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Phenix.refine question
by lbetts0508 18 Mar '22

18 Mar '22

I am refining a small protein crystal model with 1.3 A data, there is a Tyrosine that won't stay put where it looks to me it should go (see below in it's original position, in the negative density; I moved the ring into the positive Fo-Fc density). After I move it into the positive density, save the coordinates, and do another refinement with the new coordinates, I find it right back in the negative density, even if I only refine ADP or OCC. Is there some trivial reason this is happening, or can I tell it to not refine that residue? https://docs.google.com/document/d/1RkZSH312q2Pimxb9gKLjibm1XbpsVpyzmrX4wGx… THanks Laurie Betts

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Postdoctoral position in the MRC Laboratory of Molecular Biology
by Roger Williams - MRC LMB 16 Mar '22

16 Mar '22

Our group has an opening for a postdoctoral fellow to be funded on a Cancer Research UK programme aimed at understanding lysosomal control of cell proliferation and stress responses in cancer cells. The programme involves cryo-electron microscopy, X-ray crystallography, H/D exchange mass spectrometry, molecular dynamics as well as other biophysical and biochemical approaches. The post will focus on the reconstitution of large signalling assemblies that detect nutritional and stress signals on and off membranes. The candidate will join a vibrant team of researchers investigating structures, regulation, kinetics and dynamics of phosphoinositide 3-kinase family members reconstituted with their regulators on membrane surfaces. This programme concerns regulation of the lipid kinase VPS34 and protein kinase mTOR and ATM-containing complexes. The research combines biochemical, biophysical and cell biological methods with structural approaches. This is a unique opportunity to play a major role in exciting programme, introduce new ideas, and disseminate research results, while working in a collaborative and supportive environment. The position is available immediately, with an application closing date of 11 April 2022. For more details, please see https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-rog… <https://www.nature.com/naturecareers/job/postdoctoral-scientist-pnac-dr-rog…> Please contact Roger Williams at rlw(a)mrc-lmb.cam.ac.uk <mailto:[email protected]>, if you have any questions. Dr. Roger Williams, FMedSci, FRS rlw(a)mrc-lmb.cam.ac.uk MRC Laboratory of Molecular Biology Francis Crick Avenue Cambridge CB2 0QH UK Phone: +44 1223 267094

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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 08 Mar '22

08 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 02 Mar '22

02 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 02 Mar '22

02 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 25 Feb '22

25 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 02 Feb '22

02 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 22 Jan '22

22 Jan '22

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

22 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 22 Jan '22

22 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 17 Jan '22

17 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 13 Jan '22

13 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 13 Jan '22

13 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 07 Jan '22

07 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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