- phenixbb - phenix-online.org

phenix.autosol and phenix.hyss now optimized for weak SAD data
by Terwilliger, Thomas C 05 Feb '14

05 Feb '14

Hi Phenix users! You might notice some big differences in HySS and AutoSol in the new 2014 versions of Phenix (starting with current nightly builds and the soon-to-be-released Phenix-1.8.5). The big changes are parallelization, the use of Phaser completion in HySS, iterative Phaser completion using maps and models in AutoSol, and on-the-fly optimization of parameters in AutoSol for cases with weak anomalous signal. Now HySS and AutoSol can solve structures with very weak SAD phase information that previous versions could not solve. More details will be in the Phenix newsletter that will come out shortly! You can see documentation on the new HySS at: http://phenix-online.org/version_docs/dev-1613/hyss.htm#anch8 and on the new AutoSol at: http://phenix-online.org/version_docs/dev-1613/autosol.htm#anch118 --Tom Terwilliger, Randy Read, Gábor Bunkóczi, Nat Echols

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Computational Crystallography Newsletter - Volume 5, Number 1
by Nigel Moriarty 05 Feb '14

05 Feb '14

Dear Colleagues, I am pleased to announce the publication of the latest issue of the Computational Crystallography Newsletter: http://www.phenix-online.org/newsletter/ A listing of the articles and short communications is given below. Please note that the newsletter accepts articles of a general nature of interest to all crystallographers. Please send any articles to me at NWMoriarty(a)lbl.gov noting that there is a Word Template on the website to streamline production. Articles -------- FEL Detectors and ImageCIF Quantum Mechanics-based Refinement in Phenix/DivCon Short communications -------------------- Short Communications Phenix tools for interpretation of BIOMT and MTRIX records of PDB files Coping with BIG DATA image formats: integration of CBF, NeXus and HDF5 Fitting tips #7 - Getting the Pucker Right in RNA Structures Cheers Nigel -- Nigel W. Moriarty Building 64R0246B, Physical Biosciences Division 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: CCP4 crystallographic summer school in USA, at APS, June 24-July 2
by Nathaniel Echols 03 Feb '14

03 Feb '14

---------- Forwarded message ---------- From: Nukri Sanishvili <rsanishvili(a)anl.gov> To: <phenixbb(a)phenix-online.org> Date: Mon, 3 Feb 2014 18:12:09 -0600 Subject: CCP4 crystallographic summer school in USA, at APS, June 24-July 2 Dear Colleagues, We are pleased to announce the seventh annual CCP4 crystallographic summer school at Advanced Photon Source (APS), Argonne National Laboratory (ANL). All details can be found at http://www.ccp4.ac.uk/schools/APS-2014/index.php<https://mail.anl.gov/owa/redir.aspx?C=Qww5V7BVpECZd8A2kldFSf7_-DvC9NAIxdFZE…> *Title:*"CCP4 crystallographic school: From data collection to structure refinement and beyond" *Dates*: June 24 to July 2. *Site:* Advanced Photon Source, Argonne National Laboratory, Argonne, Illinois (Near Chicago), USA *The school content: *Data collection workshop the first two days: beamline training and data collection on GM/CA@APS beamlines 23ID-B and 23ID-D. For data collection, only the participants' crystals will be used. Software workshop: The rest of the time after data collection will feature many modern crystallographic software packages taught by authors and other experts. It will be organized in three sections - lectures, tutorials and hands-on trouble-shooting. There will be model data sets available for tutorials but data, provided by participants, will have higher priority for the hands-on sessions. *Applicants*: Graduate students, postdoctoral researchers and young scientists at the assistant professor level are encouraged to apply. Only 20 applicants will be selected for participation. Participants of the workshop are strongly encouraged to bring their own problem data sets or crystals so the problems can be addressed during data collection and/or computation workshops. *Application*: Application deadline is April 11. The application form, the program, contact info and other details can be found at http: http://www.ccp4.ac.uk/schools/APS-2014/index.php<https://mail.anl.gov/owa/redir.aspx?C=Qww5V7BVpECZd8A2kldFSf7_-DvC9NAIxdFZE…> *Fees: *There is no fee for the workshop. The students will be responsible for their transportation and lodging. The workshop organizers can help make the reservations at economical lodging at the Argonne Guest House. The workshop will also cover the expenses for all meals and refreshments. We hope to see you at the school, Garib, Ronan and Nukri -- Ruslan Sanishvili (Nukri) Macromolecular Crystallographer GM/CA@APS X-ray Science Division, ANL 9700 S. Cass Ave. Argonne, IL 60439 Tel: (630)252-0665 Fax: (630)252-0667rsanishvili(a)anl.gov

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Re: [phenixbb] autosol error// phaser error
by Terwilliger, Thomas C 03 Feb '14

