- phenixbb - phenix-online.org

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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Rosetta cannot Rebuild
by Perry, Kay H. 09 May '19

09 May '19

I am having a problem with mr_rosetta where I cannot make it past the rebuild step. I have made fragment files using the old Robetta Server and I am using a hhpred alignment file, but even if I try with a model_already_placed when I reach rebuilding, I get the following error. protocols.looprelax: === protocols.looprelax: === Remodel protocols.looprelax: === ERROR: frag_libs().size() > 0 ERROR:: Exit from: src/protocols/comparative_modeling/LoopRelaxMover.cc line: 47 7 My PHENIX_ROSETTA_PATH is pointed at /share/apps/necat/programs/rosetta3.4 so I believe I am using version 3.4 of rosetta. Kay Perry NE-CAT 9700 S. Cass Ave. Bldg. 436 E007 Argonne, IL 60439 630-252-0692

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Fwd: NIH/NSF-Funded Research Specialist Position in Structural Biology at the University of Illinois at Chicago
by Yury Polikanov 08 May '19

08 May '19

NIH/NSF-Funded Research Specialist Position in Structural Biology at the University of Illinois at Chicago The Polikanov Laboratory at the University of Illinois at Chicago (IL, USA) is looking for talented, skillful, and highly motivated researchers to fill the NIH/NSF-funded Visiting Research Specialist positions to study the structure and function of the bacterial ribosome. The research in the Polikanov Laboratory is focused on understanding the basic principles of protein synthesis in bacteria, the modes of action of ribosome-targeting antibiotics, and the mechanisms of drug resistance at a structural level. More information about Dr. Polikanov research can be obtained from the most recent publications ( https://www.ncbi.nlm.nih.gov/sites/myncbi/yury.polikanov.1/bibliography/503…) or found on the laboratory web-page ( https://bios.uic.edu/bios/people/faculty/yury-polikanov). The successful candidate will be involved in determination of high-resolution structures of ribosome functional complexes with various protein translation factors, tRNAs, and antibiotics using macromolecular X-ray crystallography techniques. Basic qualifications: • BS degree in chemistry, biochemistry, biophysics, or a related field is required; • MS degree or higher is preferred;• Minimum of 3 years of laboratory research experience is required; • Strong background in biochemistry and molecular biology is required; • Practical skills with the most standard methods currently used in molecular biology, and biochemistry (such as protein expression, purification); • Experience in structural biology (cryo-EM or X-ray crystallography) is not required but is highly desirable; • Experience in RNA biology field is not required but is highly desirable; The successful candidate is also expected to: • Act independently in terms of planning and executing the experiments; • Compile, analyze, and prepare data for publications; • Assist with training of graduate and undergraduate students. Interested candidates should submit their CV, cover letter, and contact information for three references at https://jobs.uic.edu/job-board/job-details?jobID=113640&job=visiting-resear… by June 28, 2019. Cover letter should be describing how previous research accomplishments and scientific interests of a candidate fit with the scope of the research in the Polikanov Lab. The University of Illinois at Chicago is an Equal Opportunity, Affirmative Action employer. Minorities, women, veterans and individuals with disabilities are encouraged to apply. The University of Illinois may conduct background checks on all job candidates upon acceptance of a contingent offer. Background checks will be performed in compliance with the Fair Credit Reporting Act *Jacquelyn DeLaurentis* *Human Resource Associate* *Department of Biological Sciences* *The University of Illinois at Chicago* *845 W Taylor St. * *3238 SES, MC 066* *Chicago, IL 60607* *(312) 996-2213 * *jdelaur(a)uic.edu <jdelaur(a)uic.edu>* [image: UIC Logo]

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phenix-1.15.2-3472 crashes with multiple CIF's
by oleg＠quantumbioinc.com 03 May '19

03 May '19

phenix-1.15.2-3472 crashes at the very end of the refinement when multiple CIF's are given at the command line (see below). Please have a look. Thanks 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 ============================== Exporting results ============================== Writing refined structure to PDB file: /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.pdb n_use = 9639 n_use_u_iso = 9639 n_use_u_aniso = 0 n_grad_site = 0 n_grad_u_iso = 0 n_grad_u_aniso = 0 n_grad_occupancy = 0 n_grad_fp = 0 n_grad_fdp = 0 total number of scatterers = 9639 Writing refined structure to CIF file: /home/oleg/TEST2/astex/full_set/astex_oniom_qm5_5_01_19/1N2J/1N2J-H_refine_001.cif Traceback (most recent call last): File "/home/oleg/phenix-1.15.2-3472/build/../modules/phenix/phenix/command_line/refine.py", line 11, in <module> command_line.run(command_name="phenix.refine", args=sys.argv[1:]) File "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/command_line.py", line 162, in run refine_object.write_model_cif_file(f_cif_model) File "/home/oleg/phenix-1.15.2-3472/modules/phenix/phenix/refinement/driver.py", line 984, in write_model_cif_file additional_blocks=[cif_block]) File "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 964, in model_as_mmcif restraints = self.extract_restraints_as_cif_blocks() File "/home/oleg/phenix-1.15.2-3472/modules/cctbx_project/mmtbx/model/model.py", line 862, in extract_restraints_as_cif_blocks if '_chem_comp_plane_atom.comp_id' in loop.keys(): AttributeError: 'NoneType' object has no attribute 'keys'

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Computational Crystallography Newsletter (CCN) submissions
by Nigel Moriarty 02 May '19

02 May '19

Folks Calling for articles and short communications of interest to structural biologists. The deadline for submission for the July 2019 issue is 20 May 2019. The previous issue is available http://phenix-online.org/newsletter/ and contains the following. January 2019 <http://phenix-online.org/newsletter/CCN_2019_01.pdf> Short Communications - MARCO: The Machine Recognition of Crystallization Outcomes <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=7> - Building a model the way you do: Map-to-model version 2 <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=9> Fitting tips #16 – Asn and Gln are remarkably different <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=1> FAQ - Are the defaults the best for refinements? <http://phenix-online.org/newsletter/CCN_2019_01.pdf#page=6> 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 <https://urldefense.proofpoint.com/v2/url?u=http-3A__www.phenix-2Donline.org…>. Cheers Nigel 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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geometry_restraints.edits.scale_restraints
by Wei Wang 02 May '19

02 May '19

Dear PHENIX developers, I would like to know if the refinement.geometry_restraints.edits.scale_restraints still a valid option for tightening local restraints. I didn’t see this option from the phenix —show-defaults=all. I saw this option on the FAQ webpage. thx Wei

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