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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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A chance to develop new therapies through AI molecular screening
by Tessa Van Grack 12 Nov '20

12 Nov '20

Hi PhenixBB community, We are excited to announce the opening of the AIMS Awards Fall 2020 cycle! Collaborate with us to find novel active compounds for your protein target of interest. Our AIMS Awards program provides non-profit researchers with virtual screening and compounds for physical testing at no cost. 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. The program is open to investigators, postdocs, and graduate students worldwide. You can apply 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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phenixbb Digest, Vol 180, Issue 1 : Using a CryoEM density for MR
by Claudia Millán Nebot 10 Nov '20

10 Nov '20

Dear Almudena, I'm assuming that you were testing the full mr phaser section in phenix and tried the add map ensemble. This expects an mtz containing structure factors, and where certain preparation has been done. A full description of the steps required can be found in a prior publication ( https://www.nature.com/articles/nprot.2015.069?proof=t) from our group. In short, you'll need to first convert your mrc map to structure factors (there a command line utility for this in phenix, called map_to_structure_factors). But you can't input this directly as an ensemble, a series of other steps involving placing the map in a large P1 cell using phenix.cut_out_density (wit the option for_phaser set to True) will also be required for it to work, and you'll need to give information about the center and the extent of your map, as well as an estimation of the errors in the map (in form of an rmsd). Only then you'll be able to use the density for MR. Within the framework of the new version of phaser under development, phasertng, we are working on facilitating this MR approach, making it automatic and robust, and investigating about the best ways to treat the maps and to parameterise their search. This is work in progress but we have already some modes for map preparation for MR within phasertng, so we will also be happy, if you share with us the file off-line, to provide you with the prepared structure factors file. Otherwise, if you need any help in following the steps of the previous protocol, we will also provide the support. Best wishes, Claudia El jue., 5 nov. 2020 a las 12:41, <phenixbb-request(a)phenix-online.org> escribió: > Send phenixbb mailing list submissions to > phenixbb(a)phenix-online.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://phenix-online.org/mailman/listinfo/phenixbb > or, via email, send a message with subject or body 'help' to > phenixbb-request(a)phenix-online.org > > You can reach the person managing the list at > phenixbb-owner(a)phenix-online.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of phenixbb digest..." > > > Today's Topics: > > 1. Re: Number of unique reflections (John Berrisford) > 2. Fwd: Re: Number of unique reflections (Boaz Shaanan) > 3. Computational Crystallography Newsletter (CCN) submissions > (Nigel Moriarty) > 4. Phenix User Workshop, 17th and 18th of November (Paul Adams) > 5. Anomalous signal (Shramana Chatterjee) > 6. Re: Anomalous signal (Roger Rowlett) > 7. Re: Anomalous signal (Gerg? G?gl) > 8. mrc maps as a molecular replacement model > (Almudena Ponce Salvatierra) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 20 Oct 2020 18:30:16 +0100 > From: "John Berrisford" <jmb(a)ebi.ac.uk> > To: "'Pavel Afonine'" <pafonine(a)lbl.gov>, "'Armando Albert'" > <xalbert(a)iqfr.csic.es>, <phenixbb(a)phenix-online.org> > Subject: Re: [phenixbb] Number of unique reflections > Message-ID: <009401d6a706$ad6c8120$08458360$(a)ebi.ac.uk> > Content-Type: text/plain; charset="us-ascii" > > Dear Armando and Pavel > > During the deposition process we compare two values > > _reflns.number_obs > > http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number_ > obs.html > <http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_reflns.number…> > And > _refine.ls_number_reflns_obs > > http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_numb > er_reflns_obs.html > <http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/_refine.ls_num…> > > We expect the number of observed reflections to be higher (or the same) as > the number of reflections used in refinement. > We would expect that these two mmCIF items handle Friedel pairs > consistently > - if the number of reflections observed is reported with Friedel pairs > separately then the number of reflections in refinement should also report > Friedel pairs separately. > > My assumption here is that there is a mismatch in reporting these values. > > Hope this helps > > John > > -----Original Message----- > From: phenixbb-bounces(a)phenix-online.org > <phenixbb-bounces(a)phenix-online.org> On Behalf Of Pavel Afonine > Sent: 20 October 2020 18:16 > To: Armando Albert <xalbert(a)iqfr.csic.es>; phenixbb(a)phenix-online.org > Subject: Re: [phenixbb] Number of unique reflections > > Hi Armando, > > > We have realise that the output mtz and mmcif files duplicate the > > number of miller indices (the number of unique reflections) with > > respect to those in the mtz input file. We guessed that this > > correspond to the friedel pairs, > > data handling machinery in Phenix (cctbx) counts F+ and F- as separately, > that is (1, 1, 2) and (-1, -1, -2) are two entries, not one. > > > but it is annoying for pdb submission, as the server warns that the > observations measured are less that those used in the refinement. > > What shall we do fro correct this issue? > > Perhaps talk to PDB stuff and suggest to make the process less annoying... > > I'm not sure what we can do at our end. I guess if we count them as one > then > I'm sure some one will come around asking 'why you are counting two > reflections as one?'. > > Pavel > > _______________________________________________ > phenixbb mailing list > phenixbb(a)phenix-online.org > http://phenix-online.org/mailman/listinfo/phenixbb > Unsubscribe: phenixbb-leave(a)phenix-online.org > > > > ------------------------------ > > Message: 2 > Date: Tue, 20 Oct 2020 18:16:16 +0000 > From: Boaz Shaanan <bshaanan(a)bgu.ac.il> > To: phenixbb <phenixbb(a)phenix-online.org> > Subject: [phenixbb] Fwd: Re: Number of unique reflections > Message-ID: <787a9a55-8840-44ad-b176-a7d3feae038c(a)email.android.com> > Content-Type: text/plain; charset="us-ascii" > > An HTML attachment was scrubbed... > URL: < > http://phenix-online.org/pipermail/phenixbb/attachments/20201020/739082e7/a… > > > > ------------------------------ > > Message: 3 > Date: Mon, 2 Nov 2020 14:38:52 -0800 > From: Nigel Moriarty <nwmoriarty(a)lbl.gov> > To: undisclosed-recipients:; > Subject: [phenixbb] Computational Crystallography Newsletter (CCN) > submissions > Message-ID: > <CANkP= > 2fyOGS1bB9Rir6A3GZU1PiyuuF2PCaWBuHnjxC0QvkLwQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Folks > > The deadline for submissions to the Computational Crystallography > Newsletter (CCN) is 15 DEC 2020. 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 are available at > www.phenix-online.org/newsletter. > > 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 >

