- phenixbb - phenix-online.org

Data processing
by Sharan Karade 07 Sep '16

07 Sep '16

Dear All, i had collected the data set on the Bruker X-ray machine (home source), it has its in built data processing software, but i want to process it on HKL2000, but the file format is .srfm and it is not read by HKL2000 soft. in our lab we have. So, i tried to change the detector type, then i came to know that we don't have license to bruker detector, So anyone know how to convert these file into .mccd or.mar, so i can process them. Thank you -- Sharan C/O Dr. J V Pratap Senior Research Fellow, CSIR-Central Drug Research Institute, Lucknow

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Post-doctoral position in membrane protein structure and function, University of Oxford, UK
by Maike Bublitz 06 Sep '16

06 Sep '16

Dear all, a post-doctoral position is available in the research group of Associate Prof. Maike Bublitz at the Department of Biochemistry, University of Oxford. The project aims to understand the structure and function of microbial membrane transport proteins identified as potential new drug targets, using a combination of state-of-the-art structural (X-ray crystallography, cryo-EM) and biochemical/biophysical techniques. Applicants should hold a PhD in a relevant subject area, such as membrane protein biochemistry or structural biology. Experience in native or recombinant membrane protein expression, purification and either structural determination or functional analysis using biochemical and biophysical techniques is essential. Ability to work in a team as well as contribute to supervision activities and excellent verbal and written communication skills are expected. Experience in protein X-ray crystallography and/or cryo-EM is an advantage. To apply for this role and for further details, including the job description and selection criteria, please click on the link below: https://www.recruit.ox.ac.uk/pls/hrisliverecruit/erq_jobspec_details_form.j… Applications for this vacancy are to be made online by 14th September 2016. PLEASE NOTE: THIS IS A READVERTISEMENT, PREVIOUS APPLICANTS NEED NOT APPLY. Best regards, Maike ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk> ************************************************* Dr. Maike Bublitz Associate Professor of Microbial Biophysics Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU United Kingdom phone: +44 (0)1865 613221 maike.bublitz(at)bioch.ox.ac.uk<http://bioch.ox.ac.uk>

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Computational Crystallography Newsletter, Volume 7, Number 2
by Nigel Moriarty 30 Aug '16

30 Aug '16

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. July 2016 <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf> Articles - Working with EIGER data <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=11> - Processing XFEL data with cctbx.xfel and DIALS <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=18> Short Communications - Using Molecular Dynamics Simulations to Enrich the Water Structure in Biomolecular Crystals <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=7> Fitting tips #12 – Twist Tells: better β strands at >3.5Å in x-ray or cryoEM <http://www.phenix-online.org/newsletter/CCN_2016_07.pdf#page=2> 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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polder map
by Kaziaa 29 Aug '16

29 Aug '16

Dear Phenix users, i am wondering if anyone has used phenix polder in Windows machine. Any kind of help would me appreciated !! Regards Kazi

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Meaning of "resolution" keyword for phenix.real_space_refine with mrc/ccp4 map input?
by Oliver Clarke 28 Aug '16

28 Aug '16

Hi, What exactly does phenix.real_space_refine do with the mandatory "resolution=" keyword when refining a model against a ccp4/mrc formatted map? Is this purely for adjusting restraints etc, or does phenix internally low-pass filter or resample the map based on this parameter? This seems like a basic question, so I apologize if the answer is staring me in the face, but I couldn't see it in the online documentation or in the output of phenix.real_space_refine --help. Cheers Oliver.

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discrepancies between completeness stats
by Kendall Nettles 23 Aug '16

23 Aug '16

Dear PHENIX developers, We are getting a group of structures ready for publication and noticed that the table 1 description of the completeness is showing higher completeness in the last shell than overall. See Table 1, attached, for one example, with completeness at 81.73 (96.75). This table was calculated from the last major release of PHENIX, and was the same on the latest nightly build. The data was highly anisotropic so we truncated it with the UCLA diffraction anisotropy server. Validation program suggests completeness is 13% in highest res shell, which makes more sense with anisotropic data. I also noticed that the refinement log lists the overall completeness at 85% while the validation and table 1 programs give 82%. Thanks for you advice! Kendall

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Merged data for "Table 1"
by Yufan Wu 10 Aug '16

10 Aug '16

Dear all, I am going to generate “Table 1” by Phenix. However, my data.mtz file was merged from 2 HKL file (2 different datasets). What should I input in “unmerged data"? Thank you in advance! Best, Yufan Regards, Yufan Wu The Plueckthun Lab www.bioc.uzh.ch/plueckthun <http://www.bioc.uzh.ch/plueckthun>Phone: +41 44 635 5574

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Mg is driving me crazy
by Almudena Ponce Salvatierra 09 Aug '16

09 Aug '16

Dear all, I am refining a structure that showed two positive peaks larger than 8 sigma. I assigned them as Mg ions, since I have them in the crystallization condition and also because it make sense, according to where they are located. However when I refine there's still all this green blob around the already properly placed Mg ions. I don't know why, they don't show large thermal factors or anything suspicious... I'm refining individual sites, individual adps, and TLS groups. The resolution I am talking about is 2.5 A. Any thoughts on this? Thank you very much Best wishes, 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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Phenix.refine peptide chain break
by Booe, Jason M (HSC) 29 Jul '16

29 Jul '16

Dear all, I am refining a structure after renumbering my chain such that there is a gap in numbering (i.e. chain A ends at 350 and then starts again at 1000) as this has numbering has been recommended for us to use by the PDB for our fusion proteins. I'm having issues with Phenix.refine not understanding that their is still a peptide bond and breaks the chain and pushes the atoms away. There is no TER card between the chains and I've used LINK records as well to no avail. I'm wondering how to properly deal with this. Thanks, Jason

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Refine pixel size of map (for EM data)?
by Oliver Clarke 26 Jul '16

26 Jul '16

Hello, I wonder whether it would be possible to add an option for phenix.real_space_refine to allow refinement of the pixel size of the map (or the unit cell dimensions - just an overall size scale factor), and write out the altered map at the end of refinement. Although we try to calibrate this as best as we are able at the time of data collection, it is never perfect - for example, in one case I have dealt with, our nominal pixel size out of the scope is 1.19 Å, but the pixel size calibrated based on a crystal structure of a fragment of the protein is 1.25 Å. This is not a huge difference, but it is sufficient I think to have a substantial impact on refinement, particularly as regards clash assessment and H-bond/sec struc restraints. In cases where one does not have a solved crystal structure to use for calibration, perhaps refining the pixel size in conjunction with the geometry might be of some use? Cheers, Oli

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