August 2020 - cctbxbb - phenix-online.org

Changes to boost_adaptbx and
by Billy Poon 18 Aug '20

18 Aug '20

Hi everyone, Two pull requests were merged today that make some important changes. 1) The boost imports were moved to boost_adaptbx.boost. This avoids claiming the main "boost" namespace. A common piece of code that will need to be changed is import boost.python ext = boost.python.import_ext("your_boost_python_ext") That can be changed to import boost_adaptbx.boost.python as bp ext = bp.import_ext("your_boost_python_ext") Otherwise, a FutureWarning will be raised. More information can be found at https://github.com/cctbx/cctbx_project/issues/458 https://github.com/cctbx/cctbx_project/pull/470 https://github.com/cctbx/cctbx_project/pull/516 2) More dependency repositories were moved from cci.lbl.gov to GitHub. If you use bootstrap.py to build cctbx, you will want to delete annlib, ccp4io_adaptbx, clipper, eigen, gui_resources, tntbx. Using a newly updated bootstrap.py, the copies from GitHub will be used instead. More information can be found at https://github.com/cctbx/cctbx_project/pull/408 Let us know if you have any questions. Thanks! -- Billy K. Poon Research Scientist, Molecular Biophysics and Integrated Bioimaging Lawrence Berkeley National Laboratory 1 Cyclotron Road, M/S 33R0345 Berkeley, CA 94720 Tel: (510) 486-5709 Fax: (510) 486-5909 Web: https://phenix-online.org

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unmerged data as mtz object
by Robert Oeffner 04 Aug '20

04 Aug '20

Hi, Does anybody know how to convert a miller array of unmerged data to an mtz object? For merged data I do something like this: mtzobj = millarr.as_mtz_dataset(column_root_label="I") But if millarr contains multiple observations with the same hkl index. Then the above code fails with the exception cctbx Error: Duplicate entries in miller_indices array. Any suggestions? Many thanks, Rob -- Robert Oeffner, Ph.D. Research Associate, The Read Group Department of Haematology, Cambridge Institute for Medical Research University of Cambridge Cambridge Biomedical Campus The Keith Peters Building Hills Road Cambridge CB2 0XY www.cimr.cam.ac.uk/investigators/read/index.html tel: +44(0)1223 763234 -- This email has been checked for viruses by AVG. https://www.avg.com

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flex.histogram giving ArgumentError when arguments correct
by Winter, Graeme (DLSLtd,RAL,LSCI) 04 Aug '20

04 Aug '20

H = flex.histogram(coords, data_min=0.0, data_max=dim, n_slots=dim) Gives Boost.Python.ArgumentError: Please report this error to dials-support(a)lists.sourceforge.net: Python argument types in histogram.__init__(histogram) did not match C++ signature: __init__(_object*, double, double, double, scitbx::af::shared<long>, unsigned long) __init__(_object*, scitbx::histogram<double, long> other, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, double relative_tolerance=0.0001) __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, double data_min, double data_max, unsigned long n_slots=1000, double relative_tolerance=0.0001) __init__(_object*, scitbx::af::const_ref<double, scitbx::af::trivial_accessor> data, unsigned long n_slots=1000) Despite coords being <scitbx_array_family_flex_ext.double object at 0x7fa8d671b5b0> with shape (31294944,) and dim being 18093576 (i.e. integer) and h = flex.histogram(a, data_min=0, data_max=100, n_slots=100) working fine in another context i.e. the calling convention is correct This has so far cost a few hours, so what gives? How can this be holding it wrong? C++ code suggests that the bin types are long so this should be fine Any hints? Thanks Graeme -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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