[phenixbb] cif file for internal bond with one of two alternative conformations

[Daqi Tu]

Hi,

I have a structure of drug bound to a protein. The drug has two 
alternative conformations, in which one of them has an internal bond 
making it a cyclic compound. How do I refine a structure like this? What 
modification should I do to its cif file, which I generated using elbow 
without the internal bond.

Thank you.

Daqi Tu
(sorry if I have double posted.)