[ccp4bb] PhD position in Structural Biology in Norway
Dear all, A 3- or 4-year PhD position in Structural Biology / Biophysics / Biochemistry starting August 2015 is available at University of Oslo, Department of Biosciences, Section for Biochemistry and Molecular Biology in the Metalloprotein group. The project is in the field of structural biology, biophysics and biochemistry with an emphasis on protein crystallography and spectroscopy (UV-vis, Raman and EPR) in combination with other biochemical and biophysical methods. The project is dealing with different redox proteins involved in oxygen activation and electron transfer. The focus will be on some enzyme systems like ribonucleotide reductase and nitric oxide synthase, their reaction mechanism and redox activation pathways. More information about the project, position and application procedure is found on the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no Applicants must hold a Master's degree or equivalent in structural biology, bioinorganic chemistry, biochemistry, biophysics, protein crystallography or related fields. We are seeking a highly motivated candidate that should have skills and experience in working with proteins or bioinorganic molecules. It would be advantageous with hands-on experience within topics like cloning, protein expression, purification, crystallisation, protein crystallography, spectroscopy, bioinorganic chemistry, protein-protein interactions, enzyme kinetics and redox-, radical- and metalloproteins. Candiates without a Master's Degree have until 30 June 2015 to complete the final exam. Application deadline is 13th April 2015 through the website: http://uio.easycruit.com/vacancy/1352831/96323?iso=no For further information please contact: Dr. Hans-Petter Hersleth, (h.p.hersl...@ibv.uio.no) -- Hans-Petter Hersleth, PhD Project Leader, Researcher and Senior Lecturer Department of Biosciences, University of Oslo Section for Biochemistry and Molecular Biology P.O.Box 1066 Blindern, NO-0316 Oslo, Norway http://www.mn.uio.no/ibv/personer/vit/hphersle/index.html ---
Re: [ccp4bb] Offtopic: Software to closely visualize interacting partnets in protein complex
Thank you all for your valuable suggestions. They have really worked well for me :) Regards, Debasish Kumar Ghosh CSIR- Junior Research Fellow (PhD Scholar) C/o: Dr. Akash Ranjan Computational and Functional Genomics Group Centre for DNA Fingerprinting and Diagnostics Hyderabad, INDIA Email(s): dkgh...@cdfd.org.in, dgho...@gmail.com Telephone: 0091-9088334375 (M), 0091-40-24749396 (Lab) Lab URL: http://www.cdfd.org.in/labpages/computational_functional_genomics.html
Re: [ccp4bb] Fwd: Structure with high B-factor
On Tuesday, 17 March, 2015 17:34:24 Manish Shah wrote: Hi All, I solved a structure using molecular replacement (Phaser) and the current R-factor and R-free is 0.2 and 0.25. The electron density looks great for residues and the ligand, however, the issue is with the B-values. The average B-value is 110 at this stage of refinement and I could not bring it down. All the residues are having a high B-values ranging from 90-120, while the R is good. I have tried several options in CCP4 (restrained refinement in Refmac) to bring it down and also used other MR programs, but still it still continues to be in the same range. I will look forward to any suggestions. Thank you. What was the Wilson B factor reported by Aimless or Truncate? What is the resolution of the data? -- Ethan A Merritt Biomolecular Structure Center, K-428 Health Sciences Bldg MS 357742, University of Washington, Seattle 98195-7742
[ccp4bb] Fwd: Structure with high B-factor
Hi All, I solved a structure using molecular replacement (Phaser) and the current R-factor and R-free is 0.2 and 0.25. The electron density looks great for residues and the ligand, however, the issue is with the B-values. The average B-value is 110 at this stage of refinement and I could not bring it down. All the residues are having a high B-values ranging from 90-120, while the R is good. I have tried several options in CCP4 (restrained refinement in Refmac) to bring it down and also used other MR programs, but still it still continues to be in the same range. I will look forward to any suggestions. Thank you.