03 Feb '14

Hi Almudena, Can you possibly say what version of Phenix you are using: phenix.version and then the columns in your mtz file: phenix.mtz.dump my_mtz_that_fails.mtz and the inputs you used for autosol and phaser (you can send the top part of the log files that should have this information). Can you also try this little test for resolve model building (that is where the "cannot read segment library" comes from): phenix_regression.wizards.test_command_line_build test_autobuild_quick That would help for diagnosing the problems. All the best, Tom T Hi everyone, I am facing some troubles with PHASER and with AutoSol (things that did not happen earlier to me). I am working with anomalous data and the first thing I do is to run HySS in order to find the heavy atoms sites. Once this is done I have two options: run PHASER or run AutoSol. Phaser gives the following error message: ERROR setting up data inputs (FATAL RUNTIME) Can not find MTZ column "F_SAD_SAD(+)" Instead Autosol gives the following: ERROR sorry can not read segment library Could anyone help me out here? Thank you very much in advance. Best, Almudena -- Almudena Ponce-Salvatierra Macromolecular crystallography and Nucleic acid chemistry Max Planck Institute for Biophysical Chemistry Am Fassberg 11 37077 Göttingen Germany

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Ten days left, many seats available: Apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 31 Jan '14

31 Jan '14

We are offering RapiData 2014, the sixteenth offering of our popular course: Rapid Data Collection and Structure Solving at the NSLS: A Practical Course in Macromolecular X-Ray Diffraction Measurement The course will be held 27 April - 2 May 2014: http://www.bnl.gov/RapiData/. Students could be at any level from advanced undergraduate to full professor. The course should accommodate 48 students total. We encourage all students to bring their own specimens for data collection, and to bring old data for the data-reduction and structure-solving tutorials. Please read the Course Announcement at http://www.bnl.gov/RapiData/. You'll see that many experts in the field will be available for lectures and tutorials. In addition to MX there will be opportunity for learning about correlated MX and spectroscopy, and SAXS. You'll find the application materials on the Course Application tab at this site. For the twelfth time we will hold a short lecture course on the fundamentals of crystallography for roughly five hours on Sunday 27 April. The body of the RapiData course really requires that students have a healthy knowledge of crystallography. For potential students who have some experience but are shaky about fundamentals, this course will help. There will be an additional fee for the fundamentals course, to pay for Saturday night accomodations and food on Sunday morning and noon. Latin American Scientists: Several scholarships are available, from the International Union of Crystallography, to pay partial travel and subsistence costs for Latin-American students and junior faculty (no more than 30 yrs). Please apply for the course, and then contact R. Sweet (sweet(a)bnl.gov) if you are interested in applying for a scholarship. In accordance with the standards of the International Union of Crystallography, we observe the basic policy of non-discrimination, affirming the right and freedom of scientists to associate in international scientific activity without regard to such factors as citizenship, religion, creed, political stance, ethnic origin, race, colour, language, age, or gender, in accordance with the Statutes of the International Council for Science. At this course no barriers will exist beyond the application procedure that would prevent the participation of bona fide scientists. Please apply yourself, or send your students to our course, Bob Sweet, Sonya Kiss, and Alex Soares Course Announcement at http://www.bnl.gov/RapiData/ ========================================================================= Robert M. Sweet E-Dress: sweet(a)bnl.gov Group Leader, PXRR: Macromolecular ^ (that's L Crystallography Research Resource at NSLS not 1) http://px.nsls.bnl.gov/ Photon Sciences and Biosciences Dept Office and mail, Bldg 745, a.k.a. LOB-5 Brookhaven Nat'l Lab. Phones: Upton, NY 11973 631 344 3401 (Office) U.S.A. 631 344 2741 (Facsimile) =========================================================================

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Output bulk solvent
by Koji Yonekura 29 Jan '14

29 Jan '14

Dear All, I am wondering if Phenix.refine has an option to output bulk solvent F to the mtz file. Best regards, Koji -- Koji Yonekura, Ph. D. Biostructural Mechanism Laboratory RIKEN SPring-8 Center Harima Institute 1-1-1 Kouto, Sayo, Hyogo 679-5148, Japan Tel: +81-791-58-2837 Fax: +81-791-58-1844 PHS: +81-791-58-0803 (7803) E-mail: yone(a)spring8.or.jp http://www.riken.jp/biostrmech/

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Postdoctoral position in macromolecular crystallography, HZI Braunschweig, Germany
by Wulf Blankenfeldt 27 Jan '14

