- phenixbb - phenix-online.org

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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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 06 Nov '20

06 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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