- phenixbb - phenix-online.org

Post-doctoral vacancy in cryoEM of viruses
by Hasan, Syed Saif 21 Dec '20

21 Dec '20

Dear Colleagues, A vacancy for a post-doctoral researcher is available immediately in my lab in the University of Maryland Center for Biomolecular Therapeutics located on the campus of Institute for Bioscience and Biotechnology Research (IBBR; https://www.ibbr.umd.edu/profiles/s-saif-hasan) in Rockville MD. We use high-resolution single particle cryoEM and X-ray crystallography to investigate how viruses utilize structural similarities with host proteins to hijack inter-organelle communication. Prior experience in insect cell culture for recombinant protein production is desirable. Expertise in cryoEM or X-ray crystallography will be advantageous. Candidates who have recently completed their PhD are encouraged to apply. IBBR is located 20 miles north-west of Washington DC. In IBBR, you will have in-house access to a 200 kV Talos Arctica with a Falcon 3EC DED and a 200 kV Glacios with a K3 DED and a Volta Phase Plate (VPP). We have a Vitrobot Mark IV and a Cp3 cryo-plunger for sample preparation. We have off-site access to a Titan Krios microscope equipped with DED and VPP. For X-ray crystallography, we have access to a Mosquito crystallization robot. Data collection is usually performed at synchrotrons. Our research is highly collaborative and is supported by wonderful colleagues who help us out with their expertise in NMR spectroscopy, lipidomics, HDX-MS, MD simulations, computer assisted drug design, and cellular imaging. Interested candidates should send their CV and a cover letter to me at sshasan(a)som.umaryland.edu ************************************************************************************************ The University of Maryland, Baltimore is an Equal Opportunity, Affirmative Action employer. Minorities, women, individuals with disabilities and protected veterans are encouraged to apply. ************************************************************************************************ Saif S. Saif Hasan, PhD Assistant Professor Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine 108 N. Greene Street, Baltimore MD 21201 https://www.medschool.umaryland.edu/profiles/Hasan-S-Saif-Hasan-Syed-Saif/ Associate Member Program in Oncology, University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center (UMGCCC) 22 S. Greene Street, Baltimore MD 21201 Office and Laboratory Address: Center for Biomolecular Therapeutics, Institute for Bioscience and Biotechnology Research (IBBR) 9600 Gudelsky Drive, Rockville MD 20850 https://www.ibbr.umd.edu/profiles/s-saif-hasan Phone: 240-314-6396 Fax: 240-314-6225

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Coot+Phenix issue
by Ashima Chopra 21 Dec '20

21 Dec '20

Hi all, I am running a refinement on Phenix for one structure, as I work on the Molprobity corrections from another refined structure in Coot. My Coot connects to Phenix so I can navigate through the Molprobity list easily, however the tmp.refine files from the first refinement keep popping up and replacing the current maps I have open. Is it possible to be connected to Phenix and define which project to display the maps/models from? Thanks, Ashima Ashima Chopra Graduate Assistant Eddy Arnold Laboratory Department of Chemistry and Chemical Biology/ Center for Advanced Biotechnology and Medicine Rutgers University, New Brunswick

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ASAPpdb - pledge to release data with preprints
by James Fraser 16 Dec '20

16 Dec '20

Fellow structural biologists - The revolution in publishing made possible by preprints calls for a re-evaluation of data disclosure practices in structural biology. While journal review processes take weeks, months, or even years, preprints allow researchers to rapidly communicate their findings to the community. However, withholding access to PDB files that accompany preprints inhibits the progress towards scientific discovery which preprints can enable. There is nothing more disappointing than reading a great preprint and not being able to open the coordinates and inspect the density! Sign the pledge to publicly release PDB files (and associated structure factor, restraint, and map files) with deposition of preprints here: https://asapbio.org/asappdb All the best, James PS> Apologies for the cross post to multiple bb's -- James Fraser - http://www.fraserlab.com - @fraser_lab jaimefraser(a)gmail.com // jfraser(a)fraserlab.com he/his/him (please do NOT use james.fraser(a)ucsf.edu)

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MicroED workshop 2020
by Johan Hattne 12 Dec '20

12 Dec '20

Dear all; We are pleased to announce the 6th MicroED workshop to be held on December 21, 2020. This will be a free virtual event. Please register at the following website to receive your link https://cryoem.ucla.edu/course Topics covered will include all aspects of microcrystal electron diffraction (MicroED) of diverse samples such as soluble proteins, membrane proteins, small molecules, natural products, and other materials. We will cover 1. Sample preparation methodologies 2. EPU-D for data collection 3. Camera systems and performance 4. FIB-milling procedures for soluble and membrane protein samples 5. Data analysis software, refinement, and structure solution The schedule is available on the registration page. // Sincerely; The organizing committee (Tamir Gonen, Brandon Mercado, Brent Nannenga)

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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 02 Dec '20

02 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 01 Dec '20

01 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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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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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 03 Nov '20

03 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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