I use the predefined mode with my ALPY but I use the file mode quite a bit with my LHIRES for cases where there is not a preconfigured setup. As well as the list of lines, the file contains the order of the fit you want and the approximate linear dispersion needed to approximately locate the lines so it is specific to a particular spectrograph and camera combination. You can generate your own file by doing a manual linear calibration first using the set (or subset) of the lines and noting the linear coefficient. (or you could try the linear coefficent from the fit generated using the predefined mode)This is then added to the list of line wavelengths along with the order of fit you want. (Note that it can fail if the dispersion is sufficiently non linear and the lines so closely spaced that the wrong line is picked. To avoid this, I suspect the predefined mode for the ALPY may allow for the non linearity of the instrument which the file mode does not allowing some more close spaced lines at the blue end to be used.) A typical file for the LHIRES looks like this for example
2
0.2461
6532.882
6598.953
6717.043
6752.834
where 2 is the order of the fit and 0.2461 is the linear dispersion (A/pixel)
(Ignore the doublespacing generated by the forum software)
Cheers
Robin