February 2020 - cctbxbb - phenix-online.org

IUCr2020 Computing School in Nove Hrady - 17th to 22nd August - Registration opened
by Claudia Millán Nebot 24 Feb '20

24 Feb '20

Dear all, We announce the IUCr Computing School in Nove Hrady (Czech Republic) which will take place between 17th and 22nd August 2020 prior to the IUCr Congress in Prague. Registration has already started. Further information about the school can be found on the website: https://www.xray.cz/iucr/workshops/nh/default.htm. Follow also our hashtag on Twitter, #IUCr2020CompSchool. Active developers of crystallographic software, tools and methods are invited to participate at this Computing School. The school is not introductory and it is recommended that participants already have some basic programming skills and crystallographic knowledge. Our aim is to discuss and exchange ideas and to tackle the challenges related to the method development in crystallography. Participants can be early-career scientists (PhD students, Postdocs, etc.) as well as established developers. Our confirmed speakers are: - Simon Billinge (Columbia University, USA) - Luc Bourhis (Bruker, France) - Paul Boyle (Western University, London, Ontario, Canada) - Iracema Caballero (Institut de Biologia Molecular de Barcelona, Spain) - Gemma de la Flor (Karlsruhe Institute of Technology, Germany) - Dorothee Liebschner (Lawrence Berkeley National Laboratory, USA) - Rafiga Masmaliyeva (Institute of Molecular Biology and Biotechnology, Azerbaijan) - Garib Murshudov (Laboratory of Molecular Biology-MRC, UK) - Reinhard Neder (Institute of Condensed Matter Physics, Erlangen, Germany) - Alexandre Ourjoumtsev (Institut de Génétique et de Biologie Moléculaire et Cellulaire, France) - Randy Read (University of Cambridge, UK) - Massimo Sammito (University of Cambridge, UK) - Arkadiy Simonov (Eidgenössische Technische Hochschule Zürich, Switzerland) - Melanie Vollmar (Diamond Light Source Ltd, Harwell Science & Innovation Campus, United Kingdom) - Thomas White (Center for Free-Electron Laser Science, Hamburg, Germany) For any questions regarding the school please contact us. Best wishes, Claudia Millán (cmncri at ibmb.csic.es) Martin Lutz (m.lutz at uu.nl) Jan Rohlicek (rohlicek at fzu.cz) PD. Please find attached a poster about the school that you can forward, together with this email, to people potentially interested in participating in the Computing School.

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map grid sizes
by GEORGE N PHILLIPS 21 Feb '20

21 Feb '20

I am confused about grid sizes of maps. When i specify a grid size for an fft_map but then pull the numpy array out for direct manimpulation, it's always 2 larger in the last dimension. Why is it not the same size? Any help appreciated. George y# Now make initial (smoothed) map using random phases with Fobs f_obs_B = f_obs1.apply_debye_waller_factors( b_iso=biso_init) phases = f_obs_B.random_phases_compatible_with_phase_restrictions(deg=False) phases_data = phases.data() e_map_coeff = f_obs_B.phase_transfer(phase_source = phases_data) e_map = e_map_coeff.fft_map(crystal_gridding = crystal_gridding, symmetry_flags = maptbx.use_space_group_symmetry) print("cgridding", crystal_gridding.n_real()) # pick initial envelope e_map_array = e_map.real_map().as_numpy_array() print("e_map", e_map_array.shape) cgridding (90, 90, 80) e_map (90, 90, 82) George N. Phillips, Jr., Ph.D. Professor Emeritus University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone 713 348 6951 (Houston)

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a little help for newbie?
by georgep 18 Feb '20

18 Feb '20

I am starting to write some python code using cctbx, but am missing how to use the C++ bindings. I am fine unless a try to access them. Something about my environment or boost of something. Can anyone point me in the right direction? I have import boost.python but am cleary missing some fundamental knowledge. George Traceback (most recent call last): File "/Users/georgep/PycharmProjects/test_env/HIO_Version3.py", line 225, in <module> S0 = percentile[rho_calc_true > percentile(rho_calc_true, solv_frac)] = 1 File "/Users/georgep/PycharmProjects/test_env/HIO_Version3.py", line 216, in percentile order = flex.sort_permutation(x) Boost.Python.ArgumentError: Python argument types in scitbx_array_family_flex_ext.sort_permutation(double) did not match C++ signature: sort_permutation(scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, bool reverse=False, bool stable=True) sort_permutation(scitbx::af::const_ref<unsigned long, scitbx::af::trivial_accessor> data, bool reverse=False, bool stable=True) sort_permutation(scitbx::af::const_ref<int, scitbx::af::trivial_accessor> data, bool reverse=False, bool stable=True) George N. Phillips, Jr. Ralph and Dorothy Looney Professor BioSciences at Rice Rice University, MS140 6100 Main Street Houston, Texas 77005-1892 Office: +1 713.348.6951 www.phillipslab.org

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