i used 1a8y protein and used the following commands
create 1a8y_a, 1a8y
alter_state 1, 1a8y_a, 1a8y,(x,y,z)=(-0.5*x + 0.886025*y, 0.886025*x + 0.5*y, -z)
then i saved the molecule in pymol from file-->save molecule-->1a8y_a.pdb
The problem is that when i open the file as text file the format is improper since the space distribution is different from actual pdb files.
I am saying this because i have to use this file to convert in tleap format and further use in a program. Is there any other way to save the molecule in pymol?