Flora PhD fellowship in Structural Biology of Metalloenzymes at NC State & Oak Ridge national Laboratory A Ph. D. research fellowship (up to 5 years) in enzyme chemistry is available with Dr. Flora Meilleur. The position is joint between North Carolina State University, the Ph. D. granting institution where the Ph. D. candidate will complete the program core coursework, and Oak Ridge National Laboratory, where research activities will be performed. The project will focus on lytic polysaccharide monooxygenase, a class of copper containing metalloenzymes involved in biomass oxidation. High resolution X-ray and neutron crystallography will be used primarily to study the enzymatic mechanism. The project will involve collaborations to include spectroscopic and biophysical methods as well as computational approaches. Key publications on the topic include (complete list here<https://scholar.google.com/citations?user=i0aLPhYAAAAJ&hl=en>): Schröder G.C., O'Dell W.B., Webb S.P., Agarwal P.K., and Meilleur F. (2021) Capture of activated dioxygen intermediates at the copper-active site of a lytic polysaccharide monooxygenase. ChemRxiv. 10.26434/chemrxiv-2021-n4c1x<https://chemrxiv.org/engage/chemrxiv/article-details/61b3cdd8689c875d6adea9…> O'Dell W. B., Aggarwal P., Meilleur F. (2017) Oxygen Activation at the Active Site of a Fungal Lytic Polysaccharide Monooxygenase. Angew. Chem. Int. Ed. 56:767-770<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340418/> The candidate should hold a degree in chemistry or biochemistry. Prior experience in molecular biology, protein expression, or protein purification is an advantage. The position is available now and applications are welcome until the position is filled. Interested candidates must email a detailed CV, a letter of motivation and the name of three scientists for reference to Flora Meilleur<mailto:[email protected]?subject=Application%20to%20NC%20State%20/%20ORNL%20PhD%20Fellowship> prior to applying to the Graduate Program in Biochemistry at NC State. For further information about the position, interested candidates can contact Flora Meilleur<mailto:[email protected]?subject=Questions%20about%20NC%20State/ORNL%20PhD%20Fellowship>. Further information about the NC State Biochemistry graduate program here<https://cals.ncsu.edu/molecular-and-structural-biochemistry/>. Further information about the neutron facilities at Oak Ridge National Laboratory here<https://neutrons.ornl.gov/>.

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refining a covalent-bound ligand (part 2)
by Sergio A. Sampieri 23 Jan '22

23 Jan '22

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refining a covalent-bound ligand (part 2) (try 2)
by Sergio A. Sampieri 23 Jan '22

23 Jan '22

Hi all, hope this message finds you well. As in a previous topic from 2018, I’m having problems refining a covalent-bounded ligand. The link shall be made between a carbon atom that is double bonded to an oxigen “SMILES C1=CC=C(C=C1)C=O” and the SG group of a Cys residue. I generated a CIF dictionary through AceDRG in COOT and CCP4i2. But after trying different approaches during refinement, (Automatic Linking parameters, Atom selection, acceptor & donnor, ligand bond cut off and so) the result keeps being a non bounded enzyme-ligand complex (“Not linked: pdbres="LIG A 401”). I readed in the phenixbb that this was solved by changing the nature of the ligand ( http://www.phenix-online.org/pipermail/phenixbb/2018-February/023718.html), but is not the way I would like to follow. Any suggestions or ideas would be greatly appreciated, thanks a lot for your time. Stay safe. -- “I’ve learned to think like a virus; no neurons, a lot of sex, and a lot of errors.” John J. Holland Biól. Sergio Aguirre Sampieri

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AlphaFold changes everything": new lecture on the Phenix tutorials channel
by Dorothee Liebschner 23 Jan '22

23 Jan '22

Hi everyone, I hope you will like "AlphaFold changes everything <https://www.youtube.com/watch?v=9IExeA_A8Xs>", the latest addition to the Phenix tutorials channel at www.youtube.com/c/phenixtutorials. In this full-length lecture, Tom Terwilliger shows how AphaFold models are great hypotheses that can help you jump-start structure determination by X-ray crystallography and Cryo-EM. The talk is from the ReNaFoBis.FRISBI webinar series organized by Jean Cavarelli (https://www.renafobis.fr/seminaires-web-renafobis). Best wishes, The Phenix team -- 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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Staff Scientist opportunity in "Single Molecule Biophysics" at Human Technopole in Milan, Italy
by Sebastiano Pasqualato 20 Jan '22

20 Jan '22

Dear all, another job post from the newly established life science Institute of Milan, Italy, Human Technopole (http://www.humantechnopole.it/en/ <http://www.humantechnopole.org/>) We are looking for a Staff Scientist to establish and manage a Single Molecule Biophysics Platform as a part of an ongoing collaboration with Lumicks. We are looking for persons with proven track record in single-molecule studies, with specific experience with Lumicks optical tweezers (C-trap and M-trap). The successful candidate will work in close collaboration with the Scientists of the Structural Biology Research Centre of Human Technopole (https://humantechnopole.it/en/research-centres/structural-biology/ <https://humantechnopole.it/en/research-centres/structural-biology/>), and their platform will be part of a larger number of research facilities and platforms, such as the Cryo-EM facility (https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/ <https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/>). More details, and how to apply can be found at the following link: https://careers.humantechnopole.it/o/staff-scientist-single-molecule-biophy… <https://careers.humantechnopole.it/o/staff-scientist-single-molecule-biophy…> Please, share this ad to anyone you think might be interested, ciao, Sebastiano PS: sorry for the double posting in different bulletin boards Sebastiano Pasqualato Biophysics Platform Manager

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Structural Biology Cryo-EM TT Asst. Professor at University of Nebraska
by Alex Vecchio 18 Jan '22

18 Jan '22

Dear PhenixBB Community, I would like to bring your attention to a Tenure-track faculty position at the rank of Assistant Professor in the Department of Biochemistry at the University of Nebraska-Lincoln (UNL). We are looking for candidates with research programs studying the structural biology of macromolecules relevant to human health or disease using cryo-EM. UNL has established a state-of-the-art cryo-EM facility that will house a Glacios 200 keV Cryo-TEM equipped with a Falcon 4i detector, a Selectris energy filter, and have capabilities for microED of crystalline samples. The candidate will be part of the Nebraska Center for Integrated Biomolecular Communication (NCIBC), an NIH-funded COBRE center, and have the opportunity to collaborate with other researchers spanning several departments across the UNL. For more information, please read our ad in Science Careers, HERE <https://jobs.sciencecareers.org/job/580579/assistant-professor-structural-b…> . To apply, please visit the UNL Employment Website, HERE <https://employment.unl.edu/postings/76851>. All the best, Alex -- *Alex J. Vecchio, Ph.D.* *Assistant Professor* *University of Nebraska–Lincoln* *Department of Biochemistry* *Center for Integrated Biomolecular Communication* 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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regarding number of unique reflections
by Viney Singh 14 Jan '22

14 Jan '22

Dear all, First of all sorry for the novice question. I *processed* one of my datasets using xds. Since I was not expecting an anomalous signal, I kept Friedel's Law = True. The number of unique reflections I got: *17,000* I used xds_ASCII.HKL after correct.LP and converted it to mtz using Phenix with 10% reflections for Rfree calculations. Now, when I am trying to* refine *the structure in Phenix, the structure is being refined against *32,300* reflections with *3230* reflections for Rfree calculation. Looks like refinement is treating Friedel's pair as two different reflections. When I am trying to upload PDB on rcsb, on the refinement tab, the number of reflections used for refinement and Rfree calculations are shown as 32,300 and 3220 respectively, while in the validation report, no. of reflections used for Rfree calculation are shown as *1700*. I would really appreciate if someone can guide me to resolve this discrepancy. Thanks in advance. Viney

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Staff Scientist opportunity in "Structural Proteomics" at Human Technopole in Milan, Italy
by Sebastiano Pasqualato 14 Jan '22

14 Jan '22

Dear all, the newly established Human Technopole Institute, based in Milan, Italy (http://www.humantechnopole.it/en/ <http://www.humantechnopole.org/>) is looking for a Staff Scientist to manage the Structural Proteomics Facility. We are looking for persons with proven track record in high-resolution MS-based proteomics, with specific experience in cross-linking- (XL) and native- MS. Structural proteomics technologies will be closely integrated with the Science Groups of the Structural Biology Research Centre of Human Technopole (https://humantechnopole.it/en/research-centres/structural-biology/ <https://humantechnopole.it/en/research-centres/structural-biology/>), and will be part of a larger number of research facilities and platforms, such as the Cryo-EM facility (https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/ <https://humantechnopole.it/en/facilities/cryo-electron-microscopy-facility/>) More details, and how to apply can be found at the following link: https://careers.humantechnopole.it/o/staff-scientist-to-manage-a-structural… <https://careers.humantechnopole.it/o/staff-scientist-to-manage-a-structural…> Please, share this ad to anyone you think might be interested, ciao, Sebastiano PS: sorry for the double posting in different bulletin boards Sebastiano Pasqualato Biophysics Platform Manager

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Re: [phenixbb] refinement of an ensemble of structures -> cryoEM variability
by Oliver Clarke 14 Jan '22

