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Re: [phenixbb] minimizing clash score
by oleg＠quantumbioinc.com 17 May '19

17 May '19

Dear Erron, We recently demonstrated that the high clash count typically seen with the conventional PHENIX refinement is likely attributed to a particular non bonded restraint function used by phenix.refine. When we employed QM/MM (ONIOM) refinement (Borbulevych et al., Acta Cryst., 2018, D74, 1063 https://doi.org/10.1107/S2059798318012913 ) that resulted in significantly better clashscore and improvements of other metrics. QM/MM refinement is available within PHENIX with the DivCon plugin. This plugin is available at no cost to academic users at http://www.quantumbioinc.com/products/software_licensing. Sincerely, Oleg Borbulevych Oleg Borbulevych, Ph.D. Staff Scientist QuantumBio, Inc. 2790 W. College Ave. State College, PA 16801 E-mail: oborbulevych(a)yahoo.com, oleg(a)quantumbioinc.com Linkedin Professional Profile: https://www.linkedin.com/in/oleg-borbulevych-b8045422 -----Original Message----- From: "Titus, Erron" <Erron.Titus(a)ucsf.edu> Sent: Friday, May 17, 2019 1:58pm To: "phenixbb(a)phenix-online.org" <phenixbb(a)phenix-online.org> Subject: [phenixbb] minimizing clash score _______________________________________________ phenixbb mailing list phenixbb(a)phenix-online.org http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: phenixbb-leave(a)phenix-online.orgHello, In order to improve model geometry of my x-ray structure, I am using real-space refinement together with reciprocal space refinement in phenix.refine. I like this, because it works very well to fix a lot of geometry issues. But clashes are a problem. Clashes tend to keep coming back. I found a clunky way to selectively use reference restraints to prevent most of the clashes from coming back, but I am wondering if there is another way of addressing this. I don't want to up-weight geometry globally, because 1) there are major regions of the x-ray map that are quite good, and 2) I don't have problems with other geometry, just clashes. I couldn't find much documentation on the "clash_guard" keyword... Thanks. Erron

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Dots and vectors of cryo em validation in Coot
by Ahmad Khalifa 17 May '19

17 May '19

Hello, In the manual, it says the red dots are clashes, what about the yellow dots and the magenta dashes (vectors)? I would also appreciate if you give an input on how you fix them. Best regards.

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On estimating Unitary Structure Factor distribution
by Andre LB Ambrosio 15 May '19

15 May '19

Dear all, We seek to calculate the distribution of Unitary Structure Factors, Uhkl, from a few datasets (at different maximum resolutions) for which the corresponding atomic models are already available at the PDB; this according to the formula (6.4), in the 2nd edition of Jan Drenth´s book: Uhkl = exp[B*(sin^2(theta)/lambda^2)] x FOBShkl / F(000) Hence, the following questions: - Is there any macromolecular crystallography software that can compute Uhkl as above, or equivalent? - If not, would it be more correct to use the Wilson-B or the mean B from the final model? - How can F(000) be best estimated from the final model, which is not necessarily always the most complete or best refined? Should we simply add together the number of electrons for all the atoms refined in the asymmetric unit (protein + ligands + solvent)? Many thanks in advance and best wishes, -- Andre LB Ambrosio

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Postdoctoral Research Assistant at University of Dundee (Alessio Ciulli)
by KH Chan 15 May '19

15 May '19

Posting on behalf of Prof. Alessio Ciulli: Professor Alessio Ciulli’s laboratory is seeking a postdoctoral researcher to undertake research in collaboration with one of the leading pharmaceutical companies supporting the Division of Signal Transduction Therapy (DSTT). The DSTT facilitates collaborations between some of the world’s major pharmaceutical companies (Boehringer Ingelheim, GlaxoSmithKline, and Merck-Serono) and leading Dundee-based researchers with a proven track record of achievement in understanding and exploiting the fundamental molecular causes of human disease in the fields of cancer, immune-regulation, neurodegeneration and hypertension resulting from disruptions in protein ubiquitylation, phosphorylation and other signalling networks. The successful applicant will be based within the Ciulli lab in Dundee ( http://www.lifesci.dundee.ac.uk/groups/alessio-ciulli). The laboratory is pioneering novel chemical structural biology approaches to target E3 ubiquitin ligases with small molecules. The applicant will employ state of the art structural biology, cell biology and biophysical approaches to conduct molecular and structural studies on disease-relevant human E3 ubiquitin ligases. The Ciulli lab has close collaborations and access to facilities available within both the MRC Protein Phosphorylation Unit ( http://www.ppu.mrc.ac.uk/) and more widely within the School of Life Sciences. This set-up will ensure the successful candidate will have access to whatever technologies required to conduct the projects that they are working on, including molecular, biochemical, mass spec proteomics, pharmacological and genetic methodologies including CRISPR/CAS9 knock-out and knock-in technologies. There will be regular opportunity for interaction and to discuss data within the group and with the collaborating pharma company. Candidate requirements: ‧ PhD with outstanding academic track record and at least one first authored publication in an internationally recognised peer-reviewed journal. ‧ Strong background in Biochemistry, Molecular Cell Biology, or Structural Biology is required. ‧ Strong interest in signal transduction research and how disruptions of these pathways are linked to human disease is expected. ‧ Experience with recombinant protein expression and purification, molecular cloning, and protein X-ray crystallography (or cryo-EM) is required. ‧ Experience with mammalian cells tissue culture, and protein-protein interaction studies inside cells e.g. pull-down, proteomics, would be highly advantageous. ‧ Experience with biophysical methods to study in vitro protein-protein and protein-peptide interactions is desirable. ‧ Capable of working in a team, but able to plan and work independently. ‧ Excellent communication skills and knowledge of the English language are essential. ‧ The candidate should have ambitions to become a successful independent researcher either in academia or the pharmaceutical/biotechnology industry. The fund for this project is available till 30th June 2020 in the first instance with a chance to renew. For informal enquiries please contact Prof Alessio Ciulli a.ciulli(a)dundee.ac.uk or Dr Kwok-Ho Chan k.chan(a)dundee.ac.uk Closing Date 31 May 2019 Job details: https://ig5.i-grasp.com/fe/tpl_uod01.asp?newms=jj&id=103176&newlang=1

