I was successfully able to calculate phi, psi, omega values for proteins, given cartesian coordinates, where
phi: C-N-CA-C
psi: N-CA-C-N
omega: CA-C-N-CA
Now I would like to calculate chi angles for the side chains, also given cartesian coordinates, where
X1 = N-Ca-Cb-x
X2 = Ca-Cb-x-x
etc. where x can be Ca/b/c/d/e/f/g/ (any carbon-with-a-subscript).... or N (if I am not mistaken)
My first question is: Is that definition correct? If so, I believe it should be quite simple because (I think) it would be the same application for what I did for phi, psi, omega values, where I was given four cartesian coordinates per angle.
My second question is: I notice in the .pdb file, there are something carbons with the same subscript. What do in that case? For instance, the following case has CG1 and CG2:
ATOM 96 N ILE A 6 1.201 -4.204 1.943 1.00 0.11 N
ATOM 97 CA ILE A 6 2.338 -5.105 2.255 1.00 0.13 C
ATOM 100 CB ILE A 6 2.067 -6.500 1.693 1.00 0.16 C
ATOM 101 CG1 ILE A 6 0.952 -7.157 2.521 1.00 0.30 C
ATOM 102 CG2 ILE A 6 3.348 -7.336 1.800 1.00 0.36 C
ATOM 103 CD1 ILE A 6 0.238 -8.228 1.683 1.00 0.33 C
ATOM 115 N LEU A 7 4.435 -3.938 2.439 1.00 0.11 N
ATOM 116 CA LEU A 7 5.682 -3.321 1.900 1.00 0.12
Thank you
Is this the same as your previous question? How to calculate bond angle in protein db file?