14 Jan '22

Hi, Just to add my two cents, I agree this would be really useful for a lot of folks. Analysis of continuously distributed variability is very common these days in cryoEM, and having a way to jointly refine an ensemble of models against a series of maps would be very handy. Cryodrgn, 3D-VA in cryosparc, ManifoldEM, multibody refinement in relion - there are many tools now for generating a series of density maps potentially corresponding to conformational modes, so having the capacity in phenix to refine models against each map would be very helpful. Cheers Oli > > > Message: 1 > Date: Wed, 12 Jan 2022 10:36:27 +0100 > From: vincent Chaptal <vincent.chaptal(a)ibcp.fr> > To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se>, Pavel Afonine > <pafonine(a)lbl.gov> > Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] refinement of an ensemble of structures -> > cryoEM variability > Message-ID: <ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3(a)ibcp.fr> > Content-Type: text/plain; charset="utf-8"; Format="flowed" > > Hi Guillaume, > > thanks for the backup. > It's exactly my feeling also. > > Best > Vincent > > Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?: >> Hi, >> >> I am guessing what we are talking about here are the maps generated by >> cryoSPARC 3D variability analysis. See: Punjani A & Fleet DJ (2021) 3D >> Variability Analysis: Resolving continuous flexibility and discrete >> heterogeneity from single particle cryo-EM.?Journal of Structural >> Biology: 107702 https://doi.org/10.1016/j.jsb.2021.107702 >> >> But this is not the only program that generates series of maps to >> describe continuous heterogeneity from single-particle cryoEM images, >> see also cryoDRGN:?Zhong ED, Bepler T, Berger B & Davis JH (2021) >> CryoDRGN: reconstruction of heterogeneous cryo-EM structures using >> neural networks.?Nature Methods: 1?10 >> https://doi.org/10.1038/s41592-020-01049-4 >> >> Except some ideally rigid particles like apoferritin, pretty much >> everything shows some degree of flexibility that generates continuous >> heterogeneity in cryoEM images. So, my feeling is that a user-friendly >> program to fit a series of models (ideally, auto-generated from a >> single starting model) to a map series is probably going to be a >> standard requirement pretty soon for typical single-particle cryoEM >> projects. >> >> Cheers, >> >> Guillaume >> >> >>> On 11 Jan 2022, at 17:16, Pavel Afonine <pafonine(a)lbl.gov> wrote: >>> >>> Hi Vincent, >>> >>> this looks like a very specialized task that I've never heard of >>> before! We can add a tool to do that if this becomes something that >>> more than one person does more than once. Meanwhile, a simple script >>> in a language of your?preference (python, linux shell, etc) should do >>> the job. I can help with a script if needed, let me know! >>> >>> Also.. just curious -- what is "3D variability of this map"? Is this >>> one map that is a composition of several map or an ensemble of maps? >>> >>> Pavel >>> >>> On 1/11/22 01:48, vincent Chaptal wrote: >>>> Hi Phenix-ers, >>>> >>>> I thought to ask for something that I believe you have already >>>> implemented, but I'm not sure of the best tool to use. >>>> >>>> I have a cryoEM map where I refine my "high resolution" structure. I >>>> also have the 3D variability of this map that shows?several maps >>>> varying around the consensus high-res map. I want to refine an >>>> ensemble (20) of structures, one for every 20?maps around the >>>> consensus map. >>>> Is there a tool in phenix to do this? >>>> >>>> I could refine individually the high-res structure into each map >>>> incrementally; since every map differs a little from the?original >>>> one, Real-space-refinement could move the structure a little at a >>>> time. Then I could combine all the PDBs in an?ensemble? >>>> A tool to refine variability would be very useful. Input could be a >>>> PDB and an ensemble of maps, and output would be all the?PDBs combined? >>>> >>>> Thank you. >>>> >>>> All the best >>>> Vincent >>>> >>>> >>>> -- >>>> Vincent Chaptal, PhD >>>> Director of GdR APPICOM >>>> Drug Resistance and Membrane Proteins Lab >>>> >>>> MMSB -UMR5086 >>>> 7 passage du Vercors >>>> 69007 LYON >>>> FRANCE >>>> +33 4 37 65 29 01 >>>> http://www.appicom.cnrs.fr >>>> http://mmsb.cnrs.fr/en/ >>>> >>>> >>>> >>>> _______________________________________________ >>>> phenixbb mailing list >>>> >>>> phenixbb(a)phenix-online.org >>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>> >>>> Unsubscribe: >>>> phenixbb-leave(a)phenix-online.org >>> _______________________________________________ >>> phenixbb mailing list >>> phenixbb(a)phenix-online.org >>> http://phenix-online.org/mailman/listinfo/phenixbb >>> Unsubscribe: phenixbb-leave(a)phenix-online.org >> >> Page Title >> >> >> >> >> >> >> >> N?r du har kontakt med oss p? Uppsala universitet med e-post s? >> inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om >> hur vi g?r det kan du l?sa h?r: >> http://www.uu.se/om-uu/dataskydd-personuppgifter/ >> >> E-mailing Uppsala University means that we will process your personal >> data. For more information on how this is performed, please read here: >> http://www.uu.se/en/about-uu/data-protection-policy > > -- > > Vincent Chaptal, PhD > > Director of GdR APPICOM > > Drug Resistance and Membrane Proteins Lab > > > MMSB -UMR5086 > > 7 passage du Vercors > > 69007 LYON > > FRANCE > > +33 4 37 65 29 01 > > http://www.appicom.cnrs.fr > > http://mmsb.cnrs.fr/en/ > >

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Re: [phenixbb] refinement of an ensemble of structures -> cryoEM variability
by Oliver Clarke 14 Jan '22

14 Jan '22

I guess it isn't all that different. If you run all jobs naively starting from a single model corresponding to the overall reconstruction, depending on the magnitude of the conformational changes the maps at either end of the series may be outside the radius of convergence of phenix.real_space_refine (with default parameters). Some way to initially perturb a single model to more-or-less match the series of maps would be useful (maybe morphing in real_space_refine will already work for this?). This could probably be scripted, but having it built into phenix would be useful I think. Oli > Date: Thu, 13 Jan 2022 09:26:50 -0800 > From: James Holton <jmholton(a)lbl.gov> > To: phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] refinement of an ensemble of structures -> > cryoEM variability > Message-ID: <92b5f0e3-c4b1-59f9-1c38-50fffcda0bb1(a)lbl.gov> > Content-Type: text/plain; charset=UTF-8; format=flowed > > How is that different from running parallel jobs of n models against n maps? > > On 1/13/2022 8:17 AM, Oliver Clarke wrote: >> Hi, >> >> Just to add my two cents, I agree this would be really useful for a lot of folks. Analysis of continuously distributed variability is very common these days in cryoEM, and having a way to jointly refine an ensemble of models against a series of maps would be very handy. Cryodrgn, 3D-VA in cryosparc, ManifoldEM, multibody refinement in relion - there are many tools now for generating a series of density maps potentially corresponding to conformational modes, so having the capacity in phenix to refine models against each map would be very helpful. >> >> Cheers >> Oli >> >>> >>> Message: 1 >>> Date: Wed, 12 Jan 2022 10:36:27 +0100 >>> From: vincent Chaptal <vincent.chaptal(a)ibcp.fr> >>> To: Guillaume Gaullier <guillaume.gaullier(a)icm.uu.se>, Pavel Afonine >>> <pafonine(a)lbl.gov> >>> Cc: PHENIX user mailing list <phenixbb(a)phenix-online.org> >>> Subject: Re: [phenixbb] refinement of an ensemble of structures -> >>> cryoEM variability >>> Message-ID: <ef1a3a20-a0dc-57b0-fcc3-48a9426ce2c3(a)ibcp.fr> >>> Content-Type: text/plain; charset="utf-8"; Format="flowed" >>> >>> Hi Guillaume, >>> >>> thanks for the backup. >>> It's exactly my feeling also. >>> >>> Best >>> Vincent >>> >>> Le 12/01/2022 ? 10:09, Guillaume Gaullier a ?crit?: >>>> Hi, >>>> >>>> I am guessing what we are talking about here are the maps generated by >>>> cryoSPARC 3D variability analysis. See: Punjani A & Fleet DJ (2021) 3D >>>> Variability Analysis: Resolving continuous flexibility and discrete >>>> heterogeneity from single particle cryo-EM.?Journal of Structural >>>> Biology: 107702 https://doi.org/10.1016/j.jsb.2021.107702 >>>> >>>> But this is not the only program that generates series of maps to >>>> describe continuous heterogeneity from single-particle cryoEM images, >>>> see also cryoDRGN:?Zhong ED, Bepler T, Berger B & Davis JH (2021) >>>> CryoDRGN: reconstruction of heterogeneous cryo-EM structures using >>>> neural networks.?Nature Methods: 1?10 >>>> https://doi.org/10.1038/s41592-020-01049-4 >>>> >>>> Except some ideally rigid particles like apoferritin, pretty much >>>> everything shows some degree of flexibility that generates continuous >>>> heterogeneity in cryoEM images. So, my feeling is that a user-friendly >>>> program to fit a series of models (ideally, auto-generated from a >>>> single starting model) to a map series is probably going to be a >>>> standard requirement pretty soon for typical single-particle cryoEM >>>> projects. >>>> >>>> Cheers, >>>> >>>> Guillaume >>>> >>>> >>>>> On 11 Jan 2022, at 17:16, Pavel Afonine <pafonine(a)lbl.gov> wrote: >>>>> >>>>> Hi Vincent, >>>>> >>>>> this looks like a very specialized task that I've never heard of >>>>> before! We can add a tool to do that if this becomes something that >>>>> more than one person does more than once. Meanwhile, a simple script >>>>> in a language of your?preference (python, linux shell, etc) should do >>>>> the job. I can help with a script if needed, let me know! >>>>> >>>>> Also.. just curious -- what is "3D variability of this map"? Is this >>>>> one map that is a composition of several map or an ensemble of maps? >>>>> >>>>> Pavel >>>>> >>>>> On 1/11/22 01:48, vincent Chaptal wrote: >>>>>> Hi Phenix-ers, >>>>>> >>>>>> I thought to ask for something that I believe you have already >>>>>> implemented, but I'm not sure of the best tool to use. >>>>>> >>>>>> I have a cryoEM map where I refine my "high resolution" structure. I >>>>>> also have the 3D variability of this map that shows?several maps >>>>>> varying around the consensus high-res map. I want to refine an >>>>>> ensemble (20) of structures, one for every 20?maps around the >>>>>> consensus map. >>>>>> Is there a tool in phenix to do this? >>>>>> >>>>>> I could refine individually the high-res structure into each map >>>>>> incrementally; since every map differs a little from the?original >>>>>> one, Real-space-refinement could move the structure a little at a >>>>>> time. Then I could combine all the PDBs in an?ensemble? >>>>>> A tool to refine variability would be very useful. Input could be a >>>>>> PDB and an ensemble of maps, and output would be all the?PDBs combined? >>>>>> >>>>>> Thank you. >>>>>> >>>>>> All the best >>>>>> Vincent >>>>>> >>>>>> >>>>>> -- >>>>>> Vincent Chaptal, PhD >>>>>> Director of GdR APPICOM >>>>>> Drug Resistance and Membrane Proteins Lab >>>>>> >>>>>> MMSB -UMR5086 >>>>>> 7 passage du Vercors >>>>>> 69007 LYON >>>>>> FRANCE >>>>>> +33 4 37 65 29 01 >>>>>> http://www.appicom.cnrs.fr >>>>>> http://mmsb.cnrs.fr/en/ >>>>>> >>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> phenixbb mailing list >>>>>> >>>>>> phenixbb(a)phenix-online.org >>>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>>> >>>>>> Unsubscribe: >>>>>> phenixbb-leave(a)phenix-online.org >>>>> _______________________________________________ >>>>> phenixbb mailing list >>>>> phenixbb(a)phenix-online.org >>>>> http://phenix-online.org/mailman/listinfo/phenixbb >>>>> Unsubscribe: phenixbb-leave(a)phenix-online.org >>>> Page Title >>>> >>>> >>>> >>>> >>>> >>>> >>>> >>>> N?r du har kontakt med oss p? Uppsala universitet med e-post s? >>>> inneb?r det att vi behandlar dina personuppgifter. F?r att l?sa mer om >>>> hur vi g?r det kan du l?sa h?r: >>>> http://www.uu.se/om-uu/dataskydd-personuppgifter/ >>>> >>>> E-mailing Uppsala University means that we will process your personal >>>> data. For more information on how this is performed, please read here: >>>> http://www.uu.se/en/about-uu/data-protection-policy >>> -- >>> >>> Vincent Chaptal, PhD >>> >>> Director of GdR APPICOM >>> >>> Drug Resistance and Membrane Proteins Lab >>> >>> >>> MMSB -UMR5086 >>> >>> 7 passage du Vercors >>> >>> 69007 LYON >>> >>> FRANCE >>> >>> +33 4 37 65 29 01 >>> >>> http://www.appicom.cnrs.fr >>> >>> http://mmsb.cnrs.fr/en/ >>> >>>

