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I'll take a stab at this but I'm just guessing.
OK here is a wild guess! I think you might be seeing PE superimposed onto the DEC axis. Maybe I'm crazy but trying to reason this out is giving me a headache. However, is it wrong to reason that the motion one measures is a vector sum of the motion in both axis? If the polar axis is not set very close then a component of motion in RA would have a small vector in declination. Given how extraordinarily small an arc-sec is I think this little vector in DEC might be measurable by PEMpro. The saw tooth pattern looks quite regular and might be a pinion gear perhaps. Over time the motion goes above and below the average position calculated by PEMpro. Perhaps if you know the period length of the worm you can roughly calculate if the larger scale up/down flux matches. Anyway, this is just a wild guess and I'm probably wrong!! I was never all that great in math. So there. But, on the other hand (!), I know that if we don't have a completely level mount moving the mount in either azimuth or altitude will have a small effect on the other component. The further from level the more one adjustment effects the other.....therefore, if one is not polar aligned movement in RA will also move in declination....and that led directly to this theory.
Perhaps you should just go ahead and ignore the fluctuations and make adjustments according to PEMpro. Perhaps as you get closer and closer to being polar aligned the saw tooth pattern will diminish. Given the steepness of the slope I'd say you are not very close to the pole.
Perhaps your interpretation of the image in MaxIM being "smooth" is influenced by image scale difference between a full frame picture and what PEMpro is doing with probably a very small ROI. After all, PEMpro is capable of measuring fractions of an arc-sec so motion on the PEMpro graph will look quite exaggerated.
What image scale are you at with your scope/camera combo?
Peter
PS. A final thought. I'd post these on the PEMpro forum and get Ray's opinion. I'm most curious now!
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