Calculate RDC from a known Tensor

This example shows how to calculate theoretical RDC values from a known \({\Delta\chi}\)-tensor which has been fitted from PCS data. Paramagpy allows seamless calculation of one PCS/PRE/RDC/CCR effect from a tensor fitted from another effect.

Downloads

  • Download the data files 4icbH_mut.pdb and calbindin_Er_HN_PCS_tensor.txt from here:

  • Download the script rdc_calculate.py

Script + Explanation

First the relevant modules are loaded, the protein is loaded and the metal is loaded from file. The magnetic field strength and temperature are also set.

from paramagpy import protein, metal

# Load the PDB file
prot = protein.load_pdb('../data_files/4icbH_mut.pdb')

# Load the fitted tensor
met = metal.load_tensor('../data_files/calbindin_Er_HN_PCS_tensor.txt')
met.B0 = 18.8

A loop is made over the atoms of the protein. The amide H and N atoms are selected and then the RDC value is calculated. Finally the formated data is appended to list forFile.

forFile = []
for atom in prot.get_atoms():
	if atom.name == 'H':
		residue = atom.parent
		seq = residue.id[1]
		if 'N' in residue:
			H = atom
			N = residue['N']
			rdc = met.atom_rdc(H, N)
			line = "{0:2d} {1:^3s} {2:2d} {3:^3s} {4:6.3f} 0.0\n".format(
				seq, H.name, seq, N.name, rdc)
			forFile.append(line)

The formatted data is written to file:

with open("calbindin_Er_RDC_calc.rdc", 'w') as f:
	f.writelines(forFile)

Output: [calbindin_Er_RDC_calc.rdc]

 0  H   0  N  -1.724 0.0
 1  H   1  N  -6.196 0.0
 2  H   2  N  -4.993 0.0
 4  H   4  N  -0.922 0.0
 5  H   5  N   1.783 0.0
 6  H   6  N   0.280 0.0
 7  H   7  N  -1.906 0.0
 8  H   8  N   1.056 0.0
 9  H   9  N   0.713 0.0
10  H  10  N   0.213 0.0
11  H  11  N  -0.881 0.0
12  H  12  N   2.712 0.0
13  H  13  N   0.614 0.0
14  H  14  N  -2.346 0.0
15  H  15  N   1.659 0.0
16  H  16  N   0.648 0.0
17  H  17  N   0.383 0.0
18  H  18  N   0.420 0.0
19  H  19  N  -7.863 0.0
21  H  21  N   0.973 0.0
22  H  22  N   1.026 0.0
23  H  23  N  -0.613 0.0
24  H  24  N  -5.847 0.0
25  H  25  N   1.761 0.0
26  H  26  N   6.470 0.0
27  H  27  N   5.541 0.0
28  H  28  N  -0.334 0.0
29  H  29  N   3.624 0.0
30  H  30  N   6.673 0.0
31  H  31  N   3.952 0.0
32  H  32  N   1.658 0.0
33  H  33  N   5.449 0.0
34  H  34  N   7.370 0.0
35  H  35  N   1.033 0.0
36  H  36  N   1.136 0.0
38  H  38  N  -7.378 0.0
39  H  39  N  -6.979 0.0
40  H  40  N  -4.810 0.0
41  H  41  N  -3.187 0.0
42  H  42  N   2.415 0.0
43  H  43  N   1.710 0.0
44  H  44  N  -5.977 0.0
45  H  45  N  -5.467 0.0
46  H  46  N   3.243 0.0
47  H  47  N   3.937 0.0
48  H  48  N   7.047 0.0
49  H  49  N   4.577 0.0
50  H  50  N   3.718 0.0
51  H  51  N   4.519 0.0
52  H  52  N   6.077 0.0
53  H  53  N   2.940 0.0
54  H  54  N   2.541 0.0
55  H  55  N  -7.493 0.0
56  H  56  N  -7.159 0.0
57  H  57  N   4.948 0.0
58  H  58  N  -1.078 0.0
59  H  59  N  -0.759 0.0
60  H  60  N   0.161 0.0
61  H  61  N  -1.132 0.0
62  H  62  N  -5.719 0.0
63  H  63  N   4.025 0.0
64  H  64  N   5.929 0.0
65  H  65  N   2.363 0.0
66  H  66  N   2.477 0.0
67  H  67  N   8.265 0.0
68  H  68  N   5.078 0.0
69  H  69  N   3.724 0.0
70  H  70  N   7.743 0.0
71  H  71  N   2.188 0.0
72  H  72  N   4.911 0.0
73  H  73  N   7.514 0.0
74  H  74  N  -0.001 0.0
75  H  75  N   1.119 0.0