> Is there a way for me to define a plane of atoms say 4 Nitrogens in a > heme complex and then determine how far out-of-plane the Fe atom is? If so > either in Pymol or another program I'd love to know the secret.
Hello Kristl, have you tried to just individually add up the x, y, and z coordinates of the four nitrogens and calculate the mean? This will give you a virtual centre point of the plane. Finally, just create a new pdb file containing the pseudo atom, load it into PyMOL and determine the distance between this pseudo atom and your iron atom. Best regards, Bartholomeus
