[cctbxbb] Electron density hitogram from MTZ file

Pavel Afonine pafonine at lbl.gov
Mon Oct 27 07:31:11 PDT 2014


Hi Marcelino,

for example, see implementation of phenix.map_comparison (Map comparison 
and statistics. For details see: Acta Cryst. (2014). D70, 2593-2606. 
Metrics for comparison of crystallographic maps. A. Urzhumtsev, P. V. 
Afonine, V. Y. Lunin, T. C. Terwilliger and P. D. Adams).

Relevant file is:
cctbx_project/mmtbx/command_line/map_comparison.py

This gives you map histogram object:
h = maptbx.histogram(map=map_data, n_bins=10000)

You can print it like this:
for a,c,v in zip(h.arguments(), h.c_values(), h.values()):
     print a,c,v

Another option would be to use flex.histogram:

def show_histogram(data, n_slots, data_min, data_max):
   hm = flex.histogram(data = data, n_slots = n_slots, data_min=data_min,
     data_max=data_max)
   lc_1 = hm.data_min()
   s_1 = enumerate(hm.slots())
   for (i_1,n_1) in s_1:
     hc_1 = hm.data_min() + hm.slot_width() * (i_1+1)
     print "%6.2f - %-6.2f : %6.4f : %d" % (lc_1, hc_1, (lc_1+hc_1)/2,n_1)
     lc_1 = hc_1

but this does not work well for crystallographic maps.

Finally, to get a Fourier map from Fourier map coefficients (miller 
array with complex-type data):

- if you want to use your custom gridding:
   fft_map = miller.fft_map(
     crystal_gridding     = crystal_gridding,
     fourier_coefficients = map_coeffs)
   fft_map.apply_sigma_scaling()
   map_data = fft_map.real_map_unpadded()

- using gridding based on resolution:
fft_map = map_coeffs.fft_map(resolution_factor = 1./4)

Pavel

On 10/27/14 5:45 AM, castro at biochem.mpg.de wrote:
> Hi everybody,
>
> I am new in crystallogrphy and in the use of cctbx.
> I am interested in building a electron density histogram from a mtz file.
> Could somebody give a hint on how to accomplish this task using cctbx 
> libraries (I am scripting in python)?
>
> Let's say that I already have the columns of interest as "miller arrays".
> Then (I think), a grid (on the real space) needs to be created based 
> on unit cell parameters, to finally make the fft.
>
> I think that most of my doubts are about the grid.
> How small the grid should be with respect to the low-resolution limit?
> Does the space group information needed or it is enough with the the 
> cell parameters?
>
> Is there all ready a routine doing this?
>
> Thanks a lot for your help.
>
> Marcelino
>
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