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  "rotate" can be used to rotate the atomic coordinates of a
  molecular object.  Behavior differs depending on whether or not the
  "object" parameter is specified.

  If object is None, then rotate rotates the atomic coordinates
  according to the axes and angle for the selection and state
  provided.  All representation geometries will need to be
  regenerated to reflect the new atomic coordinates.

  If object is set to an object name, then selection and state are
  ignored and instead of translating the atomic coordinates, the
  object's representation display matrix is modified.  This option
  is for use in animations only.


  rotate axis, angle [,selection [,state [,camera [,object [,origin]]]]]


   cmd.rotate(list-or-string axis, string selection = "all", int state = 0,
              int camera = 1, string object = None)


  rotate x, 45, pept


  if state = 0, then only visible state(s) are affected.
  if state = -1, then all states are affected. 
Electrostatic Map Caveat

If you have an electrostatic map and it's not rotating with the molecule as you expect it to, see the Turn command. Turn moves the camera and thus the protein and map will be changed.