Hi Pavel,
Thanks a lot for your help.
:)
Marcelino
Quoting Pavel Afonine
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, [email protected] 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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