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refinement of an ensemble of structures -> cryoEM variability
by vincent Chaptal 12 Jan '22

12 Jan '22

Hi Phenix-ers, I thought to ask for something that I believe you have already implemented, but I'm not sure of the best tool to use. I have a cryoEM map where I refine my "high resolution" structure. I also have the 3D variability of this map that shows several maps varying around the consensus high-res map. I want to refine an ensemble (20) of structures, one for every 20 maps around the consensus map. Is there a tool in phenix to do this? I could refine individually the high-res structure into each map incrementally; since every map differs a little from the original one, Real-space-refinement could move the structure a little at a time. Then I could combine all the PDBs in an ensemble? A tool to refine variability would be very useful. Input could be a PDB and an ensemble of maps, and output would be all the PDBs combined? Thank you. All the best Vincent -- Vincent Chaptal, PhD Director of GdR APPICOM Drug Resistance and Membrane Proteins Lab MMSB -UMR5086 7 passage du Vercors 69007 LYON FRANCE +33 4 37 65 29 01 http://www.appicom.cnrs.fr http://mmsb.cnrs.fr/en/

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Excellent Opportunity for Postdoc in Ion-Channel Structural Biology
by Pramod Kumar 08 Jan '22

08 Jan '22

Dear Structural Biology Scholars, I would like to bring your attention to an excellent opportunity to unravel the structure-function details of ion-channels as a postdoc. The Grosman lab at the University of Illinois at Urbana-Champaign is actively looking to fill a recent opening of NIH-funded postdoctoral position. The laboratory has an excellent record in combining high-resolution electrophysiology, molecular simulations, and structural biology to address fundamental questions about ion-channel mechanisms. Previous experience with the purification of eukaryotic membrane proteins is a plus and structure determination using single-particle cryo-EM is highly preferred. Salary commensurate with the experience level. The University of Illinois Urbana Champaign is an excellent place for research and life with an easy commute, lower-cost housing, easy access to all needs, and a vibrant community with easily accessible cities like Chicago, Indianapolis, St. Louis. Interested individuals should contact Prof. Claudio Grosman ( grosman(a)illinois.edu) with a CV, a 1–2 page description of previous research, and names and contact information of 2–3 references. Students in their final year of Ph.D. training are also welcome to apply. Recent select publications from the Grosman lab are listed below. A complete list of publications from the Grosman lab can be found on Prof. Claudio Grosman’s NCBI bibliography page ( https://www.ncbi.nlm.nih.gov/myncbi/claudio.grosman.1/bibliography/public <https://urldefense.com/v3/__https:/www.ncbi.nlm.nih.gov/myncbi/claudio.gros…> ). *Recent Select Publications * *· Kumar P, Cymes GD, Grosman C. Structure and function at the lipid-protein interface of a pentameric ligand-gated ion channel. Proc. Natl. Acad. Sci. USA. 2021;118(23). * *doi: 10.1073/pnas.2100164118 * *· Cymes GD, Grosman C. Signal transduction through Cys-loop receptors is mediated by the nonspecific bumping of closely apposed domains. Proc. Natl. Acad. Sci. USA. 2021;118(14). doi: 10.1073/pnas.2021016118 * *doi: 10.1038/s41467-021-21680-9 * *· Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C. Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. Proc. Natl. Acad. Sci. USA. 2020;117(3):1788-1798. * *doi: 10.1073/pnas.1906823117 * -- Pramod Kumar, Ph.D.

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use mr_rosetta to prerefine structure
by Wei Wang 08 Jan '22

08 Jan '22

Dear all, I have a question regarding phenix.mr_rosetta. I manually build a model in Coot, and want to use phenix.mr_rosetta to prerefine the model. I followed the instruction on https://phenix-online.org/documentation/reference/mr_rosetta.html#rebuildin…. Basically, my scenario is like what’s written in NOTE 2: “have a model and just want to run pre-refinement and not anything else”. I noticed that if I put nproc=xx, then the job would eventually output no structures. I checked each subjob and found that they all failed. I suspect this behavior was caused by files overwritten by parallel jobs. When I don’t specify nproc, then there’s no problem. However, in this case, for number_of_prerefine_models=1000, it would take a very long time. I hope I described the behavior clearly. Is there a way of running the prerefine jobs in parallel? Thanks, Wei

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Phenix version 1.20 released
by Paul Adams 07 Jan '22

07 Jan '22

The Phenix developers are pleased to announce that version 1.20 of Phenix is now available (build 1.20-4459). Binary installers for Linux, Mac OSX, and Windows platforms, and the source installer, are available at the download site: http://phenix-online.org/download/ Highlights for the 1.20 version of Phenix include a number of tools to leverage new structure prediction methods: - New tools and methods - Phenix AlphaFold2 notebook: Run AlphaFold on Google Colab from Phenix GUI - phenix.process_predicted_model: Identify useful domains in AlphaFold model - phenix.dock_predicted_model: Dock domains of AlphaFold model into cryo-EM - phenix.rebuild_predicted_model: Rebuild AlphaFold model in cryo-EM map using docked domains - phenix.dock_and_rebuild : Process, dock and rebuild AlphaFold model with cryo-EM map - phenix.model_completion: Connect fragments and fill in gaps based on a map - phenix.rebuild_model: Rebuild a model using a map and keeping connectivity - phenix.replace_with_fragments_from_pdb: Rebuild a model using fragments from PDB - phenix.search_and_morph: SSM search PDB; morph to match target - phenix.fragment_search: Search for a fragment in PDB matching target - phenix.reverse_fragment: Reverse chain direction of a fragment - phenix.superpose_and_morph: SSM or least-squares superpose one model on another; optionally trim and morph to match - phenix.voyager.casp_rel_ellg: Calculate relative eLLG score for predicted model quality - phenix.match_maps: - Bug fix (superposed map was not matching target map) - phenix.real_space_refine: - Symmatry multiprocessing aware individual ADP and occupancy refinement - Multiple changes to improce runtime (for certain refinement strategies) - Make NQH flips symmetry aware - phenix.superpose_pdbs: - Add feature to transform additional models with matrix found with moving model - phenix.dock_in_map: - Allow splitting model into domains based on chain ID from phenix.process_predicted_model - Restraints - GeoStd updated with 12k plus entity restraints files - cis-PRO default updated to EH99 - phenix.fetch_pdb, iotbx.cif_as_mtz: - Bug fix: Multiple datasets with different unit cells in a cif file now preserved as multiple crystals in mtz file. Please note that this 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. https://doi.org/10.1107/S2059798319011471 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. The maintenance and distribution of Phenix is funded by the National Institute of General Medical Sciences (NIH) under grant R24-GM141254. We also acknowledge the generous support of the members of the Phenix Industrial Consortium. -- Paul Adams (he/him/his) Associate Laboratory Director for Biosciences, LBL (https://biosciences.lbl.gov/leadership/) Principal Investigator, Computational Crystallography Initiative, LBL (https://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute (http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source (https://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, UC Berkeley (http://bioeng.berkeley.edu) Member of the Graduate Group in Comparative Biochemistry, UC Berkeley (http://compbiochem.berkeley.edu) Building 33, Room 250 Building 978, Room 4126 Building 977, Room 268 Tel: 1-510-486-4225 http://cci.lbl.gov/paul ORCID: 0000-0001-9333-8219 Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Michael Espinosa [ MEEspinosa(a)lbl.gov ] [ 1-510-333-6788 ] Phenix Consortium: Ashley Dawn [ AshleyDawn(a)lbl.gov ][ 1-510-486-5455 ] --

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Postdoc Position at Caltech
by Hoelz, Andre 22 Dec '21

