- phenixbb - phenix-online.org

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 22 Jan '14

22 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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