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Thanks for the response!

I used some of the settings from the following page:
www.centroidcnc.com/dealersupport/tech_b...tins/uploads/295.pdf

I have Pn000 at 0010H and Pn002 at 0100H PN200 isn't set as in the document, it is set for positive pulse and direction input.
I've also gone through the sigma II manual especially the trial procedure and tried to go through the settings that seemed relevant.
I'm aware of the power reset to make some settings take effect.

I'm pivoting my design since I just ordered a CSF 45 harmonic drive for the B. The 40 will be the 4th axis on the table. I put a 10ths indicator on the harmonic drive. It has no backlash, which is crazy cool, but does have maybe 0.0001 of "flex" backlash if I put lots of stress on it with a wrench. Seems pretty sweet.

My guess is that the drives are still in analog velocity mode and need to be set to step/dir mode.

I'm retrofitting a Fryer ET-25 lathe with using a mesa 7i95 board.  The lathe has two SGDH Sigma II drives. I'm having trouble controlling them with step and direction signals from the mesa board. I have the yaskawa sigwin software connected to the drive. I have the axis moving with the jog function in the software. I have disconnected the voltage reference signals from the old controller, but haven't removed them from the drive or grounded them.  I've got the contactor coming on for the drive. The only thing that doesn't look remotely positive is that the SEN signal is off, but I have an incremental encoder and it is my understanding that it shouldn't therefore matter. I can see the pulses accumulate as information in the yaskawa software, I can see both the step and direction change when the appropriate direction is picked. I have bypassed the overtravel signals and linked the P-con signal to the power pin 40.  I feel like there has to be a simple setting I'm missing. Maybe I'm not doing something right on the ini file as well? I'm assuming its at least good enough to make some movement since i'm getting an indication on the drive software, but maybe thats not accurate. All of the similar retrofits I have found end up using voltage reference even though everyone recommends step and direction to begin with, so I haven't found anything to go by really, if there's anything I've missed on that front, please let me know that as well.   Any help would be appreciated.
Howard

1) What is the typical following error for an axis with a linear scale of 0.001mm resolution(1 micron)? In steady state it is able to position the axis within +-0.005 accuracy. Do you think it is possible to get more from that scale resolution?

Typically, some I term is added to reduce the static error.

During acceleration and deceleration, an error jumps up to 0.1mm at 1500mm/min speed. What is a typical result for well well-tuned PID loop?

That mostly depends on the characteristics of the controlled device (delays, linearity etc)

Can you post a Halscope plot of following error and velocity?