September 2014 - cctbxbb - phenix-online.org

new cctbx-plus installers
by Nathaniel Echols 23 Sep '14

23 Sep '14

Hi all-- We now have improved installers for CCTBX with all optional third-party dependencies, including numpy, wxPython, and matplotlib; these are basically just a simplified Phenix installer (minus anything that isn't open-source, obviously). For anyone doing visualization these are probably preferable to the default packages. More useful for doing active development is that since these include the pre-build Python, if you are working directly with the CCTBX sources you can bootstrap from these packages. Yesterday's build is here: http://cci.lbl.gov/cctbx_build/plus_bundles/2014_09_08_0005/ and in general the latest version can be obtained here: http://cci.lbl.gov/cctbx_build/plus_bundles/current although today's build isn't finished yet. The next build will also incorporate IPython. I still need to fix the download page so these are listed alongside the old bundles. Once this is done we'll probably declare an official "release". -Nat

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Tests which randomly pass or fail (nag)
by Graeme.Winter＠diamond.ac.uk 16 Sep '14

16 Sep '14

Hi Folks Quick nag if I may... if people have tests which employ random inputs (e.g. random unit cell, random amplitudes and phases) please could they set a seed or select from some seeds which should give random values which work, or fix their tests so that all random values work (ideally!) That way when tests fail people know something is wrong, rather than everything is fine but the random values drawn are troublesome... Sorry for sounding grumpy! Cheerio 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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order bias in flex.random_permutation
by Keitaro Yamashita 11 Sep '14

11 Sep '14

Dear cctbx developers, I happened to notice that the implementation of flex.random_permutation (scitbx/random.h) results in biased order because each element is always swapped with the element randomly selected from entire range of array. For details, please see the second paragraph and the right figure of http://en.wikipedia.org/wiki/Fisher%E2%80%93Yates_shuffle#Implementation_er… I reproduced the plot using flex.random_permutation. Actually this seems to have less impact because flex.random_permutation is rarely used in cctbx or phenix as far as I know. If needed, I would commit the corrected version (using the algorithm in the wikipedia article above). Best regards, Keitaro

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IPython with cctbx
by Oliver Zeldin 09 Sep '14

09 Sep '14

Dear Devs, Has anyone tried to get IPython working with cctbx? I'd really like to be able to use IPython notebooks for examples/tutorials/documented experiments, and was wondering if anyone else had thought the same thing. Cheers, Oli

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