Hi Kate, The pixels size is usually not too critical whe using the H alpha lines as there are no other lines nearby but it can be super critical with the calibration module where it needs to distinguish between some very closely spaced lines
I find Christian Buil’s tip here
works well for calculating the pixel value to use:
“A tip for calculate the scaling factor p (or virtual pixel size). Use the formula:
p = 3123 / dx
where dx is the distance between the H alpha and H beta lines measured in pixels along the horizontal axis in a raw image. Try to find the distance to the nearest pixel (the reading of the mouse pointer is sufficient). In the example, the H alpha line is at x = 882, while the H beta line is at x = 535. So dx = 882-534 = 347, and thus the pixel size to adopt is p = 3123/347 = 9.00 pixels.”
Another trick is to keep an eye on the RMS value that ISIS generates in the running commentary on the “go” page when it is running the calibration fit. If you keep on repeatedly running varying the pixel size slightly, it should be obvious when the program locks onto the right lines as the RMS will suddenly tumble to a very low value.
Finally double check you are picking the H alpha line and not the nearby Telluric band as the reference point. (It has been known !)