- phenixbb - phenix-online.org

Submission Deadline on December 14th
by Tessa Van Grack 07 Dec '20

07 Dec '20

Hi PHENIX community, The AIMS Awards Fall 2020 application deadline is just one week away! For anyone with a protein target of interest, the AIMS Award program can help you discover new molecular tools, start new drug development programs, and get published. We encourage investigators, postdocs, and graduate students worldwide to apply. The AIMS Awards program provides non-profit researchers with virtual screening and compounds for physical testing at no cost. Collaborate with us to find novel active compounds for your protein target of interest. You can fill out the short application form directly on the website: atomwise.com/aims <https://hubs.la/H0z3sT80>. Please don't hesitate to reach out to me if you have any questions! Kind regards, Tessa *Tessa Van Grack, M.S.* Partnering Associate Atomwise <https://www.atomwise.com/> | Better Medicines Faster ᐧ -- Confidentiality Notice: The information contained herein is for informational purposes only. This message is private and the information contained in this message, including any attachments, contains information that may be confidential, privileged and/or proprietary. It is intended to be read only by the individual or entity to whom it is addressed. If you are not the intended recipient, please notify the sender by replying to this message, delete the material immediately from your system and note that you must not review, disclose, copy, distribute or take any action in reliance on or in reference to this message, including any attachments. No confidentiality, privilege, or property rights are waived or lost by any errors in transmission. Any unauthorized use or disclosure of the contents of this message is not permitted and may be unlawful.

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Re: [phenixbb] [ccp4bb] Phenix refine distorting a sidechain despite correct density
by Folmer Fredslund 03 Dec '20

03 Dec '20

Dear Igor There's a phenix bulletin board for question like this, which is where you should post the question. ( I crosspost here) I would choose to not do the real space refinement in phenix.refine during the last rounds of refinement of a model, when sidechain positions are essentially correct. I hope this helps Folmer tor. 3. dec. 2020 05.48 skrev Igor Petrik <petrik1(a)illinois.edu>: > I am refining a 1.71A X-ray structure with phenix refine. I have > everything modelled in - ~150 residues in the ASU and a heme - and my > R-work/R-free is 0.17/0.22. But when I went to deposit it, PDB pointed out > that two of my sidechains have distorted geometries. One is a His, and > looking at it in Coot, I can clearly see the 2Fo-Fc density for the correct > geometry, but the actual coordinates that phenix refine produce don't lie > in that density; there are significant difference map peaks showing that > the coordinates are in the wrong place. If I use real space refine in Coot > to put the coordinates back into the correct density and refine it again in > phenix, they get distorted again. > > What settings in phenix should I check to try to get it to properly refine > the coordinates? > > Thanks, > - Igor Petrik, PhD > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >

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Re: [phenixbb] 2x Postdoc positions and Lab Manager position
by Gordon Joyce 03 Dec '20

03 Dec '20

The Joyce Laboratory, Henry M. Jackson Foundation supporting the Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research have openings for two postdoctoral positions and a Lab Manager position in Structural Biology of Emerging Infectious Diseases. One postdoctoral position involves the structural and biochemical characterization of small molecule inhibitors against Emerging Infectious pathogens including SARS-CoV-2, as part of an integrated drug development pipeline at WRAIR. One postdoctoral position involves the structural and biochemical characterization of viral glycoproteins from Emerging Infectious pathogens including SARS-CoV-2 to enable vaccine development, antibody therapeutics and small molecule inhibitors. The Lab manager position will oversee day-to-day activities in the lab including lab inventory, ordering and routine mammalian cell culture and transient transfection. These positions offer a unique opportunity to gain extensive structural biology experience focused on vaccine and therapeutic development for pandemic prevention. Interested candidates should apply at the sites indicated below, or with a cover letter and a current CV directly to Gordon Joyce gjoyce(a)eidresearch.org<mailto:[email protected]> Postdoctoral Fellow: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… Postdoctoral Fellow: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… Lab Manager: https://recruiting.ultipro.com/HEN1006HMJ/JobBoard/3a6861f3-0883-4466-8b7d-… M. Gordon Joyce, Ph.D. Chief, Structural Biology The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF) In support of the Emerging Infectious Diseases Branch (EIDB) and the US Military HIV Research Program (MHRP) Walter Reed Army Institute of Research (WRAIR) 1N33, 503 Robert Grant Ave, Silver Spring, MD 20910 Office: 301-319-7528 Cell: 240-672-4311 https://eidresearch.org/our-team/m-gordon-joyce-phd gjoyce(a)eidresearch.org<mailto:[email protected]> ********************************************************************** This message contains information that may be confidential, privileged, proprietary, or otherwise protected. If you are not the intended recipient, notify the sender immediately and delete/destroy all copies of this message and any attachments. This message is not intended to constitute or include either an electronic record or an electronic signature unless otherwise specifically indicated.