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Table 1 Issue 2
by Xavier Brazzolotto 10 Nov '20

10 Nov '20

I've downloaded the 1.19rc5-4047 version of Phenix and the Table 1 issue is still present. Table 1 does not output macromolecule, ligand and water specific values for « Number of non-hydrogen atoms » and « Average B-factor » items. Still on OSX Xavier

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Table 1 issue
by Xavier Brazzolotto 07 Nov '20

07 Nov '20

I’m experiencing a small bug with Phenix 1.19rc4-4035 Running Table 1 does not output the macromolecules, ligands and water specific values for "Number of non-hydrogen atoms" and "Average B-factor ». Running on OSX Take good care Xavier

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Anomalous signal
by Shramana Chatterjee 05 Nov '20

05 Nov '20

Hi, How can I find anomalous signal for Zn-metal to be sure whether Zn is binding or not, for an already processed dataset? It would be very helpful if I get any suggestion. Thank you in advance.

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mrc maps as a molecular replacement model
by Almudena Ponce Salvatierra 05 Nov '20

05 Nov '20

Hi everybody, I would like to use a cryo-EM map for MR, however, I get an error message as I try to provide it to phaser: "Phenix did not recognize the file type for xxx.mrc" My Phenix version is 1.17.1-3660-000 What should I do? Thank you very much

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Phenix User Workshop, 17th and 18th of November
by Paul Adams 04 Nov '20

04 Nov '20

Dear Colleagues, The Phenix developers will be holding an online *Phenix User Workshop on the 17th and 18th of November at 8am-12pm PDT.* These times will work best for researchers in North and South America, Europe and Africa. We plan to hold a future workshop at a time better suited to researchers in Asia and Australasia. The format of the workshop will be demos of the use of Phenix programs combined with slides to explain the theory. We expect an interactive meeting where attendees can ask questions for the Phenix team to answer. The workshop will cover aspects of macromolecular crystallography in Phenix, with the final emphasis based on the applicants’ research interests. To apply please fill out this form <https://forms.gle/Q8P6ZC9fYqTkS7qD7>. We will make every effort to accommodate all applicants, but may need to defer some requests to a future workshop if demand is high. We are hoping this workshop will be a success, in which case we plan to host more in the future. Cheers, The Phenix Developer Team -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, LBL ( http://biosciences.lbl.gov/divisions/mbib) Principal Investigator, Computational Crystallography Initiative, LBL ( http://cci.lbl.gov) Vice President for Technology, the Joint BioEnergy Institute ( http://www.jbei.org) Principal Investigator, ALS-ENABLE, Advanced Light Source ( http://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, U.C. Berkeley ( http://bioeng.berkeley.edu) Adjunct Professor, Comparative Biochemistry, U.C. Berkeley ( http://compbiochem.berkeley.edu) Building 33, Room 347 Building 978, Room 4126 Building 977, Room 180C Tel: 1-510-486-4225 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Ashley Dawn [ AshleyDawn(a)lbl.gov <LBenvenue(a)lbl.gov> ] [ 1-510-486-5455 ]

