If I correctly remember, in one of the latest ISIS versions was adopted a new algorithm for sequence spectra wavelength registration. Christian told us that accuracy has been improved (on condition that the single spectra show numerous and contrasted lines).
I have previously used quite regularly the ISIS WR option on Be star spectra anyway with good results. I understand that the cross-correlation method requires several contrasted lines but it seems to me that old algorithm could usefully be used with hot stars h-alpha region (hi-res). With WR I obtained more sharp lines and a better wavelenght calibration before H2O check and shift correction.
With the new algorithm seems that often enough is introduced a moderate wavelength calibration error on Be star spectra (but is perfect with cooler stars).
Here is an example with the same 5 Cnc data just after process end (note H2O reference). Release 5.0.2 vs 5.2.1:
With 5.2.1 I very often see a high value of first Delta X (strange?), followed by more "regular" intervals. Note this behavior repeats similar for other hot stars.
I wonder if it would be useful to have the old algorithm option or, generally speaking, to implement an algorithm (available as an option) that works with profile shape matching (low frequency intensity variations, not sharp lines, as is often observed in Be stars Ha region). I know we have the "manual option", that is, re-sync by eye the individual sequence spectra but it seems probably less accurate than a mathematical fit.
Mechanical flexure and thermal effect on Lhires III are important problems. It's a pity not be able to use the ISIS WR powerful function to solve. Wavelength calibration is correctable thanks to telluric lines (if visible) but spectral resolution remains compromised.
Ciao
Paolo