Discrepencies between load and save when internal and external index are differents

[Jonathan Barnoud]

Pymol seems to have two different index for each atom: an internal one you can use for selection using the "index" keyword and an external one which is accessible through he "id" selection keyword. The use of the "index" keyword caused selection errors in some cases so commit f1e6430 replaced it bu the "id" keyword fixing the selection issue. However it seems that the internal index is written when ndx_save is used. Then when the internal and the external index are different the output index file is different from the input index file.