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Power disruption (12/1 11 pm to 12/2 2 pm)
by Billy Poon 02 Dec '20

02 Dec '20

Hi everyone, Sorry for the short notice, but due to some electrical work in our building, several of the Berkeley servers will be shut down later tonight at 11 pm Pacific and will return tomorrow afternoon at 2 pm Pacific. This will affect: - The Phenix web site (http://phenix-online.org/) - The CCI web site (http://cci.lbl.gov/) - The Structural Biology Technology Portal (http://technology.sbkb.org/) Bug reports and emails requesting help should be queued and we will receive them once the servers are back online. We apologize for any inconvenience. -- Billy K. Poon 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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alpha-Fold 2?
by lbetts0508 01 Dec '20

01 Dec '20

all - I just read the blurb in Nature Briefing about the DeepMind AI having made a big advance in the CASP protein fold prediction. Does it sound really transformational, does it work for membrane proteins - all the usual questions come to mind. Do we know enough yet about it? Signed an old protein crystallographer, L. Betts

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map_to_model input labels
by Schnicker, Nicholas J 20 Nov '20

20 Nov '20

Hi All, I'm trying to run map_to_model via command line for the first time (clearly) with an mtz file from an X-ray dataset. I have tried different iterations, but I can't seem to come up with the correct syntax for suppling the input labels. It gives me the list of available labels below, but what is the correct syntax to provide for input? Available labels: ['IMEAN,SIGIMEAN', 'I(+),SIGI(+),I(-),SIGI(-)', 'F,SIGF,DANO,SIGDANO,ISYM', 'F(+),SIGF(+),F(-),SIGF(-)', 'FreeR_flag'] Sorry I have checked the documentation, but still managed to fail. Thanks for your help, Nick

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Ensemble refinement with covalent ligands - bond length > 5Å
by Schulz, Eike-Christian 18 Nov '20

18 Nov '20

Dear all, I am running phenix.ensemble_refinement on a covalent protein-ligand complex providing the same parameter-files used for phenix.refine. I also included the .def and .cif files generated by phenix.ligand_linking. However, in quite a few of the ensemble structures, the covalent link exceeds 5Å, which is obviously wrong. How can I obtain ensemble structures with reasonable covalent bond length? Best, Eike ———————————————————————————— Dr. Eike C. Schulz Max Planck Institute for the Structure and Dynamics of Matter Luruper Chaussee 149 | 22761 Hamburg | Germany Building 99 (CFEL) | Office O2.101 Phone +49 (0)40 8998-6264<tel:%2B49%20%280%2940%208998-6264> | Fax +49 (0)40 8994-6264<tel:%2B49%20%280%2940%208994-6264> | Website www.mpsd.mpg.de<http://www.mpsd.mpg.de/>

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phenix.refine last cycle often break geometry for no obvious improvement
by Clement Degut 18 Nov '20

18 Nov '20

Hi, I regularly encounter this problem with phenix.refine, happened to me with several structures, at wildly different resolution, so as described in the title, phenix.refine seems to break perfect geometry in its last cycle (put 3 5 or 10 it's the last), for no obvious improvement in term of other metrics, actually getting the temporary file just before the last cycle had given me very good result in the past. Is there a reason for this behaviour? A way to get back PDB at a certain point of the refinements cycles would be really great actually. example of what I refer to: [image: image.png] Cheers, Clément Dégut PDRA Dr M Plevin's group University Of York

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Diamond-II MX beamlines letters of support
by David Briggs 18 Nov '20

18 Nov '20

Dear all, (Apologies for the slightly off-topic cross-post - hopefully, this will be of interest to all MX practitioners, not just Diamond light source users.) As Diamond User Committee MX representatives, we'd just like to remind you that the deadline for letters of support for Diamond-II beamline upgrades is this Friday, 20th November. As you are perhaps aware, the Diamond machine is scheduled for a major upgrade to a 4th generation source 2025-2027. Further information about the upgrade can be found here<https://www.diamond.ac.uk/Home/About/Vision/Diamond-II.html>. All MX beamlines will benefit from a brighter, more focused source – however, two MX beamlines have been selected as flagship projects for significant upgrades. I04-1 > K04 Ultra XChem. The I04-1 fixed wavelength beamline used for the XChem fragment screening will be completely rebuilt as K04. Briefly, K04 will allow higher throughput fragment screening (meaning more projects and more fragments can be screened) and it is hoped the improved characteristics of the Diamond-II beam will allow XChem methodologies to be extended to more difficult targets such as transmembrane proteins. The K04 proposal outline can be found here<https://www.diamond.ac.uk/dam/jcr:bd879384-900b-4a2c-897d-a8e0e818c6e8/MX%2…> [PDF]. I24 > KMX Kinetic micro crystallography. The I24 microfocus beamline will be upgraded to enhance the capabilities of I24 and allowing analysis of smaller crystals, radiation-sensitive crystals, and expanding the serial synchrotron crystallography (SSX) functionality of the beamline. The abilities to conduct room temperature SSX will also be enhanced to allow in-crystal kinetic analysis, with various on-line spectroscopic (Raman, UV-Vis, XES) detectors built into the end station. The KMX proposal outline can be found here<https://www.diamond.ac.uk/dam/jcr:add3277b-5bc2-4e8b-93a2-25d1e0e585f6/MX%2…> [PDF] Having read these proposals you will obviously be very excited by the possibilities and will want to submit your letters of support for both of them, by Friday, 20th November Letters of support can be submitted via this link<https://forms.office.com/Pages/ResponsePage.aspx?id=dLonnQABDU2B_x1yja6N9sO…>. Thanks in advance, Dave & Arnaud. -- Dr David C. Briggs Senior Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == Diamond User Committee MX representative == about.me/david_briggs The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT