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Research Associate (Fixed Term) at the MRC Mitochondrial Biology Unit, University of Cambridge
by Jonathan Ruprecht 15 May '19

15 May '19

Posting on behalf of Dr Edmund Kunji: The University of Cambridge wishes to appoint a Postdoctoral scientist to join the research group of Dr Edmund Kunji in the MRC Mitochondrial Biology Unit of the University of Cambridge. The postholder will work within a programme focussed on mitochondrial transporters. Transport processes are crucial for the functioning of mitochondria and mutations in transport proteins cause of a wide range of metabolic, neuromuscular and developmental diseases. Basic molecular understanding of their structure and mechanism is required to understand their role in health and disease. The goal of the project is to study their structures in different conformational states by electron cryo-microscopy and/or x-ray crystallography. The post-holder will participate in every stage of the process, from the generation of expression strains or cell lines, isolation of mitochondria, purification and sample preparation, data acquisition and processing, and structure model building and interpretation. There will also be an opportunity to study their role and mechanism using a wide range of biochemical and biophysical techniques. This project is part of a collaborative SNF Sinergia grant together with Profs. Hediger and Lochner of the University of Bern. Candidates will have a PhD in Structural Biology/Biophysics or related disciplines, and a track record of research achievements. Knowledge of protein purification and experience in structural biology are essential. Further details about the job may be found here: http://www.jobs.cam.ac.uk/job/21519/ The MRC Mitochondrial Biology Unit is a world-renowned centre for mitochondrial research. Additional information can be found at www.mrc-mbu.cam.ac.uk. Fixed-term: The funds for this post are available for 3 years in the first instance. The closing date for applications is Wednesday 12th June 2019 with interview date yet to be confirmed. Informal enquiries may be made to Dr Edmund Kunji (ek(a)mrc-mbu.cam.ac.uk).

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Cutting out a fragment from cryoEM map
by Sunandan Mukherjee 14 May '19

14 May '19

Hi, I want to build an RNA model using cryo-EM density. The structure is of a protein-RNA complex and the map consists regions with protein subunits. Is it possible to separate the portion of the map which represents the RNA only? Thanks and regards, Sunandan -- Sunandan Mukherjee (PhD) Research Assistant Laboratory of Bioinformatics and Protein Engineering International Institute of Molecular and Cell Biology (IIMCB) ul. Ks. Trojdena 4, 02-109 Warsaw, Poland

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Low resolution structure determination workshop at ECM32
by Paul Adams 14 May '19

14 May '19

Dear Colleagues, I’d like to draw your attention to a workshop that we’ll be hosting at the 32nd European Crystallographic Meeting in Vienna: Low resolution structure determination and refinement of biological macromolecules by crystallography and cryo-EM Organizers: Paul Adams, Dorothee Liebschner (Lawrence Berkeley Laboratory, Berkeley, USA) Date: 18th August 2019 Time: 9 a.m. – 5 p.m. More details: https://www.ecm2019.org/satellites/ Meeting and satellite registration: https://www.ecm2019.org/submission-registration/registration/online-registr… Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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AUC2019 – early bird registrations closing soon....
by Renwick Dobson 13 May '19