22 Dec '21

The Hoelz laboratory at the California Institute of Technology seeks to recruit an outstanding postdoctoral scientist in structural cell biology. Our laboratory focuses on the structure-function relationships of the nuclear pore complex and associated nucleocytoplasmic transport machinery. This position requires a recent Ph.D. degree in biochemistry/biophysics with a strong background in biochemistry, x-ray crystallography, or cryo-electron microscopy/tomography. The successful applicant should be a highly motivated individual with good organizational, communication, and interpersonal skills. The laboratory is well-funded and equipped with modern biophysical instrumentation. Importantly, Caltech has an exceptional infrastructure for structural biology, including access to a high intensity, completely automated, state-of-the-art crystallography beamline at the Stanford Synchrotron Radiation Lightsource (SSRL), as well as an excellent cryo-electron microscopy facility with access to FEI Arctica and Titan Krios microscopes equipped with Gatan K3 cameras. The position is available immediately and funded for 3+ years. Depending on performance, the position can be extended for additional years. To apply, please send your CV, a statement of research interests, and the names and contact information of at least two references to André Hoelz (hoelz(a)caltech.edu). Selected Recent Publications Bley, C.J., Nie, S., Mobbs, G.W., Petrovic, S., Gres, A.T., Liu, X., Mukherjee, S., Harvey, S., Huber, F.M., Lin, D.H., Brown, B., Tang, A.W., Rundlet, E.J., Correia, A.R., Chen, S., Regmi, S.G., Dasso, M., Patke, A., Palazzo, A.F., Kossiakoff, A.A., Hoelz, A. (2021). BioRxiv (https://doi.org/10.1101/2021.10.26.465790). Petrovic, S., Samanta, D., Perriches, T., Bley, C.J., Thierbach, K., Brown, B., Nie, S., Mobbs, G.W., Liu, X., Hoelz, A. (2021). Architecture of the linker-scaffold in the nuclear pore. BioRxiv (https://doi.org/10.1101/2021.10.26.465796). Lin, D. H., Hoelz, A. (2019). The structure of the nuclear pore complex (an update). Annu. Rev. Biochem. 88, 725-783. Lin, D. H., Correia, A.C., Cai, S.W., Huber, F.M. Jette, C.A., Hoelz, A.* (2018). Structural and functional analysis of mRNA export regulation by the nuclear pore complex. Nat. Commun., 2319. Huber, F., Hoelz, A., (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation, Nat. Commun. 8, 14354. Lin, D., Stuwe, T., Schilbach, S., Rundlet, E.J., Perriches, T., Mobbs, G., Fan, Y., Thierbach, K., Huber, F.M., Collins, L.N., Davenport, A.M., Jeon, Y.E., Hoelz, A. (2016). Architecture of the symmetric core of the nuclear pore, Science 352, aaf1015. [Cover] Stuwe, T., Bley, C.J., Thierbach, K., Petrovic, S., Schilbach, S., Mayo, D.J., Perriches, T., Rundlet, E.J., Jeon, Y.J., Collins, L.N., Huber, F.M., Lin, D.H., Paduch, M., Koide, A., Lu, V., Fischer, J., Hurt, E., Koide, S., Kossiakoff, A., Hoelz, A.* (2015). Architecture of the fungal nuclear pore inner ring complex, Science 350, 56-64. Stuwe, T., Correia, A., Lin, D. H., Paduch, M., Lu, V. T., Kossiakoff, A. A., Hoelz, A.* (2015). Architecture of the nuclear pore complex coat. Science 347, 1148-1152. Hoelz, A., Debler, E.W., Blobel, G. (2011). Structure of the Nuclear Pore Complex, Annu. Rev. Biochem. 80, 613-643.

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Query re individual sites (real space)
by Oliver Clarke 21 Dec '21

21 Dec '21

Hi, While refining an X-ray structure using phenix.refine (v1.20-4444), I get the attached table during real-space refinement of coordinates. What are the criteria for selecting the correct weighting factor? I assumed it would be the delta between R/Rfree and/or the clash score, but it doesn't seem to exactly match either in this table (and the same for other iterations of refinement). Is it just incorrectly writing the clash score in the "Accepted refinement result" line? Shouldn't this match the line from the selected weight (here 0.125 so should be 6.1, not 7.1)? Cheers Oli

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Phenix.metal_coordination not working in 1.20-4444
by Oliver Clarke 21 Dec '21

21 Dec '21

Hi, When I try to run phenix.metal_coordination in v1.20-4444 (as phenix.metal_coordination whatever.pdb), I get the attached error. Traceback (most recent call last): File "/Applications/phenix-1.20-4444/build/../modules/elbow/elbow/command_line/metal_coordination.py", line 50, in <module> from metal_coordination_params import master_phil_string ImportError: No module named metal_coordination_params Cheers Oli

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Re: [phenixbb] sequence file error in phenix map-to-model
by Raja Dey 21 Dec '21

21 Dec '21

Hi Sharan, I am getting the same error saying , 'is not a known sequence type'. Also, please see the image enclosed below that tells how the template sequence file should look like. I tried with/without space after '>' sign and getting the same error message. [image: image.png] Any suggestion from anyone would be appreciated. Thanks, Raja On Mon, Dec 20, 2021 at 3:29 PM Sharan Karade <sharankarade(a)gmail.com> wrote: > Hi Raja, > > Try to use the file attached here. I hope it works. > > On Mon, Dec 20, 2021 at 3:27 PM Raja Dey <rddey80(a)gmail.com> wrote: > >> Sorry, the error message is >> D41-st-Trx-sequence.txt is not a known sequence type. >> >> Can someone help solving this problem? >> >> Best regards, >> Raja >> >> On Mon, Dec 20, 2021 at 12:02 PM Raja Dey <rddey80(a)gmail.com> wrote: >> >>> Hi, >>> I am getting an error with the sequence file attached. Could you please >>> tell me what's wrong with this file? The error is enclosed below: >>> Starting phenix >>> on Mon Dec 20 11:45:46 2021 by rdey >>> >>> =============================================================================== >>> >>> Processing files: >>> >>> ------------------------------------------------------------------------------- >>> >>> Found phil, >>> /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff >>> >>> Processing PHIL parameters: >>> >>> ------------------------------------------------------------------------------- >>> >>> Adding PHIL files: >>> ------------------ >>> >>> /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff >>> >>> Processing files from PHIL: >>> >>> ------------------------------------------------------------------------------- >>> >>> Found real_map, >>> /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc >>> >>> Files not used by program: >>> -------------------------- >>> /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt >>> /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec >>> >>> Final processed PHIL parameters: >>> >>> ------------------------------------------------------------------------------- >>> data_manager { >>> real_map_files = >>> "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" >>> default_real_map = >>> "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" >>> phil_files = >>> "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" >>> default_phil = >>> "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" >>> } >>> input_files { >>> map_file = >>> /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc >>> seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt >>> ncs_file = >>> /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec >>> } >>> reconstruction_symmetry { >>> symmetry = """D2""" >>> } >>> control { >>> nproc = 2 >>> } >>> job_title = """D41-st-Trx-19Dec21""" >>> >>> >>> Starting job >>> >>> =============================================================================== >>> Validating inputs >>> >>> >>> Thanks a lot for your time. >>> Regards, >>> Raja >>> >>> _______________________________________________ >> phenixbb mailing list >> phenixbb(a)phenix-online.org >> http://phenix-online.org/mailman/listinfo/phenixbb >> Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > -- > Sharan Karade > Postdoc-fellow > IBBR-UMD, 9600 Gudelsky Dr, > Rockville > Maryland 20850 > > >

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sequence file error in phenix map-to-model
by Raja Dey 21 Dec '21

21 Dec '21

Hi, I am getting an error with the sequence file attached. Could you please tell me what's wrong with this file? The error is enclosed below: Starting phenix on Mon Dec 20 11:45:46 2021 by rdey =============================================================================== Processing files: ------------------------------------------------------------------------------- Found phil, /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing PHIL parameters: ------------------------------------------------------------------------------- Adding PHIL files: ------------------ /atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff Processing files from PHIL: ------------------------------------------------------------------------------- Found real_map, /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc Files not used by program: -------------------------- /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" default_real_map = "/atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc" phil_files = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" default_phil = "/atavium/home/jfrench/rdey/st_JF/.phenix/project_data/map_to_model_8.eff" } input_files { map_file = /atavium/home/jfrench/rdey/st_JF/cryosparc_P11_J139_008_volume_map_half_A.mrc seq_file = /atavium/home/jfrench/rdey/st_JF/D41-st-Trx-sequence.txt ncs_file = /atavium/home/jfrench/rdey/st_JF/p11_j140_sharpened-map_box.ncs_spec } reconstruction_symmetry { symmetry = """D2""" } control { nproc = 2 } job_title = """D41-st-Trx-19Dec21""" Starting job =============================================================================== Validating inputs Thanks a lot for your time. Regards, Raja

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model shifts after real space refinement
by Ashok Nayak 16 Dec '21

16 Dec '21

Hi, Is there a way to say keep_origin=False in phenix real space refinement. I used it in the command line version of v3958. It didn't take that. There is a model shift after the refinement which I think is because the program brings the map to the origin and hence the refined model as well. Thanks, Ashok -- Post-Doctoral Fellow Department of Biochemistry and Molecular Biology, Sidney Kimmel cancer Center Thomas Jefferson University 1020 Locust Street, JAH Philadelphia, PA, 19107 Phone: 804-661-4620

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Job Opportunities at Surrozen Inc (SFO Bay Area)
by Parthasarathy Sampathkumar 15 Dec '21

15 Dec '21

Dear All, I would like to bring to the attention of suitable candidates the following exciting job opportunities at Surrozen Inc, located in South San Francisco. Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines with a focus on unlocking the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Our vision is to engage the body’s own biological tissue repair mechanisms with our targeted regenerative antibodies, overcoming research and development hurdles that have been previously intractable, and have held back drug development efforts in the promising area of Wnt biology. *Research Associate/Senior Research Associate, Biochemistry and Biophysics:* https://apply.workable.com/surrozen/j/ACBA0B0D96/ *Scientist, Protein Sciences: * https://apply.workable.com/surrozen/j/DF4518083F/ *Research Associate, Protein Purification:* https://apply.workable.com/surrozen/j/7D64A01556/ Many Thanks, Best Wishes, Partha Sampathkumar PhD Principal Scientist Surrozen Inc Email: partha(a)surrozen.com

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NIH-funded Postdoc, Membrane Protein Structural Biology
by Alex Vecchio 14 Dec '21

14 Dec '21

Dear Phenix Community, I would like to bring your attention to an NIH-funded Postdoc position in the Vecchio Lab <https://vecchio-lab.unl.edu> at the University of Nebraska studying membrane proteins and membrane protein assemblies using X-ray crystallography and cryoEM. We are looking for a Ph.D., with experience in membrane proteins and/or crystallography. Potential exists for the candidate to *acquire cryoEM expertise* during the postdoc training via an NSF fellowship. For more information, please read our ad HERE <https://jobrxiv.org/job/vecchio-lab-at-university-of-nebraska-27778-nih-fun…> . To apply or for specific questions, please contact me at avecchio(a)unl.edu. All the best, Alex -- *Alex J. Vecchio, Ph.D.* *Assistant Professor* *University of Nebraska–Lincoln* *Department of Biochemistry* *Center for Integrated Biomolecular Communication* 1901 Vine Street N113 / N114 Beadle Center [Lab / Office] Lincoln, NE 68588 avecchio(a)unl.edu 1 [402] 472-2933

