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So, I've made a small space station (skylab) which has  an Advanced Reaction Wheel Module on it. When I dock an Apollo sized ship and disconnect the pod reaction wheels everything seems normal. When I switch to IVA, the ship starts to wobble, only to stop if I switch back to external view. Doesn't happen if the pod reaction wheels are working too. The ship is docked with a Clamp-O-Tron Docking Port Jr.

 

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That is an unfortunate effect of a combination of features of KSP (each of which is nice on its own) when SAS is active on a complex craft.

When you use the IVA view for a pod, the control-from-here point is changed to that pod (so the control inputs are aligned to that pod).
The SAS tries to slow the rotation of control-from-here pod.
The control torques are applied at the reaction wheels.
Joints between parts flex.
Large craft have wobbling resonances, where the control-from-here pod might be yawing right while the part of the craft housing the reaction wheel is rotating left.

So by trying to slow a rotation to the right by commanding a turn left, the SAS is making the reaction wheel (already turning left) turn left even faster, and thus pumping up the wobble.

You can solve the wobble by removing any link in that causal chain.   I like turning SAS off.

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7 hours ago, OHara said:

That is an unfortunate effect of a combination of features of KSP (each of which is nice on its own) when SAS is active on a complex craft.

When you use the IVA view for a pod, the control-from-here point is changed to that pod (so the control inputs are aligned to that pod).
The SAS tries to slow the rotation of control-from-here pod.
The control torques are applied at the reaction wheels.
Joints between parts flex.
Large craft have wobbling resonances, where the control-from-here pod might be yawing right while the part of the craft housing the reaction wheel is rotating left.

So by trying to slow a rotation to the right by commanding a turn left, the SAS is making the reaction wheel (already turning left) turn left even faster, and thus pumping up the wobble.

You can solve the wobble by removing any link in that causal chain.   I like turning SAS off.

You can go into the game settings and turn off the IVA view control point reset. Should help.

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12 hours ago, OHara said:

That is an unfortunate effect of a combination of features of KSP (each of which is nice on its own) when SAS is active on a complex craft.

When you use the IVA view for a pod, the control-from-here point is changed to that pod (so the control inputs are aligned to that pod).
The SAS tries to slow the rotation of control-from-here pod.
The control torques are applied at the reaction wheels.
Joints between parts flex.
Large craft have wobbling resonances, where the control-from-here pod might be yawing right while the part of the craft housing the reaction wheel is rotating left.

So by trying to slow a rotation to the right by commanding a turn left, the SAS is making the reaction wheel (already turning left) turn left even faster, and thus pumping up the wobble.

You can solve the wobble by removing any link in that causal chain.   I like turning SAS off.

Seems that only happens when I control the ship from the pod instead from the Probodobodyne probe onboard the station. 
Solved it just lowering the torque from the station reaction wheels.
Actually is not a complex craft, didn't happen on more complex stations, but probably since using a Jr. Docking port could lead to this, having such lightweight station with that powerful reaction wheels, docked with a probably heavier ship.

4 hours ago, Xd the great said:

Kerbal Joint reinforcement may help.

Thanks for the suggestion but I try to not to use this mod, by now.

4 hours ago, RealKerbal3x said:

You can go into the game settings and turn off the IVA view control point reset. Should help.

Thanks, that helped to stop wobbling while in IVA, unless I switch the control to the pod.

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