[cctbxbb] Computing E^4 from an mtz file

Graeme.Winter at diamond.ac.uk Graeme.Winter at diamond.ac.uk
Fri Dec 14 12:19:19 PST 2012

Thanks Nat, that hit the spot.

For reference the final code I got was

def main():
    import sys
    from iotbx import reflection_file_reader

    for argv in sys.argv[1:]:
        reflection_file = reflection_file_reader.any_reflection_file(
            file_name = argv)
        if reflection_file.file_type() is None:
        miller_arrays = reflection_file.as_miller_arrays()

        for ma in miller_arrays:
            print ma.info().label_string(), E4(ma)

def E4(ma):
    f = ma.as_intensity_array()
    f = f.array(data=f.data()/f.epsilons().data().as_double())
    f.setup_binner(auto_binning = True)
    sm = f.second_moment(use_binning = True)
    moments = [sm.data[j] for j in f.binner().range_used()]
    return sum(moments) / len(moments)

if __name__ == '__main__':

Best wishes,


On 13 Dec 2012, at 16:29, Nathaniel Echols wrote:

> On Thu, Dec 13, 2012 at 8:18 AM,  <Graeme.Winter at diamond.ac.uk> wrote:
>> That gave me six and a bit: specifically
>>    sm.show()
>>    print f.second_moment(use_binning = False)
>> 6.46063790107
>> The E^2 = I/<I> need to be computed in bins. After that (E^2)^2 should be fine. This got me confused - it must be in there somewhere
> Ah, I think I see - look at the "data" attribute:
> sm = f.second_moment(use_binning=True)
> print sm. data
> [None, 2.3279309836355044, 2.8099112859261517, 2.1769967857271175,
> 2.200637763782145, 2.2919308734359407, 2.000356888782398,
> 1.7555453224108684, 1.4836662688931992, None]
> (using a dataset from the PDB)  I've never fully understood what the
> first and last elements are supposed to mean (at least one is for
> "unused" data) - but you can get the elements of interested this way:
>  for i_bin in f.binner().range_used() :
>    # etc.
> -Nat
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