HI David dials/command_line/rfactor.py contains some useful hints - you want to work with miller arrays and common sets All the best Graeme

On 14 Aug 2018, at 11:37, David Waterman wrote:

Hi all,

I have a script that extracts Fobs and Fcalc from an MTZ file produced by Refmac for some analysis. I was just doing this in a trivial way:

fobs = m.extract_reals("F").data fc = m.extract_reals("FC_ALL").data

and this worked fine, until I came across a file with missing observations, so that the lengths of fobs and fc do not match.

Can anybody advise a better way to do this please? I'm inexperienced with iotbx.mtz. I don't need anything other than the values of the structure factors, but I need each element of fobs and fc to contain the equivalent values.

Thanks

-- David _______________________________________________ cctbxbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/cctbxbb

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Hi David, I would do something like this: $ cat tst.py def run(mtz): from iotbx.reflection_file_reader import any_reflection_file miller_arrays = any_reflection_file(mtz).as_miller_arrays() for ma in miller_arrays: print ma.info().labels fobs = [ma for ma in miller_arrays if ma.info().labels == ['F', 'SIGF']] fc = [ma for ma in miller_arrays if ma.info().labels == ['FC_ALL', 'PHIC_ALL']] assert len(fobs) == 1, len(fobs) assert len(fc) == 1, len(fc) fobs = fobs[0] fc = fc[0] fobs.show_summary() fc.show_summary() if __name__ == '__main__': import sys run(sys.argv[1]) $ dials.python tst.py dimple/final.mtz ['FreeR_flag'] ['F', 'SIGF'] ['FC', 'PHIC'] ['FC_ALL', 'PHIC_ALL'] ['FWT', 'PHWT'] ['DELFWT', 'PHDELWT'] ['FOM'] ['FC_ALL_LS', 'PHIC_ALL_LS'] Miller array info: dimple/final.mtz:F,SIGF Observation type: xray.amplitude Type of data: double, size=14217 Type of sigmas: double, size=14217 Number of Miller indices: 14217 Anomalous flag: False Unit cell: (68.2317, 68.2317, 108.095, 90, 90, 90) Space group: P 43 21 2 (No. 96) Miller array info: dimple/final.mtz:FC_ALL,PHIC_ALL Observation type: None Type of data: complex_double, size=14551 Type of sigmas: None Number of Miller indices: 14551 Anomalous flag: False Unit cell: (68.2317, 68.2317, 108.095, 90, 90, 90) Space group: P 43 21 2 (No. 96) Cheers, Richard Dr Richard Gildea Data Analysis Scientist Tel: +441235 77 8078 Diamond Light Source Ltd. Diamond House Harwell Science & Innovation Campus Didcot Oxfordshire OX11 0DE ________________________________ From: [email protected] on behalf of David Waterman Sent: 14 August 2018 11:37:29 To: cctbx mailing list Subject: [cctbxbb] Extracting data from MTZ Hi all, I have a script that extracts Fobs and Fcalc from an MTZ file produced by Refmac for some analysis. I was just doing this in a trivial way: fobs = m.extract_reals("F").data fc = m.extract_reals("FC_ALL").data and this worked fine, until I came across a file with missing observations, so that the lengths of fobs and fc do not match. Can anybody advise a better way to do this please? I'm inexperienced with iotbx.mtz. I don't need anything other than the values of the structure factors, but I need each element of fobs and fc to contain the equivalent values. Thanks -- David -- 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