Delete atoms

[almisrati ali]

Hello everyone, 

I need some assistance please . I would like to know how to permanently delete atoms from a crystal structure. Whenever I use the selection tool to delete atoms, they reappear when I reopen the file. 

when I delete them from the structure parameters. This persistence of atoms is due to the e periodicity of the crystal. In my latest attempt, I exported the file in XYZ format after deleting the atoms, and they were successfully removed. However, when I repened xyz file  and exported  to the  POSCAR  format, the structure appeared inside a box. I'm wondering why this is happening.

Thanks for your help in advance