On 13/07/2022 19:18, Ravikumar wrote:
I would like to calculate One-dimension electron density profiles of
the different number of ions bound to an ion channel. Are there any
programs in CCP4/ Phenix which can do the same job as the MAPMAN
(UPPSALA electron density server) program to extract the electron
density values to plot electron density values versus pore axis? I
have attached an example figure.
Here's how to do it in Coot (see attached).
Paul.
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from __future__ import print_function
import math
imol = read_pdb('pdb6qkc.ent')
imol_map = read_ccp4_map('emd_4572.map', 0)
n_steps = 250
start_point = [154, 154, 133]
end_point = [154, 154, 180]
imol_map_smooth = sharpen_blur_map_with_resampling(imol_map, 0.0, 2.3)
delta = [x - y for x, y in zip(end_point, start_point)]
delta_step = [ x/float(n_steps) for x in delta]
delta_step_size = math.sqrt(sum([x*x for x in delta_step]))
print(delta)
print(delta_step)
print(delta_step_size)
with open('line-of-density.table', 'w') as f:
for i_step in range(n_steps + 1):
p = [x + i_step * y for x, y in zip(start_point, delta_step)]
r = density_at_point(imol_map_smooth, p[0], p[1], p[2])
d = delta_step_size * i_step
f.write('{} {} {} {} {}\n'.format(p[0], p[1], p[2], d, r))
