I am not sure if this question is relevant here, but I have a very basic doubt. I have a .cif file of a crystal, it has _atom_site_disorder_group and _atom_site_disorder_assembly for some of the atoms. I understand that it means there are multiple sites for those atoms possible with similar potential energy. But to use the structure in any computation, we have to assign some position and connectivity to those atoms. How can we do that? Is there any standard method to deal with such disorder?
There are no standard methods. By making choices you need to create a structure with no symmetry (P1) so that all atom positions are defined.