August 2015 - cctbxbb - phenix-online.org

dependency on phenix
by Roger Martin 26 Jan '16

26 Jan '16

Hi, looking through http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/minimi… shows at line 61 from phenix.refinement import weight_xray_chem and http://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/mmtbx/refinement/occupa… line 134 Is weight_xray_chem.py code that could move to cctbx? (cctbx_project/mmtbx/refinement/weight_xray_chem.py) Are there other cross dependencies?

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tst_miller failing
by markus.gerstel＠diamond.ac.uk 26 Aug '15

26 Aug '15

Hi everyone, particularly Pavel I guess, I had a look at one intermittently failing test: cctbx/regression/tst_miller.py, run with parameter P31 The relevant piece of code is: def exercise_randomize_amplitude_and_phase(): xrs = random_structure.xray_structure( space_group_info=sgtbx.space_group_info(number=1), elements=["C"]*300) fc = xrs.structure_factors(d_min=1).f_calc() def run(a,p): fc_ = fc.randomize_amplitude_and_phase(amplitude_error=a, phase_error_deg=p, random_seed=1312425) d1, d2 = flex.abs(fc.data()), flex.abs(fc_.data()) r = flex.sum(flex.abs(d1-d2))/flex.sum(flex.abs(d1+d2))*2 return (r, fc.mean_phase_error(phase_source=fc_)) # assert approx_equal(run(0,0), (0,0)) for v in list(xrange(0,91, 10)): r = run(v/100.,v) assert approx_equal(r[0], v/100., 0.01) assert approx_equal(r[1], v, 1) The test fails in the last line for varying values of v. I saw that the values of r[] increase proportionally to v, so I ran the test 2000 times for v=90, plotting the values of r[0] and r[1]; results attached. With the current statistics the r[1] test is expected to fail in 1 run out of every 80. Could you please have a look at this, and either increase the tolerance on the test or identify whether these values are true unexpected outliers indicating a problem in the code? Don't know what the r[1] distribution should look like, but that's clearly not normal. :) -Markus -- 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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Structure factor calculation for Si
by Allan Lyckegaard 26 Aug '15

26 Aug '15

Dear CCTBX-list I am trying to reproduce the (scaled) intensities for Si reported here: http://rruff.geo.arizona.edu/AMS/xtal_data/DIFfiles/15285.txt based on this information: http://rruff.geo.arizona.edu/AMS/CIF_text_files/15285_cif.txt I am using CCTBX in Python: from cctbx.array_family import flex from cctbx import sgtbx, crystal, miller, xray sgnum = 227 sg = sgtbx.space_group_info(sgnum).group() latticepar = [5.43070, 5.43070, 5.43070, 90, 90, 90] dmin = 1.0 atompos = [['Si',(0.0, 0.0, 0.0)]] scatterers = flex.xray_scatterer() scatterers.append(xray.scatterer(label=atompos[0][0], site=atompos[0][1])) pg = sg.build_derived_point_group() sym = crystal.symmetry(space_group=sg,unit_cell=latticepar) sps = crystal.special_position_settings(crystal_symmetry=sym) structure = xray.structure(special_position_settings=sps,scatterers=scatterers) F = structure.structure_factors(d_min=dmin,algorithm='direct').f_calc() list(F.amplitudes()) This gives: [((0, 2, 2), 0.0), ((0, 4, 0), 120.21765812638594), ((1, 1, 1), 84.18849550806966), ((1, 3, 1), 65.48371727205928), ((1, 3, 3), 57.45438308324155), ((1, 5, 1), 51.48759686950681), ((2, 2, 2), 128.54540698861973), ((2, 4, 2), 0.0), ((3, 3, 3), 51.48759686950681)] How come CCTBX give an amplitude of 0.0 for (0,2,2) and (2,4,2)? The measured intensities in the DIFfile above does not show this. Am I missing something? Cheers, /Allan

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Computational Crystallography Newsletter - Volume 6, Number 2
by Nigel Moriarty 25 Aug '15

25 Aug '15

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 2015 <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf> Articles - A context-sensitive guide to RNA & DNA base-pair & base-stack geometry <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=22> Short Communications - New Phaser-MR search panel in Phenix <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=7> - Quantum chemical techniques for minimising ligand geometries in the active site <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=10> - 13 typical occupancy refinement scenarios and available options in *phenix.refine* <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=12> Fitting tips #10 – How do your base pairs touch and twist? <http://www.phenix-online.org/newsletter/CCN_2015_07.pdf#page=3> Cheers Nigel --- Nigel W. Moriarty Building 33R0349, Physical Biosciences Division 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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Shelx HKL file with original indices from unmerged MTZ
by Graeme.Winter＠diamond.ac.uk 06 Aug '15

06 Aug '15

Hi Folks Using reader = any_reflection_file(hklin) intensities = [ma for ma in reader.as_miller_arrays(merge_equivalents=False) if ma.info().labels == ['I', 'SIGI']][0] help(intensities) with open('%s.hkl' % prefix, 'wb') as f: intensities.export_as_shelx_hklf(f, normalise_if_format_overflow=True) to get a file for input to shelx and it appears to have only indices in the ASU not the Fridel pairs. What do I need to do to output with original indices (ie. P1 indices?) I assume that this has been solved before... 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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Tonights build/testing failures
by markus.gerstel＠diamond.ac.uk 05 Aug '15

05 Aug '15

Hi everyone, tonights test (cctbx) or build (dials) failures were caused by changes to the CBFlib in r568. http://sourceforge.net/p/cbflib/code-0/commit_browser Error messages may include ImportError: (..)/build/lib/_pycbf.so: undefined symbol: cbf_airy_disk_volume Do we have a red phone to cbflib folks? -Markus -- 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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