[RASMB] counterbalance functions

[Borries Demeler]

> 
> Xin,
> 
> What Virgil said is mostly correct, but it is only part of the story. The
> counterbalance is also required for "delay" calibration of the absorbance
> optics (to set the timing of the lamp pulses). This calibration happens
> every time you start a run or when the rotor speed is changed by more than
> 2000 rpm.
> 
> Radial calibration needs only to be done intermittently (I recommend doing
> it only when the service tech has done something to the instrument). Since
> the optical components are entirely independent of which rotor is used the
> radial calibration is independent of the rotor, so I have to disagree with
> what Virgil said about needing to recalibrate for each rotor. 
> 
> If the counterbalances are machined accurately then they all should give the
> same radial calibration also. Again, remember the optical components do not
> move or change when you change counterbalances. If different counterbalances
> give different calibrations then it is impossible to say which one is more
> accurate. In that situation I would recommend adopting one of them as
> 'correct' and sticking to its calibration. Otherwise your results are
> potentially different from one experiment to another depending on which
> counterbalance you used for radial calibration.
> 
> If you are not using the absorbance optics then in fact the counterbalance
> is not required and an additional interference or fluorescence sample can be
> run in that hole. 
> 
> John

Yes, that is a chicken and egg sort of conundrum, if you cannot trust your
counterbalance you cannot trust your radial calibration. However, you 
can get a little closer to the truth with some software I wrote.
One way to check if the counterbalance is correctly calibrated is with
the UltraScan3 rotor calibration program. While the main purpose of the 
program is to calculate the rotor's stretching function, you can also
use it to "measure" the counterbalance and cell housing and centerpiece
combinations. 

The way it works is that you would scan the counterbalance (or
centerpiece) in intensity mode at multiple speeds, generating a sharp
boundary at each edge. The edge would move with each speed, as the rotor
stretches. If the edges are truly centered at 5.85 and 7.15 cm, then the
center should be at 6.5 cm, which is how the rotor has been machined.
The program will take the differences between the edges at successive
speeds and extrapolate these differences with a second order polynomial
to zero speed. The positions at rest should be 7.15 for the bottom then
and 5.85 for the top, and the center (which is also calculated by the
program) should then be at 6.5 cm. If the center is not at 6.5 cm, then 
that is an indication that something is wrong with the counterbalance.

In addition to the counterbalance dimensions, you will get the rotor
stretching function from this calculation. By scanning centerpieces in
different cell housings you will also get the true bottom of the cell
this way for each cell housing/centerpiece combo.  This is helpful if you
want to do mass conservation calculations in equilibrium experiments (the
stretching function will predict the offsets at each speedi). See
the recent posts on this topic.

Regards, -borries