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Ligand CIF file in real space refinement
by Fadini, Alisia 07 Dec '21

07 Dec '21

Hello, I am trying to use phenix.real_space_refine to improve the fit between my protein's ligand and the electron density. I include a CIF file that has worked well for reciprocal space refinement, made through JLigand. It seems to me that the CIF file is read properly, it does not produce errors and the restrains are stated correctly in the output .cif file that includes all protein + ligand atoms. However, the output pdb shows a distorted ligand, where specific bond angles and bond lengths have been modified past what should be allowed by the restrains. Any insights on how to improve/the causes of this effect would be very welcome! My command is : phenix.real_space_refine model.pdb map.ccp4 ligand.cif resolution=1.63 Thank you, Alisia

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phenix installation problem
by princeadam＠163.com 04 Dec '21

04 Dec '21

Dear all I tried to install Phenix on my virtual machine(Ubuntu) in win11. And got the following error message. ========================================================================== Phenix Installation version: 1.19.2-4158 machine type: intel-linux-2.6-x86_64 OS version: 5.11.0-40-generic destination: /usr/local/phenix-1.19.2-4158 # of processors: 1 ========================================================================= Configuring Phenix components... Traceback (most recent call last): File "./bin/install.py", line 245, in <module> installer(sys.argv[1:]).install() File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 200, in install self.install_from_binary() File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 349, in install_from_binary self.reconfigure(log=log) File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/install_distribution.py", line 431, in reconfigure call(args=args, log=log, verbose=self.options.verbose) File "/media/sf_Virtual_Shared_Folder/phenix-installer-1.19.2-4158-intel-linux-2.6-x86_64-centos6/lib/libtbx/auto_build/installer_utils.py", line 55, in call raise RuntimeError("Call to '%s' failed with exit code %d" % (args, rc)) RuntimeError: Call to '/usr/local/phenix-1.19.2-4158/conda_base/bin/python /usr/local/phenix-1.19.2-4158/modules/cctbx_project/libtbx/configure.py --current_working_directory /usr/local/phenix-1.19.2-4158/build --command_version_suffix 1.19.2-4158 phenix phaser solve_resolve labelit dials xia2 iota prime amber_adaptbx --use_conda' failed with exit code 127 I searched phenixbb, and got the similar information from http://www.phenix-online.org/pipermail/phenixbb/2015-November/022456.html It's a pity , that the answer was not suiable for me. I have root access to write to usr/local. And under /usr/local/phenix-1.19.2-4158 , I can see four folders:build, conda_base, doc, modules. Any one has suggestions? all the best Adam

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opportunity for experienced crystallographer
by Mooers, Blaine H.M. (HSC) 30 Nov '21

30 Nov '21

Associate Director of the Laboratory of Biomolecular Structure and Function The Laboratory of Biomolecular Structure and Function (LBSF) at the University of Oklahoma Health Sciences Center (OUHSC) seeks an experienced crystallographer to run the daily operations of the LBSF. The position is at the Assistant Professor of Research level. The candidate will be responsible for working with PIs to advance their structural biology projects. These efforts will include routine technical operations, developing new protocols to overcome challenging problems, and training the staff of user labs in protein purification, crystallization, data collection, and structure determination. The ideal candidate for this position will have a PhD and ten years of experience in macromolecular crystallography. The candidate will not be expected to write grant applications. Pluses in a candidate's background include experience with membrane protein purification and LCP crystallization, experience with Cyro-EM, or experience with other structural biology methods like microED, SAXS, SANS, XAFS, NMR, or XFELS. The LBSF is part of a suite of core labs supported in part by the OUHSC Vice President of Research. The LBSF is also part of the Biomolecular Structure Core (BSC) for the Oklahoma Center of Biomedical Research Excellence in Structural Biology (OCSB), which is based on the main campus in Norman. The BSC has contributed to the awarding of 23 million dollars in grant funding and 33 publications in the past nine years. The OCSB has been the focal point of Oklahoma's structural biology community for nine years. The community includes 50 labs at three major research institutions. The BSC will be a vital part of a new Center for Therapeutic Science. The center will coordinate and foster the drug development pipeline with the BSC playing a central role in structure-based drug design. The LBSF will be working closely with Dr. Matt Hart (https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/hart-matthew-phd-1), Director of the newly established Center for High Throughput Screening. Most of the 12 major users of the LBSF have cancer-related projects. One project led to the 2021 publication of crystal structures of RET Kinase bound to two drug molecules recently approved by the FDA for the treatment of non-small cell lung cancer. Most of the major users are members of the Stephenson Cancer Center, a National Cancer Institute-designated cancer center. The compensation level for this full-time position includes a generous benefits package. The position is based in Oklahoma City -- an affordable place to raise a family. To apply, please submit a cover letter, CV and contact information (name and email) for three references to Blaine Mooers, Director of the Laboratory of Biomolecular Structure and Function at OUHSC, at blaine-mooers at http://ouhsc.edu. The position will remain open until filled. Application review will begin immediately. OUHSC is an equal opportunity employer and is committed to creating a diverse and inclusive environment for all employees. Best regards, Blaine Blaine Mooers, Ph.D. Associate Professor Department of Biochemistry and Molecular Biology, College of Medicine Director of the Laboratory of Biomolecular Structure and Function Academic Director, Biomolecular Structure Core, COBRE in Structural Biology Full Member, Cancer Biology Program, Stephenson Cancer Center University of Oklahoma Health Sciences Center Mailing Address: 975 NE 10th Street, BRC 466 Oklahoma City, OK 73104-5419 Office: 405-271-8300 Lab: 405-271-8312 Websites: Faculty page: https://basicsciences.ouhsc.edu/bmb/Faculty/bio_details/mooers-blaine-hm-phd BSC-OKC (LBSF): https://research.ouhsc.edu/Core-Facilities/Laboratory-of-Biomolecular-Struc… COBRE in Structural Biology: https://www.ou.edu/structuralbiology

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iotbx.merging_statistics on Python 3: too memory consuming
by Martin Malý 30 Nov '21

30 Nov '21

Dear PHENIX & CCTBX developers and users, I tried to calculate merging statistics with CCTBX tools using Python 3. I realized that the memory requirements are much higher comparing with Python 2... I closed all programs firstly so I had just 1.6 GB RAM used of 7.6 GB total RAM. Then I ran these two lines of code in the cctbx.python shell: import iotbx.merging_statistics i_obs = iotbx.merging_statistics.select_data(file_name="XDS_ASCII.HKL", data_labels=None) Python 2.7: The RAM usage went to 4.8 GB and then I was able to calculate merging statistics. Python 3.7: The module import was successful. Then the RAM usage went to total 7.6 GB and then the process was killed by the operating system (CentOS 7). Please, do you have any suggestion how to use this module "more carefully" and save memory? Thank you! Best regards, Martin Malý ----- Upozornění: Není-li v této zprávě výslovně uvedeno jinak, má tato e-mailová zpráva nebo její přílohy pouze informativní charakter. Tato zpráva ani její přílohy v žádném ohledu Biotechnologický ústav AV ČR, v. v. i. k ničemu nezavazují. Text této zprávy nebo jejích příloh není návrhem na uzavření smlouvy, ani přijetím případného návrhu na uzavření smlouvy, ani jiným právním jednáním směřujícím k uzavření jakékoliv smlouvy a nezakládá předsmluvní odpovědnost Biotechnologického ústavu AV ČR, v. v. i. Disclaimer: If not expressly stated otherwise, this e-mail message (including any attached files) is intended purely for informational purposes and does not represent a binding agreement on the part of Institute of Biotechnology of the Czech Academy of Sciences. The text of this message and its attachments cannot be considered as a proposal to conclude a contract, nor the acceptance of a proposal to conclude a contract, nor any other legal act leading to concluding any contract, nor does it create any pre-contractual liability on the part of Institute of Biotechnology of the Czech Academy of Sciences.

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Job vacancy: Institute Research Investigator within the Therapeutics Discovery Division at MD Anderson Cancer Center
by Leonard,Paul G 19 Nov '21

19 Nov '21

Hi, The Structural Chemistry group, within the Therapeutics Discovery Division of MD Anderson Cancer Center is looking for a highly motivated individual with a strong background in structural biology, using X-ray crystallography and/or single particle cryo-EM to determine high resolution structures of proteins and protein complexes. Our mission is to integrate novel biological insights with drug discovery expertise to accelerate the development of innovative, targeted, small-molecule therapeutics for the treatment of cancer or neurodegenerative diseases. Our work is conducted in a team science environment that brings together excellence in both academic and pharmaceutical discovery. The structural chemistry group provides structural biology support for several drug discovery programs in our pipeline, spanning from early stage drug discovery through lead optimization. For a full job description and to submit an application please use the following link... https://jobs.mdanderson.org/search/jobdetails/institute-research-investigat… kind regards, Paul Leonard Senior Institute Research Scientist MD Anderson Cancer Center 1881 East Road Houston TX 77054 USA The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.

