Open each file in separate pymol and save them ...

File --- save molecule --- one file.. in this fashion

Again open both in a single pymol and align together.

Hope, your problem will be solved :)

The yellow lines show which atom was fitted to which in the alignment process. If you look at the object menu on the right side of the display menu, you'll see that a new object was generated, whose name starts with "aln"and also contains the name of the two objects you aligned. This object both shows the alignment lines and the governs the alignment in the sequence view. Click on the object in the object menu to disable it (lines will no longer be showns and the sequence view will no longer show the alignment) or delete it to permanently get rid of it.

Actually, the lines indicate a very bad alignment. Try using the command "cealign" instead. (type "cealign object1, object2" in the command line, where object1 stands for the name of the molecule you want to align to and object2 for the name of the molecule that moves in the alignment process.

The command "align" decides based on the sequence alignment which atoms have to be aligned to which, and works well only for very closely related sequences, while "cealign" does a structural alignment. There are many more ways to tweak the alignment of structures in pymol - consult the pymol wiki (https://pymolwiki.org/index.php/Main_Page) for details.

PS: In a good alignment between very similar structures, the yellow lines are also there but so short that they are not visible. To get an alignment object when using a command line command like "cealign", you need to specify this (https://pymolwiki.org/index.php/Cealign):

cealign selection1, selection2, object

object = string: name of alignment object to create