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 02 Nov '20

02 Nov '20

Folks The deadline for submissions to the Computational Crystallography Newsletter (CCN) is 15 DEC 2020. 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 are available at www.phenix-online.org/newsletter. 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

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Fwd: Re: Number of unique reflections
by Boaz Shaanan 20 Oct '20

20 Oct '20

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Number of unique reflections
by Armando Albert 20 Oct '20

20 Oct '20

Dear all, We have realise that the output mtz and mmcif files duplicate the number of miller indices (the number of unique reflections) with respect to those in the mtz input file. We guessed that this correspond to the friedel pairs, but it is annoying for pdb submission, as the server warns that the observations measured are less that those used in the refinement. What shall we do fro correct this issue? Armando

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What can iNEXT-Discovery do for us?
by a.perrakis＠nki.nl 20 Oct '20

20 Oct '20

Dear all, We are happy to announce a webinar series highlighting some of the experimental possibilities offered by iNEXT-Discovery facilities. iNEXT-Discovery is an H2020 program, that allows scientists from all over Europe (and outside Europe, to some extent) to access state of the art facilities for Structural Biology (X-rays, cryo-EM, NMR, Biophysics). Our offers extend beyond the use of machines, to hands-on expertise and (in many cases) help in designing experiments and interpreting data and of course remote services! Access to iNEXT-Discovery is free (often including samples shipment or visitor expenses) and is on the basis of (rapid) independent peer-review, for projects with a translational research component; the offer extends to industry partners under specific rules. These webinars will be short presentations (20 minutes) presented by experts in the various facilities, and will not be in-depth science talks, but mostly geared towards user awareness for the technical and scientific capabilities we can offer! We will offer one webinar every Monday at 16:00 CET, until Xmas, and then a few more! We will cover topics like cryo-EM single particles and tomography, X-ray tomography, fragment screening by X-ray crystallography, in-cell NMR, and more. Every presentation will be followed by a live discussion. A more detailed program is at: https://inext-discovery.eu/events/what-can-inext-discovery-do-for-us/ Registration is open at: https://zoom.us/webinar/register/WN_ZPGVwe7xR9GIyqESRS-dxA Best regards on behalf of the iNEXT-Discovery team, A. Perrakis Prof. Dr. Anastassis Perrakis, PhD Group leader, Dept. of Biochemistry, Netherlands Cancer Institute Professor of Macromolecular Structures, University of Utrecht Oncode Institute Investigator Coordinator iNEXT-Discovery H2020

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Mask used for map-to-model FSC
by Yang Shi 20 Oct '20

20 Oct '20

Hi all, Does anyone happen to know how to control the tightness of a mask for map-to-model FSC calculation? I have tried the "atom radius" in Map/Model CC tab of "Comprehensive validation (cryo-EM)", but it was not working for me. The reason I am asking this question is that I can only model a small region in the cryoEM map, the rest is unknown to me. Then the CC in low-frequency was 0.4-0.6 in the FSC curve, while the overall masked cc was 0.85. I would like to find an easy way to make the FSC curve look better. Any suggestions would be appreciated! Best wishes, Yang

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Opening Coot through Phenix in Window
by Thomas, Leonard M. 14 Oct '20

14 Oct '20

Hello, Most likely a simple problem, I am helping a some of our students setup their computers to use Phenix and Coot for both their own work and a class. One has installed both Phenix and Coot but cannot get Phenix to open Coot and display the model or maps on a Windows box, Coot is opening just not displaying. I admit I don’t work with Windows that often and I am not sure what the problem could be. Thank you in advance for any insight. Cheers, Len Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Oklahoma COBRE in Structural Biology Price Family Foundation Institute of Structural Biology University of Oklahoma Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center 101 Stephenson Parkway Norman, OK 73019-5251 Office: (405)325-1126 lmthomas(a)ou.edu<mailto:[email protected]> http://www.ou.edu/structuralbiology/cobre-core-facilities/mcl

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phenix.resolve_cryo_em resolution and real space refinement
by David Lawson (JIC) 14 Oct '20

