March 2012 - phenixbb - phenix-online.org

Fwd: Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 02 Mar '12

02 Mar '12

Sue: I am not sure they are being included... I have the option checked, but the R values and difference maps tell me otherwise Pavel: A bug? That would be consistent with the behavior I observe. Even when I enable refinement with hydrogens individual or riding, i see essentially no difference in maps or Rfree values. -- Yuri Pompeu

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Hi Res Model. Maybe its time to Include Hydrogens?
by Yuri 02 Mar '12

02 Mar '12

Dear users, I am refining a 400 aa protein with data out to 1.16 A (real data). I am almost finished with refinement. I have good geometry, complete model and ligands Rw 0.11 Rf 0.13. Difference maps seem to be asking for more. See attached screen shot.Both maps 2Fo-Fc (non-filled) and Fo-Fc are contoured at 3 sigma. How should I handle this? I have used hydrogens all along (riding). Thanks for your time -- Yuri Pompeu

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phenix.reciprocal_space_arrays question
by Michael Thompson 01 Mar '12

01 Mar '12

Hi All, I have a very simple question about phenix.reciprocal_space_arrays. I apologize if this is obvious, but I could not find any info in the documentation or the bb archives. I just want to make sure that I am actually doing what I think I am doing. If I provide phenix.reciprocal_space_arrays with an .mtz file containing Fobs and a .pdb file for which I would like to calculate Fmodel and PHImodel, will the resulting Fmodel (and Fcalc, Fmask, Fbulk, etc.) be scaled to the Fobs from the input .mtz? Thanks for the help! Mike T. -- Michael C. Thompson Graduate Student Biochemistry & Molecular Biology Division Department of Chemistry & Biochemistry University of California, Los Angeles miket(a)chem.ucla.edu

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BCA/CCP4 Summer School 2012
by Airlie McCoy 01 Mar '12

01 Mar '12

Applications are now open for the BCA/CCP4 Summer School in Protein Crystallography to be held at Diamond (UK) from Tuesday 28th August to Sunday 2nd September 2012. Applications close 1st May 2012. The BCA/CCP4 Protein Crystallography Summer School is intended for students and researchers new to crystallography. Its dual aims are to provide comprehensive training in crystallography and to promote best practise within the British crystallographic community. The lectures cover the gamut of techniques required for a structure solution, from protein expression through to structure validation. Intensively supervised computer tutorials enable students to relate the theory presented in the lectures to practice. Although CCP4 programs will primarily be used in these tutorials, the aim will be to approach crystallographic questions in a software-agnostic manner. There will also be a crystal manipulation and cooling workshop. (Note that the course is scheduled during Diamond synchrotron downtime, so there will not be active data collection at the Diamond beamlines.) For more information on eligibility, cost, and applications see: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012.html Application form: http://www.diamond.ac.uk/Home/Events/BCA-Summer-School-2012/Application-Pag…

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