January 2014 - phenixbb - phenix-online.org

labelit distl_minimum_number_spots_for_indexing
by Christian Roth 21 Sep '15

21 Sep '15

Dear Phenix-Team I installed the latest nightly build 1.8-1069. I tried to index some diffraction images and to overwrite the minimum usable spots for indesing I tried the suggested command. However If I try this command, it seems that it does not exist. At least in the list of the possible distl commands it does not show up. Do I have to install some additional stuff or change some preferences to get this command? Best Regards Christian

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exporting results, reduce
by jp d 10 Feb '14

10 Feb '14

hi, we have a large complex at low resolution (7A) and just want to see general conformational changes. Occasionally phenix gets stuck at 'Exporting Results' and top shows 'reduce' running and using lots of RAM . so much RAM that it starts using swap. is there a way to bypass or limit the reduce step. thanks jpd

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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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phenix.refine wxc weight
by rainfieldcn 17 Jan '14

17 Jan '14

Hi All, I am doing refinement on some low resolution structures ( around 4A ). I used wxc_scale=0.15 before on phenix.refine: 1.8.2_1309 I got: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 BOND : 0.006 0.048 24993 REMARK 3 ANGLE : 1.049 11.841 33849 REMARK 3 CHIRALITY : 0.044 0.323 3843 REMARK 3 PLANARITY : 0.005 0.053 4276 REMARK 3 DIHEDRAL : 14.080 87.581 8889 REMARK 3 MIN NONBONDED DISTANCE : 2.098 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 10.49 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.10 % REMARK 3 ALLOWED : 3.84 % REMARK 3 FAVORED : 96.06 % REMARK 3 ROTAMER OUTLIERS : 3.87 % REMARK 3 CBETA DEVIATIONS : 0 now, phenix is updated to phenix.refine: 1.8.4_1496. and I got: REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD MAX COUNT REMARK 3 BOND : 0.016 0.237 24993 REMARK 3 ANGLE : 2.262 36.773 33853 REMARK 3 CHIRALITY : 0.099 2.724 3847 REMARK 3 PLANARITY : 0.010 0.102 4280 REMARK 3 DIHEDRAL : 14.585 89.962 8889 REMARK 3 MIN NONBONDED DISTANCE : 1.923 REMARK 3 MOLPROBITY STATISTICS. REMARK 3 ALL-ATOM CLASHSCORE : 17.57 REMARK 3 RAMACHANDRAN PLOT: REMARK 3 OUTLIERS : 0.32 % REMARK 3 ALLOWED : 4.07 % REMARK 3 FAVORED : 95.61 % REMARK 3 ROTAMER OUTLIERS : 4.22 % REMARK 3 CBETA DEVIATIONS : 39 So I am wondering if there is some bug in phenix.refine that wxc_scale doesn't work? Thanks, Lei

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MR
by Swastik Phulera 17 Jan '14

17 Jan '14

Dear All, I am trying an MR, it looks like there would be 16 dimers in the asymmetric unit, Upon running Phaser once it could easily fit two copies. I now wish to use this solution to perform further MR runs in order to locate the other dimers. I was just wondering what shall be the right way to go about it. Regards Swastik

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Re: [phenixbb] phenixbb Digest, Vol 98, Issue 2
by Kay Diederichs 14 Jan '14

14 Jan '14

Am 14.01.14 21:00, schrieb phenixbb-request(a)phenix-online.org: > PS. It's possible I'm still misunderstanding the meaning of FRIEDEL'S_LAW=TRUE. > Under what circumstances does XDS output anomalous vs. non-anomalous data? This keyword affects the way the statistics are calculated in CORRECT.LP: with FRIEDEL'S_LAW=FALSE the members of Bijvoet pairs are treated as separate reflections, which almost doubles the number of unique reflections, affecting the reported completeness and R-values, I/sigmas and so on. The reflection output file XDS_ASCII.HKL has unmerged intensities in all cases (whether FRIEDEL'S_LAW=TRUE or FALSE). Phenix should ignore the FRIEDEL'S_LAW setting in XDS_ASCII.HKL. hope this helps, Kay

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XDS data
by Tim Gruene 14 Jan '14

14 Jan '14

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Dear all, I would like to run Phaser-EP through the phenix GUI. When I first uploaded the XDS_ASCII.HKL file, there was an error message about "No valid observed reflections found in this file". Subsequently I uploaded an unmerged hklf4 file. The GUI tells me I need to let phenix know about it being hklf4 by appending '=hklf4'. However, when I do so, there is an error message the file did not exist and the Data file line goes red. Where should I correctly append '=hklf4'? At the bottom, the message states it would be best to recover the original reflection data such as [...] XDS [...]. This suggests that the original XDS_ASCII.HKL could be used. Is this correct in if so, how do I put it into phenix? Best, Tim - -- - -- Dr Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.12 (GNU/Linux) Comment: Using GnuPG with Icedove - http://www.enigmail.net/ iD8DBQFS1TDEUxlJ7aRr7hoRArKdAKDpXBrs4wsWMvWw0JNo8F746fY76ACfeFuG geGY6T6se8peE9dEGz8ETow= =AaLk -----END PGP SIGNATURE-----

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Refining coordinates
by Subhani Bandara 10 Jan '14

