David,
The spectral assistant does not work with the file mode (the response assistant yes of course). Some info here:
http://www.astrosurf.com/buil/isis/tuto ... ion_us.htm
The ISIS algorithm is very simple. First, ISIS find approximative X coordinates position of the lines (in pixels) by using dispersion law coefficient (a) from the file and constant (b) from the Calibration tab : X = a (wavelength) + b
It is a first guest. Next ISIS search in the range {X-dx, X + dx} the exact X position for each wavelength (max pixel intensity pixel and next, a gaussian fit of the line position).
Finally, ISIS fit a polynomial function lambda = A X'^2 + B X' + C (for example), with X' the exact (fractional ) X position of the lines.
I suggest order 2 or 3 for the spectral law fit (max).
The principal problem concern the initial linear fit. No real problem if the LISA spectrograph (or Lhires of course) is concerned, the base dispersion is correctly linear. The situation is more complex with Aply600 because the dispersive element is a grism. For the Alpy600, the predefined mode use is a 2nd order polynomial function for line search (internally coded).
Your line list seem correct and a 0.5 A RMS is normal (note the low contrast of some lines). I recommand acquisition in bin 1x1 for the best result.
Here a typical line list (for Alpy 600 is line mode) :
3
2.4548
3948.98
4158.59
4199.45
4545.05
4657.90
4764.87
4965.12
5400.56
5495.87
5852.49
5944.83
6143.06
6266.49
6334.43
6506.53
6678.28
7067.22
Christian