[cctbxbb] Asymmetric Unit with cctbx

[Philipp Heuser]

Hi Ralf,

Thank you very much for your quick and detailed reply! It almost does 
what I am looking for, but I am not sure if I really got how it works...

Am I right if I assume that adding lines 5 and 6 to your code:

1 for grid_point in flex.nested_loop(tag_array.focus()):
2       if (tag_array[grid_point] < 0):
3             number_of_symmetry_unique_grid_points += 1
4             sum_of_asu_data += real_map[grid_point]
5       else:
6              print real_map[grid_point], real_map[tag_array[grid_point]]


should print twice the same value? It doesn't. Could you be so kind to 
give me a hint where my error in thinking is?
Is there any reason for the different sizes of the tag_array and the 
real_map? real_map.last() and tag_array.last() show different results.

Kind regards
Philipp


Ralf W. Grosse-Kunstleve schrieb:
> Hi Philipp,
>
> You can find an expanded version of your script here:
>
>   http://cci.lbl.gov/~rwgk/tmp/cctbx_examples/2007_06_17/ 
> <http://cci.lbl.gov/%7Erwgk/tmp/cctbx_examples/2007_06_17/>
>
> Use this command to generate a fake mtz file:
>
>   iotbx.python random_f_calc.py P31
>
> Then this command:
>
>   iotbx.python mtz_to_map_and_back.py random_f_calcs.mtz FC1 FC2
>
> This illustrates how to convert a manipulated map back to Fourier
> coefficients (via .structure_factors_from_map()) and write these
> out in MTZ format.
>
> In the example, the map manipulation is simply squaring the map.
> You can do anything else with the map from Python.
>
> For the FFT back to Fourier coefficients, you need a map over the
> unit cell. For maps, we don't have continuous asymmetric units
> (the map code pre-dates the ASU gallery). Instead, we have a "tag
> array" of integer values with the same gridding as the data map. An 
> integer value less than 0 means "this grid point is unique under
> symmetry", values >= 0 are the 1D indices of the symmetry-related
> unique point. See the code near the end of mtz_to_map_and_back.py.
> It shows a loop over the grid points accessing both the tag_array and
> the real_map. This loop is slow, of course, since it is in Python. It
> should be fast enough for prototyping, but I'd expect the final
> version to be implemented in C++, unless your manipulation can
> be formulated with existing array algebra, e.g. the flex.pow2()
> in the example, which already runs at C++ speed.
>
> Cheers,
>         Ralf
>
>
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-- 

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Dr Philipp Heuser
Postdoctoral fellow

EMBL-Hamburg 
c/o Building 25A, DESY
Notkestrasse 85
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phone:   +49 40 89902 188
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mail:    philipp.heuser at embl-hamburg.de
web:     www.philipp-heuser.de

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