14 Oct '20

Hi All, I have run phenix.resolve_cryo_em using half maps at 7.5 A resolution (the postprocessed map is at 7.1 A) and I just wanted to clarify a couple of things (I have pasted the end of the logfile below this message). I set the resolution to 7.52 A but didn't supply a resolution for density modification - it seems to have chosen a value of 5.671 A (1) It states "Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A" suggesting to me that it agrees with the postprocessed resolution. Is this the value of 7.08 on this line: "FSCref=0.5: 7.08 6.69 6.63"? (2) I understand that the actual process of real space refinement doesn't care about the resolution of the map, but you need to supply it to get meaningful CC values. So my question is what resolution should I supply to RSR if I use the density modified map? I realise that a value of "-0.450 A" is at the upper end of what to expect from density improvement, but I can report that the DM map does look noticeably better than the postprocessed map, especially in regions that are less well defined. Many thanks in advance for any advice Dave Lawson ----------------------------------- d-values (A) where FSCref=0.5: 7.08 6.69 6.63 Estimated improvement in d_cc_star=0.5: -0.450 A This is new current best working_map_coeffs_info. Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A Done testing....R-value: 0.530 Try: 1 ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None A**2'] Best density modification cycle 1 is try 1 with Methods used: ['database 5', 'resolution: 5.67 ', 'dm_resolution: 5.67 ', 'density_modify_unsharpened_maps:False', 'apply_cc_star:True', 'b_iso: None A**2'] R-value: 0.530 Estimated improvement of -0.450 A to d_min(FSCref=0.5): 6.628 A Result: -0.450 A to d_min(FSCref=0.5): 6.628 A R-value: 0.530 Wrote working map to /home/lawsond/phenix/ResolveCryoEM_1/map_denmod.ccp4 =============================================================================== SUMMARY AFTER CYCLE OF DENSITY-MODIFICATION =============================================================================== Overall best density modification Cycle 1 try 1 Estimated improvement: -0.450 A to d_min(FSCref=0.5): 6.628 A R-value: 0.530 Denmod resolution: 5.671 A Database: 5.000 A Writing out final map files... ------------------------------- Prof. David M. Lawson Department of Biological Chemistry, John Innes Centre, Norwich, NR4 7UH, UK. Tel: +44-(0)1603-450725 Web: https://www.jic.ac.uk/people/david-lawson Email: david.lawson(a)jic.ac.uk

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Quest for resolution-sensitive substructure determination cases
by Randy Read 11 Oct '20

11 Oct '20

Dear members of the BBs, When determining the anomalous substructure as part of SAD phasing, one of the most important parameters can be the choice of resolution limit for the data provided to the substructure determination algorithm. Extending to too high resolution can hamper the search by introducing too much noise. The resolution limit is varied internally in phenix.hyss, but is provided as a parameter to SHELXD. There are various rules of thumb that people use to make a first choice of resolution limit, such as half-dataset anomalous correlation or the average precision of the anomalous differences, or even just adding 0.5 to dmin. We’re currently exploring some alternative measures and we would like to test them on a significant number of relevant test cases. It turns out that a large proportion of SAD data deposited in the PDB have such good signal-to-noise that substructure determination succeeds with a wide variety of parameters, so we’ve only collected a few cases so far. It would be great if you could let us know of cases that you’re aware of, where substructure determination succeeds with the right choice of resolution limit but fails with the full resolution range of data. Of course, these have to be cases where the diffraction data have been deposited at the PDB or otherwise been made available. We prefer data for which the intensities, and not just the amplitudes, are available, but we won’t be too picky if that would limit the number of examples too much! If you email me directly, I’ll post a summary to the BBs. Thanks! Randy Read ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Fax: +44 1223 336827 Hills Road E-mail: rjr27(a)cam.ac.uk Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk

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questions regarding phenix.table_one
by Wei Wang 09 Oct '20

09 Oct '20

Dear all, I’m using phenix.table_one to prepare the statistics to include in the paper, and came up with a question regarding the number of reflections being reported. For example, one of the structures has the following statistics: Unique reflections: 70764 (7064) Reflections used in refinement: 70731 (7019) Reflections used for Rfree : 3523 (371) Clearly 70731+3523 is greater than 70764. So I’m puzzled here. I guess “Reflections used in refinement” number actually equals to the sum of "Reflections used for Rfree”+”Reflections used for Rwork”. If this is true then I would just do a simple calculation myself to get the ”Reflections used for Rwork”. Another question is I’m seeing “Reflections used in refinement” always a little smaller than “Unique reflections”. I guess it’s because there’s an outlier rejection in certain step but not sure. I’d be grateful for any clarification. thanks ! Regards, Wei

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phenix.refine read .geo file
by Sheila Boreiko 08 Oct '20