27 Jan '14

Postdoctoral Position in Macromolecular Crystallography The Helmholtz Centre for Infection Research (HZI) in Braunschweig (Germany) announces an opening for a postdoctoral researcher in macromolecular crystallography. The position is associated with the department “Structure and Function of Proteins” headed by Prof. Wulf Blankenfeldt. The department focuses on unraveling molecular mechanisms of uncharacterized processes in the metabolism, regulation and virulence of pathogenic microorganisms. About the institute More than 800 people work at the HZI, a research institution in the Helmholtz Association of German Research Centres funded jointly by the Federal Republic of Germany and the Federal State of Lower Saxony. The centre’s task is to undertake biomedical research in the field of infection biology to expand knowledge of the fundamental mechanisms behind medically relevant infectious diseases with the aim of providing the key for the development of new therapeutics and vaccines. The Department “Structure and Function of Proteins” offers excellent working conditions, state-of-the-art technical platforms and equipment (including bacterial, insect cell and mammalian protein expression systems; access to a rotating anode X-ray source and several synchrotrons, crystal imaging and liquid handling systems; biophysical characterization of proteins), a lively scientific community and excellent support for the development of personal soft-skills. Projects All projects in our department aim at the identification and elucidation of the molecular function and mechanism of uncharacterized genes in pathogenic microorganisms. A better understanding of these “white spaces” of the genome map will not only unravel interesting new molecular processes but also provide novel targets for pharmaceutical intervention. To achieve our goal, we employ a gamut of methods including – in addition to structural biology – microbiological, biophysical and metabolomic techniques. Because our department is also the prime partner for structural biology-related questions at the HZI, the Technical University of Braunschweig and the German Centre for Infection Research (http://www.dzif.de/en/) the successful candidate will have the opportunity (and is expected) to take leading roles within our existing and emerging collaborations. Prerequisites Candidates should hold a Ph.D. in a life sciences related subject at the time of their employment. They should have a strong background in all aspects of macromolecular crystallography, including techniques of recombinant protein production and biophysical characterization. Experience in handling and manipulating pathogenic bacteria (biosafety level 2) is a plus. The handicapped Qualified applicants with a disability will be given preference. Job details The position is available immediately for three years with a six month probation period. Salary is according to level E14 of the collective labor agreement for public service (TVöD). Application details Candidates are asked to submit a full CV including a publication list, a cover letter outlining their interest in this position, a brief summary of current and past research experience (max. 2 pages) and contact data of at least two referees. All documents and information should be provided in English or German. Applications should refer to code 05/2014 and be sent by 28.02.2014 to: Helmholtz Centre for Infection Research Dept. of Human Resources Inhoffenstraße 7 38124 Braunschweig Germany E-Mail: JobsHZI(a)helmholtz-hzi.de For further information, please contact Prof. Dr. Wulf Blankenfeldt, phone: +49-531-6181-7000, e-mail: wulf.blankenfeldt(a)helmholtz-hzi.de ________________________________ Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de Das HZI ist seit 2007 zertifiziertes Mitglied im "audit berufundfamilie" Vorsitzende des Aufsichtsrates: MinDir’in Bärbel Brumme-Bothe, Bundesministerium für Bildung und Forschung Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Franziska Broer Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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Re: [phenixbb] measuring the angle between two DNA duplexes
by Xiang-Jun Lu 26 Jan '14

26 Jan '14

Hi Xiang, Since you mentioned "or in other software", I think I can chime in to this topic. The short answer is to see "How to calculate DNA bending angle?" ( http://forum.x3dna.org/faqs/how-to-calculate-dna-bending-angle/). 3DNA, following the original NewHelix algorithm, calculates a best-fitted linear global helix (where sensible) using equivalent C1'...C1', RN9/YN1...RN9/YN1 atom pairs along each strand. The so-called global helical axis parameters are no longer widely used, but the best-fitted linear helical axis is a useful concept, and has been kept in 3DNA and DSSR [ http://forum.x3dna.org/rna-structures/dssr-software-for-defining-the-(secon… ]. HTH, Xiang-Jun -- Xiang-Jun Lu (PhD) Email: xiangjun(a)x3dna.org Web: http://x3dna.org/ Forum: http://forum.x3dna.org/ > > > On 1/20/14, 5:48 AM, ?? wrote: > > > > Hi, > > > > I have a DNA model which is composed of two DNA duplexes. I want to > > measure the angle between the two duplexes and if there a way to do it in > > PHENIX or in other software? > > > > Thanks you very much for your help! > > > > Sincerely, > > Xiang > > > > -- > > Li Xiang > > Department of chemistry, > > Purdue University > > Email?lixiang1642(a)gmail.com > >

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non-bonded
by Leonard Thomas 23 Jan '14

23 Jan '14

Hello All, We are trying to refine a complex that was solved using Phaser. We have run a round of rigid body refinement using Refmac and now want to run a simulated annealing run in Phenix. Visually the complex looks pretty. The resolution we currently are at is 3.6 A. When we go to run phenix.refine the program quits with a Number of non-bonded interactions < 0.0001 error. Is there a way to loosen this up a bit or get around it or should we go about this in a different way? Best Regard, Leonard Thomas, Ph.D. Macromolecular Crystallography Laboratory Manager 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 http://barlywine.chem.ou.edu http://structuralbiology.ou.edu

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measuring the angle between two DNA duplexes
by 李翔 21 Jan '14

21 Jan '14

Hi, I have a DNA model which is composed of two DNA duplexes. I want to measure the angle between the two duplexes and if there a way to do it in PHENIX or in other software? Thanks you very much for your help! Sincerely, Xiang -- Li Xiang Department of chemistry, Purdue University Email：lixiang1642(a)gmail.com

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