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Research Associate position in structural biology at Takeda in San Diego
by L Qin 18 Nov '21

18 Nov '21

Dear PHENIX user mailing list members, The Structural Biology group at Takeda Pharmaceuticals in San Diego California has an open position for a Research Associate. I invite interested candidates to apply through the following link: https://www.takedajobs.com/job/san-diego/research-associate-structural-biol… Please feel free to contact me for further information. Best regards, Ling Ling Qin PhD Structural Biology Takeda Development Center Americas 9625 Towne Centre Dr, San Diego, CA 92121 <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> Virus-free. www.avg.com <http://www.avg.com/email-signature?utm_medium=email&utm_source=link&utm_cam…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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MizzouForward faculty hiring campaign
by Tanner, John J. 18 Nov '21

18 Nov '21

Dear Colleagues: The University of Missouri has initiated a major faculty hiring campaign, called MizzouForward, which intends to hire 150 new faculty members over the next 5 years. Successful candidates must be research leaders with a passion for collaboration and a proven track record of active, external research funding, particularly from federal agencies like NIH. This initiative coincides with the recent grand opening of the NextGen Precision Health research building, which houses a newly upgraded imaging center with a Krios G4 and Aquilos Cryo-FIB. Other investments in structural biology include a share of ALS beamline 4.2.2 and a Bruker 800 MHz NMR with cryoprobe. For more information, please see: https://provost.missouri.edu/mizzou-forward/ -- Jack Tanner (tannerjj(a)missouri.edu<mailto:[email protected]>) and Lesa Beamer (BeamerL(a)missouri.edu<mailto:[email protected]>) Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211

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Low resolution refinement
by Armando Albert 17 Nov '21

17 Nov '21

Dear all, I have got a very promising MR solution at 5A resolution. Can I refine this structure? Any hint would be very much appreciated Armando

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RapiData 2020 applications open
by Smith, Clyde 16 Nov '21

16 Nov '21

Applications are now open for the 2020 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 in sunny California at the Stanford Synchrotron Radiation Lightsource (SSRL) located on the SLAC National Accelerator Laboratory campus in Menlo Park, CA, from March 30 - April 4 2020. Course organizers for 2020 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-2020/ and use the links on the "registration" page to apply for the course. The application deadline is November 10 2019. Successful applicants will be notified shortly thereafter, 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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Thresholding for N/Q/H errors in phenix.refine?
by Nicholas Gao 16 Nov '21

16 Nov '21

Hi, For the correction of N/Q/H errors in phenix.refine: is this option binary (that is, can it only be turned on or off)? Or can it be adjusted to be on but its stringency adjusted to an arbitrary scale? https://phenix-online.org/documentation/reference/refinement.html#id19 <--suggests its binary, but asking here for thoroughness. Sincerely, Nicholas Gao

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superpose mrc maps (and also mtz files)
by Georg Mlynek 16 Nov '21

16 Nov '21

Dear Scientific community, I got a few .mrc maps from collaborators. Is there a way in phenix to superpose models and corresponding mrc maps. Using superpose maps I get the error:" This file format CCP4 map is not supported as input for this field; only files of type 'Reflections' are allowed. Also the program Structure comparison does not recognize .mrc files. On top there are also a few mtz files I would like to superpose on the .mrc files. Many thanks, br Georg.

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Phenix bug report [[email protected] - Mon Jun 22 19:42:79 2021]
by Robert Munoz 16 Nov '21

16 Nov '21

User name: Robert Munoz E-mail address: robertm(a)lbl.gov Version: 1.18.2-3874 Platform: mac-intel-osx-x86_64 Comments: Trying to refinement using locscale out map Traceback: RuntimeError : cctbx Internal Error: /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/cctbx/maptbx/resolution.h(38): CCTBX_ASSERT(sum_all != 0.) failure. Traceback: File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 181, in run return_value = self.target() File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/libtbx/runtime_utils.py", line 76, in __call__ result = self.run() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 908, in run self.result = run(args=self.args, validated=True, log=sys.stdout) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 581, in __init__ self.caller(func = self.initialize, prefix="Initialize") File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 619, in caller status = func(prefix=prefix, **kwargs) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 696, in initialize self.inputs = self.process_inputs() File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 675, in process_inputs return process_inputs_stage_1(process_inputs_stage_0_object=pis_0, log=self.log) File "/Applications/phenix-1.18.2-3874/modules/phenix/phenix/command_line/real_space_refine.py", line 403, in process_inputs_stage_1 crystal_symmetry = model.crystal_symmetry()).result.d99 File "/Applications/phenix-1.18.2-3874/modules/cctbx_project/cctbx/maptbx/__init__.py", line 117, in __init__ d_max = self.d_max) Platform info: __FILE__ = /Users/builder/slave/phenix-nightly-mac-intel-osx-x86_64/modules/cctbx_project/boost_adaptbx/meta_ext.cpp __DATE__ = May 17 2020 __TIME__ = 22:35:27 __TIMESTAMP__ = Thu Feb 27 10:57:04 2020 __x86_64__ __APPLE_CC__ = 6000 __GNUC__ = 4 __GNUC_MINOR__ = 2 __GNUC_PATCHLEVEL__ = 1 __clang__ __clang_major__ = 11 __clang_minor__ = 0 __clang_patchlevel__ = 0 __clang_version__ = 11.0.0 (clang-1100.0.33.17) __llvm__ __GXX_WEAK__ = 1 __LP64__ = 1 __VERSION__ = 4.2.1 Compatible Apple LLVM 11.0.0 (clang-1100.0.33.17) FE_INEXACT = 32 FE_DIVBYZERO = 4 FE_UNDERFLOW = 16 FE_OVERFLOW = 8 FE_INVALID = 1 FE_ALL_EXCEPT = 63 __SSE2__ = 1 BOOST_LIB_VERSION = 1_63 PY_VERSION = 2.7.15 PYTHON_API_VERSION = 1013 sizeof(bool) = 1 sizeof(short) = 2 sizeof(int) = 4 sizeof(long) = 8 sizeof(std::size_t) = 8 sizeof(void*) = 8 sizeof(long long) = 8 sizeof(float) = 4 sizeof(double) = 8 sizeof(long double) = 16 sizeof(boost::int32_t) = 4 sizeof(boost::uint32_t) = 4 sizeof(wchar_t) = 4 __PTRDIFF_TYPE__ Py_USING_UNICODE sizeof(PY_UNICODE_TYPE) = 2 BOOST_ADAPTBX_TYPE_ID_SIZE_T_EQ_UNSIGNED_LONG boost/TAG: None os.name: posix sys.platform: darwin sys.byteorder: little platform.platform(): Darwin-17.7.0-x86_64-i386-64bit platform.architecture(): ('64bit', '') floating_point_exceptions.division_by_zero_trapped: False floating_point_exceptions.invalid_trapped: False floating_point_exceptions.overflow_trapped: False number of processors: 4 Memory total: 17,179,869,184 Memory free: unknown import thread: OK "hello" = ['h', 'e', 'l', 'l', 'o'] u"hello" = ['h', '\x00', 'e', '\x00', 'l', '\x00', 'l', '\x00', 'o', '\x00'] u"\u00C5" = ['\xc5', '\x00'] as utf-8 = ['\xc3', '\x85'] LATIN CAPITAL LETTER A WITH RING ABOVE = Å

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Double difference anomalous maps
by Mark Saper 10 Nov '21

10 Nov '21

I tried the "Isomorphous difference map” action and specified a file for input 1 containing F1+, F1– at one wavelength, and the file input 2 containing F2+,F2– at another wavelength. I selected the appropriate Labels for the columns containing the anomalous data. I then specified in "Advanced Options” to use anomalous differences instead of amplitudes. Will this procedure use the following coefficients for the difference Fourier? ( F1(+) – F1(–) ) – ( F2(+) – F2(–) ), alpha(calc) Can someone confirm if this is indeed what is calculated? Many thanks, Mark Saper __________________ Mark A. Saper, Ph.D. Visiting Professor at the Faculty of Medicine Hebrew University of Jerusalem Ein Kerem Jerusalem ISRAEL saper(a)umich.edu mobile +972 52 815-0480‬ Powered by Mailbutler <https://www.mailbutler.io/?utm_source=watermark&utm_medium=email&utm_campai…>, the email extension that does it all

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Parameters in "reference_model" during "real space refinement"
by Coudray, Nicolas 09 Nov '21

09 Nov '21

Hi, I would be interested in understanding more the exact meaning of the options related to "reference model" when doing "real space refinement" (in https://phenix-online.org/documentation/reference/real_space_refine.html): * hydrogens = False * main_chain = True * side_chain = True * fix_outliers = True * strict_rotamer_matching = False * auto_shutoff_for_ncs = False * secondary_structure_only = False It is a bit unclear what setting each of them to "True" would exactly imply or what the difference between them are. Does anyone have more information? Thanks, Best, Nicolas ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================