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Postdoctoral position in cryo-EM and translation regulation
by Loveland, Anna 13 Nov '20

13 Nov '20

Postdoctoral position in cryo-EM and translation regulation ‒ from bacteria to neurons Korostelev Lab, University of Massachusetts Medical School We study how the ribosome interacts with numerous cellular components to achieve high accuracy and efficiency of gene expression. We’d like to understand the key roles of translation and ribosomes in: (1) Neurodevelopment and neurodegenerative diseases; (2) Bacterial stress signaling and gene regulation (e.g. coupling with transcription); and other aspects of gene expression (https://www.umassmed.edu/korostelev-lab/). We use a range of approaches, including cryo-EM and biochemistry (see selected references below). Our laboratory is housed at the RNA Therapeutics Institute, a vibrant and highly interactive research community: https://www.umassmed.edu/rti/about-the-rti/faculty-members/. Our colleagues are interested in nearly all aspects of RNA biology, from small to large RNAs to RNA chemistry and therapeutics development. We seek a highly motivated person who very recently received a PhD, or will soon receive a PhD. Applications sent prior to the dissertation defense date are welcome. If you are interested in using single-particle cryo-EM and in situ (cellular) EM to elucidate cellular mechanisms, submit the following information to ann.powers(a)umassmed.edu<mailto:[email protected]>: 1) Your CV (including your publication list); 2) Cover letter (less than 2 pages) describing: (i) your previous work - focusing on your most interesting finding(s), (ii) your scientific interests, (iii) which aspects of translation regulation are of interest to you. 3) Email addresses of three references. Selected publications (accessible via the provided links): • Carbone CE, Demo G, Madireddy R, Svidritskiy E, Korostelev AA. “ArfB can displace mRNA to rescue stalled ribosomes<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.natur…>”. Nature Commun. 2020. • Loveland AB, Demo G, Korostelev AA. “Cryo-EM of elongating ribosome with EF-Tu GTP elucidates tRNA proofreading<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.natur…>”. Nature. 2020. • Loveland AB, Svidritskiy E, Susorov D, Lee S, Park A, Demo G, Gao FB, Korostelev AA. “Ribosome inhibition by C9ORF72-ALS/FTD-associated poly-PR and poly-GR proteins revealed by cryo-EM<file:///C:/Users/PowersA/Dropbox%20(UMass%20Medical%20School)/Korostelev/Job%20Postings/Susorov%20D%20et%20al.%20%22Termi-Luc:%20a%20versatile%20assay%20to%20monitor%20full-protein%20release%20from%20ribosomes>”. bioRxiv. 2020. • Susorov D, Egri S, Korostelev AA. "Termi-Luc: a versatile assay to monitor full-protein release from ribosomes<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Frnajourna…>”. RNA. 2020. • Svidritskiy E, Demo G, Loveland AB, Xu C, Korostelev AA. “Extensive ribosome and RF2 rearrangements during translation termination<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felifescie…>”. eLife. 2019. • Loveland AB, Demo G, Grigorieff N, Korostelev AA. “Ensemble cryo-EM elucidates the mechanism of translation fidelity<https://nam10.safelinks.protection.outlook.com/?url=http%3A%2F%2Fem.rdcu.be…>”. Nature. 2017. • Demo G, Rasouly A, Vasilyev N, Svetlov V, Loveland AB, Diaz-Avalos R, Grigorieff N, Nudler E, Korostelev AA. “Structure of RNA polymerase bound to ribosomal 30S subunit<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felifescie…>”. eLife. 2017. • Abeyrathne PD, Koh CS, Grant T, Grigorieff N, Korostelev AA. “Ensemble cryo-EM uncovers inchworm-like translocation of a viral IRES through the ribosome<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.ncbi.…>”. eLife. 2016. • Loveland AB, Bah E, Madireddy R, Zhang Y, Brilot AF, Grigorieff N, Korostelev AA. “Ribosome•RelA structures reveal the mechanism of stringent response activation<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Felifescie…>”. eLife. 2016. https://twitter.com/korostelevlab<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftwitter.c…> --- Anna Loveland, Ph.D. anna.loveland(a)umassmed.edu 617 610 4321 (cell) Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential, proprietary and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender immediately and destroy or permanently delete all copies of the original message.

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