13 May '19

Dear AUC and Structural biology community, AUC2019<https://auc2019.uleth.ca/>, the 24th AUC Workshop and Symposium, will be held at the University of Canterbury, Christchurch (New Zealand) from 24-29 August 2019. Registrations are now open and details can be found at this website: https://auc2019.uleth.ca/. Early Bird Registrations close on 15th June. As the scientific program<https://auc2019.uleth.ca/symposium.php> for AUC2019 emerges, events will be uploaded to the website. We strongly encourage you to submit abstracts for talks and posters<https://auc2019.uleth.ca/abstracts.php>. The format of the event is a 2-3 day workshop<https://auc2019.uleth.ca/workshops.php> offering parallel, hands-on training in experimental design and the latest AUC data analysis software from the world experts in this area followed by a 2 day research symposium on AUC and complementary approaches: methodological development, combination with orthogonal techniques (SAXS, SANS, SPR, MST, SEC-MALLS etc), application in biosciences and material sciences. The meeting is also timed such that delegates can also attend the Biomolecular interactions and Engineering Symposium<https://www.queenstownresearchweek.org/bio-interactions/>, which is part of the Queenstown Molecular Biology Conference (this is in Queenstown, NZ), although note that this is a separate conference. Lastly, The European Biophysics Journal has kindly agreed to run a special issue to celebrate the research presented at AUC2019. Therefore, we invite those who wish to extend their talks to a journal publication to consider contributing original research articles to this issue. Please indicate your interest for inclusion in this volume below. Deadline for registration of a contribution is August 30 2019. We look forward to welcoming you to Christchurch, New Zealand next Spring(-ish)! Ren Dobson, Chair AUC2019 On behalf of the AUC2019 Scientific Organising Committee ---- Prof. Ren Dobson Co-Director, Biomolecular Interaction Centre (BIC) http://www.bic.canterbury.ac.nz/ School of Biological Sciences | Te Kura Pūtaiao Koiora University of Canterbury | Te Whare Wānanga o Waitaha Private Bag 4800 Christchurch | Ōtautahi New Zealand | Aotearoa E: renwick.dobson(a)canterbury.ac.nz<mailto:[email protected]> T: ++64 (03) 369-5145 x 95145 F: ++64 (03) 364-2590 W: http://dobsonlab.org/

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Electron microscopy software tools workshop at ACA
by Paul Adams 12 May '19

12 May '19

Dear Colleagues, I’d like to draw your attention to a workshop that we’ll be hosting at the American Crystallographic Associate meeting in Covington: Introduction to PHENIX for Electron Cryo-Microscopists Organizers: Paul Adams (Lawrence Berkeley Laboratory, Berkeley, USA) Date: Saturday, July 20, 2019 Time: 9 a.m. – 5 p.m. More details: https://www.aca2019mtg.com/workshops Meeting registration: https://www.aca2019mtg.com/registration Cheers, Paul -- Paul Adams Division Director, Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley Lab Division Deputy for Biosciences, Advanced Light Source, Lawrence Berkeley Lab Adjunct Professor, Department of Bioengineering, U.C. Berkeley Vice President for Technology, the Joint BioEnergy Institute Laboratory Research Manager, ENIGMA Science Focus Area Building 33, Room 347 Building 978, Room 4126 Tel: 1-510-486-4225, Fax: 1-510-486-5909 http://cci.lbl.gov/paul Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 33R0345 Berkeley, CA 94720, USA. Executive Assistant: Louise Benvenue [ LBenvenue(a)lbl.gov ][ 1-510-495-2506 ] --

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MR-Rosetta installation
by Taberman, Helena 09 May '19

09 May '19

Dear Phenix bb, I am facing a problem when trying to instal Rosetta locally. I have installed Rosetta 3.9, set a local environment to my c-shell (setenv PHENIX_ROSETTA_PATH "/Applications/rosetta_src_3.10_bundle") and compiled with ./scons.py -j4 mode=release bin in main/source/ folder. When I try to run rosetta.run_test I get the following error:"OSError: [Errno 2] No such file or directory: '/Applications/rosetta_src_3.10_bundle/main/source/bin' " though the folder is there. Could you please help me? Cheers, Helena -- Helena Taberman, PhD Postdoctoral Researcher Helmholtz-Zentrum Berlin for Materials and Energy Macromolecular Crystallography (HZB-MX) Albert-Einstein-Str. 15 12489 Berlin, Germany Tel: +49 30 8062 14376 Email: helena.taberman(a)helmholtz-berlin.de<mailto:[email protected]> Web: http://www.helmholtz-berlin.de/bessy-mx ________________________________ Helmholtz-Zentrum Berlin für Materialien und Energie GmbH Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V. Aufsichtsrat: Vorsitzender Dr. Karl Eugen Huthmacher, stv. Vorsitzende Dr. Jutta Koch-Unterseher Geschäftsführung: Prof. Dr. Bernd Rech (kommissarisch), Thomas Frederking Sitz Berlin, AG Charlottenburg, 89 HRB 5583 Postadresse: Hahn-Meitner-Platz 1 D-14109 Berlin

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