Re: [ccp4bb] OS X yosemite
Hi Mirek: I haven’t encountered anything (CCP4, phenix, coot. pymol, etc) that doesn’t work, but also haven’t found a single compelling advantage (or even a non-compelling advantage) to upgrading. You get to see more of the spinning beachball of death while waiting for file dialog boxes to materialize. YMMV, Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott On Mar 17, 2015, at 4:30 PM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I am thinking of upgrading the os on my mac to Yosemite. Are there any known issues for crystallographic software that I should pay attention to? Thanks, Mirek
Re: [ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop
Hi Marc, I have an Intel Iris Pro graphics chip on a Late 2013 MacBook Pro which works impressively well with all these programs, even on a 15 inch Retina display. I don’t know if the Nvidia one is better though... Bonne chance, Mark On 17 Mar 2015, at 16:12, Marc Graille marc.grai...@polytechnique.edu wrote: Hello, I would like to buy a MacBook Pro laptop that will allow me among others to solve structures, build models and visualize electron density maps using Pymol, Coot or Chimera. I have the choice between between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is fine for the programs I want to run. Can some of you share advices/feedback with me? Thanks a lot for your answer. Best wishes, Marc Dr Marc GRAILLE Directeur de recherche CNRS Team: Translation and degradation of eukaryotic mRNAs Team supported by the ATIP-Avenir CNRS program Laboratoire de Biochimie ECOLE POLYTECHNIQUE - UMR7654 CNRS 91128 PALAISEAU CEDEX Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 Office 033012B Email: marc.grai...@polytechnique.edu mailto:marc.grai...@polytechnique.edu http://bioc.polytechnique.fr/spip.php?rubrique117 http://bioc.polytechnique.fr/spip.php?rubrique117
[ccp4bb] OS X yosemite
Hi, I am thinking of upgrading the os on my mac to Yosemite. Are there any known issues for crystallographic software that I should pay attention to? Thanks, Mirek
[ccp4bb] Graphics cards for Coot, Pymol, Chimera on MacBook Pro Laptop
Hello, I would like to buy a MacBook Pro laptop that will allow me among others to solve structures, build models and visualize electron density maps using Pymol, Coot or Chimera. I have the choice between between Intel Iris Pro (5200 series) and Intel Iris Pro + Nvidia GT 750M for the graphics cards but I don’t know which one is fine for the programs I want to run. Can some of you share advices/feedback with me? Thanks a lot for your answer. Best wishes, Marc Dr Marc GRAILLE Directeur de recherche CNRS Team: Translation and degradation of eukaryotic mRNAs Team supported by the ATIP-Avenir CNRS program Laboratoire de Biochimie ECOLE POLYTECHNIQUE - UMR7654 CNRS 91128 PALAISEAU CEDEX Phone : +33 (0)1 69 33 48 90 – Fax : +33 (0)1 69 33 49 09 Office 033012B Email: marc.grai...@polytechnique.edu http://bioc.polytechnique.fr/spip.php?rubrique117
[ccp4bb] Vacancy for a Scientific Programmer Bioimaging EMPIAR at PDBe
Hi all, We are looking to recruit an experienced and motivated Scientific Programmer Bioimaging EMPIAR to join the Protein Data Bank in Europe (PDBe) team at the European Bioinformatics Institute (EBI) located on the Wellcome Trust Genome Campus near Cambridge in the UK. PDBe has recently launched EMPIAR (http://pdbe.org/empiar), an archive of raw 2D image data from electron microscopy and electron tomography experiments. We now plan to extend and improve the archival, integration and dissemination of cellular imaging data from a range of other modalities including 3D scanning electron microscopy (3D-SEM), soft X-ray tomography (SXT) and correlative light and electron microscopy (CLEM). We are therefore seeking to recruit an enthusiastic scientific programmer with outstanding programming skills to join the EMPIAR development team. For more information, see: https://ig14.i-grasp.com/fe/tpl_embl01.asp?newms=jjid=53570aid=15470 For informal enquiries, please contact Ardan Patwardhan ar...@ebi.ac.uk, who is in charge of the EMPIAR project. Best wishes, --Gerard --- Gerard J. Kleywegt, PDBe, EMBL-EBI, Hinxton, UK ger...@ebi.ac.uk . pdbe.org Secretary: Pauline Haslam pdbe_ad...@ebi.ac.uk
Re: [ccp4bb] OS X yosemite
HI Mirek, You may wanna to check for codes using libpng12.0.dylib. This you have to get from other sources. Best Andy Anindito Sen. Ph.D Scientist Application Specialist in Biological Sciences JEOL LTD. 13F, Ohtemachi Nomura Bldg 2-1-1 Ohtemachi Chiyoda-Ku. Tokyo, Japan Tel: +81-3-6262-3563 Fax: +81-3-6262-3577 www.jeol.com On Mar 18, 2015, at 11:57 AM, William G. Scott wgsc...@ucsc.edu wrote: Hi Mirek: I haven’t encountered anything (CCP4, phenix, coot. pymol, etc) that doesn’t work, but also haven’t found a single compelling advantage (or even a non-compelling advantage) to upgrading. You get to see more of the spinning beachball of death while waiting for file dialog boxes to materialize. YMMV, Bill William G. Scott Professor, Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/~wgscott On Mar 17, 2015, at 4:30 PM, Cygler, Miroslaw miroslaw.cyg...@usask.ca wrote: Hi, I am thinking of upgrading the os on my mac to Yosemite. Are there any known issues for crystallographic software that I should pay attention to? Thanks, Mirek