08 Oct '20

Dear all, For the sake of some experiment, I would like to manually edit some restraints of a geometry restraint file (normally named .geo) and ask for phenix.refine to read this edited file rather than producing a new one, is this possible? What should be the command line to read this geometry restraint file be? Thank you, Sheila

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Tenure track faculty position University of Missouri
by Tanner, John J. 07 Oct '20

07 Oct '20

Dear Colleagues, My department has begun a search for a tenure track faculty position. Structural biology is among the preferred areas of biochemistry for this search. More information in available here: https://biochem.missouri.edu/open-positions/ Review of applications will begin on November 16, 2020. John J. Tanner Professor of Biochemistry and Chemistry Associate Chair of Biochemistry Department of Biochemistry University of Missouri 117 Schweitzer Hall 503 S College Avenue Columbia, MO 65211 Phone: 573-884-1280 Email: tannerjj(a)missouri.edu<mailto:[email protected]> http://faculty.missouri.edu/~tannerjj/tannergroup/tanner.html Lab: Schlundt Annex rooms 3,6,9, 203B, 203C Office: Schlundt Annex 203A

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Newcastle University Professor/Reader/Senior Lecturer of Structural Biology
by Arnaud Basle 05 Oct '20

05 Oct '20

Dear All, Newcastle University is delighted tobe recruiting for a Professor / Reader / Senior Lecturer of Structural Biology to work within the Biosciences Institute in the Faculty of Medical Sciences. https://jobs.ncl.ac.uk/job/Newcastle-ProfessorReaderSenior-Lecturer-of-Stru… Cheers, Arnaud -- Dr Arnaud Basle X-ray facilities manager Newcastle Structural Biology Laboratory Biosciences Institute Faculty of Medical Sciences Newcastle University Framlington place NE2 4HH Newcastle upon tyne Phone 0191 208 5482

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Scientist-I (Structural Biology) position at Frederick National Laboratory for Cancer Research
by Dhirendra K Simanshu 05 Oct '20

05 Oct '20

Hello everyone, The Frederick National Laboratory for Cancer Research is looking for a Scientist-I with experience in protein chemistry and structural biology. The candidate will join the structural biology group within the NCI RAS Initiative program and work on the protein-small molecule complexes. For detailed information and to apply for this position, please use this link: https://leidosbiomed.csod.com/ats/careersite/jobdetails.aspx?site=4&c=leido… Best regards Dhirendra Simanshu -- Dhirendra Simanshu Principal Scientist, Team Lead - RAS Structural Biology NCI RAS Initiative Frederick National Laboratory for Cancer Research Leidos Biomedical Research, Inc. *Office/Courier*: 8560 Progress Drive, C1012, Frederick, MD 21701 *USPS mail*: Post Office Box B, ATRF-C1012, Frederick, MD 21702 Dhirendra.Simanshu(a)fnlcr.nih.gov <Dhirendra.Simanshu(a)nih.gov>

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Postdoc positions at MRC-LMB & CCPEM/STFC
by Burnley, Tom (STFC,RAL,SC) 25 Sep '20

25 Sep '20

Dear all, For those interesting in computational cryoEM development... We are excited to announce two new PDRA positions in the Scheres’ group (MRC-LMB, UK) and the CCP-EM group (STFC RAL, UK). These two positions will work closely together as part of a wider project with the Alan Turing Institute and the Department of Applied Mathematics and Theoretical Physics at Cambridge University to investigate molecular structure from images under physical constraints. In brief, the LMB position will focus on developing and implementing new machine-learning-driven algorithms within the RELION framework. The STFC position will focus on the data capture and training for these algorithms (as well as for the wider community), alongside application to molecular modelling. For full details and application please see: LMB position: https://mrc.tal.net/vx/lang-en-GB/mobile-0/appcentre-1/brand-3/xf-15f5592f8… STFC position: https://www.topcareer.jobs/Vacancy/irc255076_10934.aspx For those interested in both positions, we encourage you to apply for both. If you are unsure or would like further information please contact us. Best wishes, Tom and Sjors This email and any attachments are intended solely for the use of the named recipients. If you are not the intended recipient you must not use, disclose, copy or distribute this email or any of its attachments and should notify the sender immediately and delete this email from your system. UK Research and Innovation (UKRI) has taken every reasonable precaution to minimise risk of this email or any attachments containing viruses or malware but the recipient should carry out its own virus and malware checks before opening the attachments. UKRI does not accept any liability for any losses or damages which the recipient may sustain due to presence of any viruses. Opinions, conclusions or other information in this message and attachments that are not related directly to UKRI business are solely those of the author and do not represent the views of UKRI.

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