Here is a Python script that will change your atom coordinates to rotate a given vector to the z axis, and another given vector into the yz plane with y > 0, and a given point is moved to 0,0,0. The vectors and point are specified each as 3 numbers separated by commas. For example, Chimera command

will change the coordinates of atoms to make the new z-axis in direction .7,.2,0 from the original coords, with 0,-.5,.5 from original coords pointing in the new yz plane with y>0 and the original point 16,7,-5 will move to the origin 0,0,0. Notice the first two vectors need not have unit length. They will be normalized by the code. This should allow you to specify your 5-fold symmetry axis as z and put the 2-fold symmetry axis in the yz plane. I only did one test so if the results look wrong, tell me. The script is attached and is also available on the Chimera Python scripts web page, called changeaxes.py