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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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