2 2

eLBOW crashes Phenix
by Xavier Brazzolotto 04 Nov '21

04 Nov '21

Hi, I am using the latest stable Phenix release (1.19.2-4158) on macOS (v12.0.1) and I do have an odd bug with Phenix eLBOW. The program by it self runs and generates the expected cif files. If I open REEL to check the models, I do see them but as soon as I exit REEL, it crashes the whole Phenix process. Is it a know bug ? I paste the crash report below if this helps. ------------------------------------- Translated Report (Full Report Below) ------------------------------------- Process: python [57745] Path: /Applications/phenix-1.19.2-4158/*/python.app/Contents/MacOS/python Identifier: com.continuum.python Version: ??? Code Type: X86-64 (Native) Parent Process: launchd [1] User ID: 501 Date/Time: 2021-11-03 18:05:27.1449 +0100 OS Version: macOS 12.0.1 (21A559) Report Version: 12 Bridge OS Version: 6.0 (19P548) Anonymous UUID: 461A1FA5-1FFE-CC49-2057-0C0BB25A7143 Sleep/Wake UUID: 335CBE5C-1D37-4713-B3EA-80B0E830794F Time Awake Since Boot: 300000 seconds Time Since Wake: 13706 seconds System Integrity Protection: enabled Crashed Thread: 0 Dispatch queue: com.apple.main-thread Exception Type: EXC_BAD_ACCESS (SIGSEGV) Exception Codes: KERN_INVALID_ADDRESS at 0x0000000000000020 Exception Codes: 0x0000000000000001, 0x0000000000000020 Exception Note: EXC_CORPSE_NOTIFY Termination Reason: Namespace SIGNAL, Code 11 Segmentation fault: 11 Terminating Process: exc handler [57745] VM Region Info: 0x20 is not in any region. Bytes before following region: 4480602080 REGION TYPE START - END [ VSIZE] PRT/MAX SHRMOD REGION DETAIL UNUSED SPACE AT START ---> __TEXT 10b109000-10b10a000 [ 4K] r-x/rwx SM=COW .../MacOS/python Thread 0 Crashed:: Dispatch queue: com.apple.main-thread 0 libobjc.A.dylib 0x7ff81e00bc4f objc_release + 31 1 Foundation 0x7ff81f1ecde8 empty + 58 2 Foundation 0x7ff81f094dd9 dealloc + 38 3 Foundation 0x7ff81f094d64 -[NSConcreteMapTable dealloc] + 54 4 libobjc.A.dylib 0x7ff81e0290fe objc_object::sidetable_release(bool, bool) + 232 5 AppKit 0x7ff8212d8c4c ___NSTouchBarFinderSetNeedsUpdateOnMain_block_invoke_2 + 2233 6 AppKit 0x7ff820d3130c NSDisplayCycleObserverInvoke + 155 7 AppKit 0x7ff820d30e97 NSDisplayCycleFlush + 952 8 QuartzCore 0x7ff8252a5434 CA::Transaction::run_commit_handlers(CATransactionPhase) + 98 9 QuartzCore 0x7ff8252a41b2 CA::Transaction::commit() + 376 10 AppKit 0x7ff820dd24e2 __62+[CATransaction(NSCATransaction) NS_setFlushesWithDisplayLink]_block_invoke + 285 11 AppKit 0x7ff821518724 ___NSRunLoopObserverCreateWithHandler_block_invoke + 41 12 CoreFoundation 0x7ff81e23bc07 __CFRUNLOOP_IS_CALLING_OUT_TO_AN_OBSERVER_CALLBACK_FUNCTION__ + 23 13 CoreFoundation 0x7ff81e23baa4 __CFRunLoopDoObservers + 543 14 CoreFoundation 0x7ff81e23af37 __CFRunLoopRun + 841 15 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 16 HIToolbox 0x7ff826e583e1 RunCurrentEventLoopInMode + 292 17 HIToolbox 0x7ff826e58008 ReceiveNextEventCommon + 284 18 HIToolbox 0x7ff826e57ed5 _BlockUntilNextEventMatchingListInModeWithFilter + 70 19 AppKit 0x7ff820c658f0 _DPSNextEvent + 886 20 AppKit 0x7ff820c63f5c -[NSApplication(NSEvent) _nextEventMatchingEventMask:untilDate:inMode:dequeue:] + 1411 21 AppKit 0x7ff820c56359 -[NSApplication run] + 586 22 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d2b0a23 wxGUIEventLoop::OSXDoRun() + 115 23 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d192ce4 wxCFEventLoop::DoRun() + 52 24 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d0c2885 wxEventLoopBase::Run() + 165 25 libwx_osx_cocoau-3.0.0.2.0.dylib 0x10d087521 wxAppConsoleBase::MainLoop() + 209 26 _core_.so 0x10bd94114 wxPyApp::MainLoop() + 84 27 _core_.so 0x10bdf7902 _wrap_PyApp_MainLoop(_object*, _object*) + 82 28 libpython2.7.dylib 0x10b4967ee PyEval_EvalFrameEx + 30382 29 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 30 libpython2.7.dylib 0x10b409a84 function_call + 388 31 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 32 libpython2.7.dylib 0x10b3ee5d4 instancemethod_call + 180 33 libpython2.7.dylib 0x10b3dcce1 PyObject_Call + 97 34 libpython2.7.dylib 0x10b4957b6 PyEval_EvalFrameEx + 26230 35 libpython2.7.dylib 0x10b49c631 fast_function + 337 36 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 37 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 38 libpython2.7.dylib 0x10b49c54a fast_function + 106 39 libpython2.7.dylib 0x10b495889 PyEval_EvalFrameEx + 26441 40 libpython2.7.dylib 0x10b48eeb3 PyEval_EvalCodeEx + 2147 41 libpython2.7.dylib 0x10b48e642 PyEval_EvalCode + 34 42 libpython2.7.dylib 0x10b4c0901 PyRun_FileExFlags + 161 43 libpython2.7.dylib 0x10b4c035f PyRun_SimpleFileExFlags + 847 44 libpython2.7.dylib 0x10b4d8dfb Py_Main + 3483 45 dyld 0x11609f4fe start + 462 Thread 1:: com.apple.NSEventThread 0 libsystem_kernel.dylib 0x7ff81e138aba mach_msg_trap + 10 1 libsystem_kernel.dylib 0x7ff81e138e2b mach_msg + 59 2 CoreFoundation 0x7ff81e23ca42 __CFRunLoopServiceMachPort + 319 3 CoreFoundation 0x7ff81e23b11b __CFRunLoopRun + 1325 4 CoreFoundation 0x7ff81e23a52d CFRunLoopRunSpecific + 563 5 AppKit 0x7ff820dd3cec _NSEventThread + 132 6 libsystem_pthread.dylib 0x7ff81e175514 _pthread_start + 125 7 libsystem_pthread.dylib 0x7ff81e17102f thread_start + 15 Thread 2: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 3: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 4:: Dispatch queue: com.apple.NSXPCConnection.user.endpoint.NSRemoteView.IMKTextInputFunctionRowItemServiceViewController 0 CoreFoundation 0x7ff81e1c5746 CFHash + 134 1 CoreFoundation 0x7ff81e1e49fb CFBasicHashAddValue + 223 2 CoreFoundation 0x7ff81e22e09c CFSetCreate + 66 3 CoreFoundation 0x7ff81e223179 CFRunLoopPerformBlock + 288 4 ViewBridge 0x7ff82572020d deferBlockOntoMainThread + 280 5 ViewBridge 0x7ff82572d4d5 deferNSXPCInvocationOntoMainThread + 130 6 Foundation 0x7ff81f0acc12 -[NSXPCConnection _decodeAndInvokeMessageWithEvent:flags:] + 1576 7 Foundation 0x7ff81f063f1a message_handler + 206 8 libxpc.dylib 0x7ff81deba530 _xpc_connection_call_event_handler + 56 9 libxpc.dylib 0x7ff81deb928c _xpc_connection_mach_event + 1387 10 libdispatch.dylib 0x7ff81dfbed63 _dispatch_client_callout4 + 9 11 libdispatch.dylib 0x7ff81dfd78b7 _dispatch_mach_msg_invoke + 452 12 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 13 libdispatch.dylib 0x7ff81dfd83fb _dispatch_mach_invoke + 484 14 libdispatch.dylib 0x7ff81dfc4b85 _dispatch_lane_serial_drain + 335 15 libdispatch.dylib 0x7ff81dfc57c8 _dispatch_lane_invoke + 366 16 libdispatch.dylib 0x7ff81dfcf7e1 _dispatch_workloop_worker_thread + 758 17 libsystem_pthread.dylib 0x7ff81e17208f _pthread_wqthread + 326 18 libsystem_pthread.dylib 0x7ff81e17101b start_wqthread + 15 Thread 5: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 6: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 7: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 8: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 9: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 10: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 11: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 12: 0 libsystem_pthread.dylib 0x7ff81e17100c start_wqthread + 0 Thread 0 crashed with X86 Thread State (64-bit): rax: 0x6000000000000000 rbx: 0x0000000000000018 rcx: 0x0000000000000000 rdx: 0x00007f8ec5973a00 rdi: 0x00007f8ea57830d0 rsi: 0x0000000000000000 rbp: 0x00007ff7b4df3260 rsp: 0x00007ff7b4df3238 r8: 0x0000000000000200 r9: 0x00007f8ec5972d20 r10: 0x00007ff85f8105d0 r11: 0x00007ff81f094d2e r12: 0x00007f8f01f8e7c0 r13: 0x00007ff85f966a01 r14: 0x00007f8f01f8e7c8 r15: 0x000000000000000d rip: 0x00007ff81e00bc4f rfl: 0x0000000000010246 cr2: 0x0000000000000020 Logical CPU: 0 Error Code: 0x00000004 (no mapping for user data read) Trap Number: 14 Thread 0 instruction stream: 34 48 89 c2 48 01 ca 72-12 f0 48 0f b1 17 74 25 4H..H..r..H...t% a8 01 75 e4 31 f6 e9 7c-d7 01 00 31 f6 e9 eb 86 ..u.1..|...1.... 00 00 48 b9 f8 ff ff ff-ff 7f 00 00 48 21 c8 f6 ..H.........H!.. 40 1c 01 74 df 48 89 f8-c3 90 90 90 90 90 90 90 @..t.H.......... 90 48 85 ff 74 76 89 f8-83 e0 01 48 85 c0 75 6c .H..tv.....H..ul 48 8b 07 48 b9 f8 ff ff-ff ff 7f 00 00 48 21 c1 H..H.........H!. [48]8b 51 20 f6 c2 04 74-54 a8 01 74 6f 48 b9 00 H.Q ...tT..toH.. <== 00 00 00 00 00 80 00 48-ba 00 00 00 00 00 00 00 .......H........ 01 48 39 c8 72 36 48 89-c6 48 29 d6 72 17 f0 48 .H9.r6H..H).r..H 0f b1 37 74 22 a8 01 75-e8 31 f6 ba 01 00 00 00 ..7t"..u.1...... e9 82 d3 01 00 48 85 c8-75 3a 48 8b 35 18 f5 99 .....H..u:H.5... 41 ff 25 f2 d2 e6 3f 48-39 ce 72 ee c3 f6 c2 02 A.%...?H9.r..... 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(*) <00000000-0000-0000-0000-000000000000> ??? External Modification Summary: Calls made by other processes targeting this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by this process: task_for_pid: 0 thread_create: 0 thread_set_state: 0 Calls made by all processes on this machine: task_for_pid: 0 thread_create: 0 thread_set_state: 0 VM Region Summary: ReadOnly portion of Libraries: Total=1.2G resident=0K(0%) swapped_out_or_unallocated=1.2G(100%) Writable regions: Total=2.6G written=0K(0%) resident=0K(0%) swapped_out=0K(0%) unallocated=2.6G(100%) VIRTUAL REGION REGION TYPE SIZE COUNT (non-coalesced) =========== ======= ======= Accelerate framework 896K 7 Activity Tracing 256K 1 CG backing stores 2528K 4 CG image 1596K 41 CG raster data 184K 21 ColorSync 228K 26 CoreAnimation 139.5M 206 CoreGraphics 12K 2 CoreImage 608K 35 CoreUI image data 2480K 21 Foundation 80K 2 Kernel Alloc Once 8K 1 MALLOC 511.7M 149 MALLOC guard page 48K 9 MALLOC_MEDIUM (reserved) 880.0M 8 reserved VM address space (unallocated) MALLOC_NANO (reserved) 384.0M 1 reserved VM address space (unallocated) STACK GUARD 56.0M 13 Stack 14.1M 13 VM_ALLOCATE 1128K 27 VM_ALLOCATE (reserved) 768.0M 1 reserved VM address space (unallocated) __DATA 41.4M 510 __DATA_CONST 23.2M 234 __DATA_DIRTY 969K 139 __FONT_DATA 4K 1 __GLSLBUILTINS 5176K 1 __LINKEDIT 682.2M 110 __OBJC_RO 81.5M 1 __OBJC_RW 3120K 2 __TEXT 529.9M 498 __UNICODE 588K 1 dyld private memory 3072K 3 mapped file 158.3M 26 shared memory 1296K 19 =========== ======= ======= TOTAL 4.2G 2133 TOTAL, minus reserved VM space 2.2G 2133 ----------- Full Report ----------- {"app_name":"python","timestamp":"2021-11-03 18:05:27.00 +0100","app_version":"","slice_uuid":"41b01d14-4c6e-3a14-a84e-812c0ee8d9cd","build_version":"","platform":1,"bundleID":"com.continuum.python","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 12.0.1 (21A559)","incident_id":"3B71C390-9A85-4125-A53A-7058CF9E1361","name":"python"} { "uptime" : 300000, "procLaunch" : "2021-11-03 18:04:29.4653 +0100", "procRole" : "Foreground", "version" : 2, "userID" : 501, "deployVersion" : 210, "modelCode" : "MacBookPro15,1", "procStartAbsTime" : 303473294854732, "coalitionID" : 1512, "osVersion" : { "train" : "macOS 12.0.1", "build" : "21A559", "releaseType" : "User" }, "captureTime" : "2021-11-03 18:05:27.1449 +0100", "incident" : "3B71C390-9A85-4125-A53A-7058CF9E1361", "bug_type" : "309", "pid" : 57745, "procExitAbsTime" : 303530973462636, "cpuType" : "X86-64", "procName" : "python", "procPath" : "\/Applications\/phenix-1.19.2-4158\/*\/python.app\/Contents\/MacOS\/python", "bundleInfo" : {"CFBundleIdentifier":"com.continuum.python"}, "storeInfo" : {"deviceIdentifierForVendor":"4FD8A66E-22D2-5A3D-904B-4E69B0B05DAE","thirdParty":true}, "parentProc" : "launchd", "parentPid" : 1, "coalitionName" : "org.pythonmac.unspecified.phenix-1.19.2-4158", "crashReporterKey" : "461A1FA5-1FFE-CC49-2057-0C0BB25A7143", "responsiblePid" : 57744, "wakeTime" : 13706, "bridgeVersion" : {"build":"19P548","train":"6.0"}, "sleepWakeUUID" : "335CBE5C-1D37-4713-B3EA-80B0E830794F", "sip" : "enabled", "vmRegionInfo" : "0x20 is not in any region. Bytes before following region: 4480602080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b109000-10b10a000 [ 4K] r-x\/rwx SM=COW ...\/MacOS\/python", "isCorpse" : 1, "exception" : {"codes":"0x0000000000000001, 0x0000000000000020","rawCodes":[1,32],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000000000000020"}, "termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"exc handler","byPid":57745}, "vmregioninfo" : "0x20 is not in any region. Bytes before following region: 4480602080\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n UNUSED SPACE AT START\n---> \n __TEXT 10b109000-10b10a000 [ 4K] r-x\/rwx SM=COW ...\/MacOS\/python", "extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0}, "faultingThread" : 0, "threads" : 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Phenix 1.20 release candidates
by Billy Poon 03 Nov '21

