Encoder wiring - Mesa 7i33

Fordperf393W wrote:

is it possible to zero out an axis at its current position?

Yes, in about three different ways, depending on what you are wanting to do.
You can zero the encoder (set the "reset" bit high through a HAL pin). Generally you don't, the encoders just hold their value and can count for about a milliion years before they run out of counts. (Seriously, the counts are held in a 64-bit number).
Normally you zero-out the axis using either "home" or "touch-off". The former says "this is zero in the absolute machine axis positions" and the latter means "for this job, I want zero to be here". Think of it as the difference between winding a manual machine to the end stops, or tweaking the micrometer thimble on the handwheel.

EMC2 has several coordinate sets available, so you can set up all 4 corners of a machine vice or whatever to suit. I suspect it is a bit early in your build to worry about it, but here is a page which explains: wiki.linuxcnc.org/emcinfo.pl?CoordinateSystems

just clicking the "home" button for each axis will make that problem go away.
(Or you can put the NO_FORCE_HOMING option in for testing)
linuxcnc.org/docs/html/config_ini_config...b:%5BTRAJ%5D-section