10 Jan '14

Dear all, I have a protein crystallized with metal chelate complexes and some of the atoms of chelators and the metals sit on the two fold axis. Is there a way that I can refine the coordinates of those atoms only along the two fold axis (let's say X) while restraining the coordinate refinement along other two axes (Y and Z)? Thanks Subhani

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fwd: Announcement: International Summer School of Crystallography - May 2014, Hamburg, Germany
by Nathaniel Echols 10 Jan '14

10 Jan '14

---------- Forwarded message ---------- From: "Oberthuer, Dominik" <dominik.oberthuer(a)cfel.de> To: phenixbb(a)phenix-online.org Date: Fri, 10 Jan 2014 16:14:08 +0100 Subject: Announcement: International Summer School of Crystallography - May 2014, Hamburg, Germany Dear colleagues, we are pleased to announce the first International Summer School of Crystallography at the Center for Free-Electron Laser Science at DESY, Hamburg (D). As part of the International Year of Crystallography 2014, Prof. Carmelo Giacovazzo will give a full week of lectures on the basics of crystallography, as well as the basics of modern phasing methods in protein crystallography. The course will cover basic mathematical understanding of crystallographic point and space groups, diffraction experiments, structure factor calculations, systematic absences, determination of space groups and many additional topics. After the discussions of theory, one afternoon will be spent to learn about modern applications of protein crystallography using advanced light sources, such as 3rd generation synchrotron and XFELs. The course will be given mainly for PhD students working in the field of crystallography, but exceptions for motivated PostDocs and MSc students can be made. The course will mostly cover mathematical background of crystallography, hence we are looking for students, having a (bio)physics background. This will NOT be a workshop covering protein crystallographic programs but rather the theory behind those programs. The course will start Sunday (11.05.2014) around lunch and will end Saturday (17.05.2014) around lunch. The registration fee is 100 EUR per person including coffee breaks and lunch. Accommodations can be made at the DESY Guest House: 70 EUR per person for 7 nights (10.-17.05.2014). Application deadline will be 28th of February 2014 and notification of accepted applications will be sent during March 2014. The applications will be managed via the DESY Indico system: https://indico.desy.de//event/ISSC14 Applicants must provide a motivation letter, as well as a CV, directly to the organizer Cornelius Gati (cornelius.gati(a)cfel.de). Places and accommodation are limited to 30 students in total. Please contact Cornelius Gati regarding further questions ( cornelius.gati(a)cfel.de). We are looking forward to welcome you in Hamburg! -- Dr. Dominik Oberthür CFEL - Center for Free-Electron Laser Science Coherent Imaging Division and University of Hamburg Laboratory for Structural Biology of Infection and Inflammation Notkestrasse 85 22607 Hamburg Germany phone: +49 (0)40 8998 6394 dominik.oberthuer(a)cfel.de obertuer(a)chemie.uni-hamburg.de

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Low F-obs Values
by 张怀东 06 Jan '14

06 Jan '14

Hi, everyone I used phenix-1.8.2-1309 to do MR and Autobuild, then Refinement, the max F-obs value of the mtz file from refinement was about 300. However, I used phenix-1.8.4-1496 to do the same work, the max F-obs value was about 3000. The resulting structure models donot seem to be any different. We tried several datasets of different proteins, and the max F-obs value are low with phenix-1.8.2-1309. So is this a real problem or not? Best regards Huaidong Zhang

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I remind you: Please apply for RapiData 2014, a course on Data Collection and Structure Solving at the NSLS.
by Robert Sweet 06 Jan '14

06 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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Postdoc positions (SGC, Diamond): fragments into crystals
by Frank von Delft 02 Jan '14

02 Jan '14

Hello, I have 3 open postdoc positions, to work on technologies around fragment screening in crystals, which is what my (joint) research team at Diamond (beamline I04-1) and SGC (PX group) is trying to make simple and accessible. Details of the project are on my website <http://www.thesgc.org/scientists/groups/oxford/crystallography>; we need smart people to: * (at SGC) test-drive with start-to-end soaking campaigns <http://www.thesgc.org/careers/oxford/crystallography-postdoc-fragment-scree…> * (at SGC) develop crystal engineering to get soakable systems (molecular biology, biochemistry) <http://www.thesgc.org/careers/oxford/crystallography-postdoc-crystal-engine…> * (at Diamond) explore soaking techniques <http://www.diamond.ac.uk/Home/Jobs/Current/DIA0886_CH.html> The application deadlines for the SGC posts are a function of the UK's charming political climate; if you're interested but from outside the EU, alert me with a direct email plus CV. phx. P.S. if you know smart undergrads who'd be interested in a DPhil in that sort of thing -- applied engineering, technology -- send them to that website too. (DPhils are what you get in Oxford - that makes it special. Or "special".)

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Multiple conformation, two ligands
by YANG HAI 31 Dec '13

31 Dec '13

Dear Phenix Community, I tried to model two ligands one of which has two conformations. In other words, the two scenarios are: 1) ligand X with conformation A (XA, 75% occupancy); 2) ligand X with conformation B (XB, 25% occupancy) plus another ligand Y. However, the problem is ligand Y will have steric clash with ligand XA. If I rename ligand X and Y to the same residue name then I do not know how to define the CIF file. I apologize if this question was asked before and I do not know how Phenix or other refinement can deal with multiple conformation a group of ligands. Thanks. Happy new year! Yang Hai Christianson Lab University of Pennsylvania

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