Hello all,
I want to know how can I calculate the geometrical properties of helices.
Consider any α-helix of proteins, how to get informations about their helical pitch length, reduced pitch length, helical angle, turn, radius (or dimeter) etc from their .pdb or .xyz files.
Any suggestions are welcome.
Thank you in advance.
unless otherwise stated, the helix can be taken in a 3 dimensional space and there will be an axis of symmetry for the helix and the plane to which the axis is normal will have a projection of the helix which appears to be the base curve. for instance, if the plane is XY - plane, then x = f(t), y= g(t) will be the parametric equations that will determine the parameters with the boundary conditions for two dimensions. the normal will be z = h(t) that also depend on the boundary conditions a
You may want to check:
https://www.researchgate.net/post/How_the_pitch_of_a_non-perfect_helix_can_be_calculated
alpha helix is a double helical path that can be parametrized with two different helical equations which differ by a period and thus, the double path appears to be a spiral staircase. so, one side or railing of this stair case can be x1 = a + bcos(t), y1 = a + bsin(t), z1 = kt . other railing of the stair case may be seen as x2 = a+bcos(t +c*pi), y2 = a + b sin(t + c*pi), z2= kt.