03 Nov '21

Hi everyone, We are doing a final Python 2.7 release of Phenix and the first release candidate is available from https://phenix-online.org/download/nightly_builds.cgi This release will contain several new features, such as tools for using AlphaFold models. The release after that is planned to be in Python 3.7. 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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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 28 Oct '21

28 Oct '21

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 11 DEC 2021. Please consider writing an article of general interest to the community. 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 is attached to this email. 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 ORCID : orcid.org/0000-0001-8857-9464

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Re: [phenixbb] Restricting real-space refinement and weights to specific atom selections
by Josh Cofsky 20 Oct '21

20 Oct '21

Thanks for that suggestion, Phil. After several weeks, I've finally found solid answers to all my questions, which I'll write here in case anyone reading this message is curious: Q1: Is there any way to apply different map weights to different pieces of the structure during refinement? A1: Pavel tells me the answer is no—this feature is not available in Phenix yet. The way I was able to accomplish something to a similar effect was by performing full-model refinements at different weights. Then, in a final refinement job, use torsion restraints from each of those output models (as reference models) across the desired stretches of residues. Clunky, but it solved a few problems for me. Q2: How is the generic "weight" parameter at the bottom of the Phenix GUI applied to the refinement? A2: The target function is T = Tmap * weight + Trestraints. At the time of writing this message, there is a typo in the Phenix Real-Space Refine documentation, which incorrectly reports the target function as "T = Tmap + weight * Trestraints" (Pavel confirmed). Q3: Why is the PDB validation telling me I have geometric issues that were not acknowledged by Phenix? A3: Phil is right. The ESD for several nucleic acid bond lengths and angles is wide as compared to the sigma tolerated by wwPDB. To fix this, I went into the CIF files within the geostd folder and made the following changes to the troublesome RNA and DNA nucleotide files: *data_AD.cif, data_TD.cif, data_CD.cif, data_GD.cif:* length: C1'-N1, ESD=0.020 C3'-O3', ESD=0.020 angles: O4'-C1'-N9/N1, ESD=0.30 *data_U.cif* angles: C5-C6-N1, ESD=0.5 C6-N1-C2, ESD=0.5 *data_C.cif* angles: C6-N1-C2, ESD=0.5 *data_A.cif* angles: N7-C8-N9, ESD=0.5 Best, Josh On Mon, Sep 13, 2021 at 7:23 AM Philip D. Jeffrey <pjeffrey(a)princeton.edu> wrote: > :: most of the outliers are not acknowledged as such (by Phenix), and I > only become > :: aware of them when the wwPDB validation tells me they are there. > > Check that the equilibrium values that PDB are using and the ones that > Phenix are using are the same. If they're not (or if the sigmas are way > different) you're not going to be able to change the outcome just by > changing weights. > > Phil Jeffrey > Princeton > > ------------------------------ > *From:* phenixbb-bounces(a)phenix-online.org < > phenixbb-bounces(a)phenix-online.org> on behalf of Josh Cofsky < > josh.cofsky(a)gmail.com> > *Sent:* Sunday, September 12, 2021 9:42 PM > *To:* phenixbb(a)phenix-online.org <phenixbb(a)phenix-online.org> > *Subject:* Re: [phenixbb] Restricting real-space refinement and weights > to specific atom selections > > I now realize that I am confused as to what the mentioned "weight" > parameter refers to. The Phenix RSR documentation contains a line that > reads "T = Tmap + weight * Trestraints"—if I'm understanding correctly > (?), this means a larger "weight" value should yield greater conformity to > geometric restraints at the expense of model/map fit. In reality, I observe > the opposite trend in my refinements (which is why I assumed it was a "map > weight"). Can someone clarify what "weight" (Refinement Settings > "Other > Options") refers to? > > The reason I am exploring these questions is that Phenix RSR is > introducing bond angle outliers into a low-resolution area of a DNA > molecule in my model—most of the outliers are not acknowledged as such (by > Phenix), and I only become aware of them when the wwPDB validation tells me > they are there. I assumed this was the result of overfitting to the map > because setting "weight" to 0.0 prevented these outliers from appearing, > but at the expense of map-model fit in the remainder of the structure > (which is why I wanted to apply different weights to different segments of > the model). > > Thanks, > Josh > > On Sun, Sep 12, 2021 at 12:21 PM Josh Cofsky <josh.cofsky(a)gmail.com> > wrote: > > Hi all, > > I'm using phenix.real_space_refine to refine a model into a cryo-EM map. > My local map resolution is highly variable across the molecule, and using a > single map weight (the parameter shown in the Refinement Settings > "Other > Options" in the GUI) on the whole model leads to poor map-to-model fit in > some locations and overfitting in others. Potential solutions could be to: > 1. assign different map weights to different segments of the model (based > on a user-specified atom selection) > OR > 2. perform iterative refinements with different weight settings, holding > different (user-specified) segments of the model fixed during each > iteration (I suspect this isn't possible based on Pavel's message here: > http://phenix-online.org/pipermail/phenixbb/2021-May/025037.html) > > Is either of these approaches (or another one that accomplishes the same > goal) possible? I am using the Phenix GUI, but if this is only possible in > command line, and you're willing to share an example command that > accomplishes either of these tasks, please let me know. > > Thanks! > -Josh > > (also, apologies if this is a duplicate message...still trying to figure > out the phenixbb listserv) > >

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Job opening: Scientist/Sr. Scientist, Structural Biology at Plexxikon Inc, South San Francisco, CA, USA
by Ying Zhang 16 Oct '21

16 Oct '21

Dear all, This post is to bring your attention to a job opportunity of a scientist/Sr. Sicentist position at Plexxikon Inc. We are looking for a highly motivated, structural biologist with expertise in crystallography. Plexxikon (https://www.plexxikon.com/) is located in South San Francisco at CA, USA. We only consider candidates based in US. This Scientist will be a critical member of the Structural Chemistry team. This is an exceptional opportunity to gain experience in structure-guided drug discovery in a successful biotech company. Plexxikon utilizes its proprietary discovery platform to successfully develop a portfolio of competitively differentiated clinical and preclinical stage compounds in a number of therapeutic areas, including two marketed drug. Zelboraf(tm) (vemurafenib) was the first precision medicine to be approved for the treatment of BRAF-mutant metastatic melanoma; Turalio(tm) (pexidartinib) was the first FDA-approved therapy for tenosynovial giant cell tumor. You can find details about this position at https://careers.jobscore.com/careers/plexxikon/jobs/scientist-structural-bi… Please apply through the link. Best Regards, Ying Zhang, Ph.D Sr Director, Research Planning Plexxikon Inc

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