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.

all you need to do is to define a custom bond for the second conformation that makes a cycle: http://phenix-online.org/documentation/refinement.htm#anch88 For example: refinement.geometry_restraints.edits { bond { action = *add atom_selection_1 = chain A and resseq 123 and name C1 and altloc A atom_selection_2 = chain A and resseq 123 and name O1 and altloc A distance_ideal = 1.35 sigma = 0.02 } bond { action = *add atom_selection_1 = chain A and resseq 123 and name C1 atom_selection_2 = chain Z and resseq 987 and name N1 distance_ideal = 1.45 sigma = 0.02 } } You can define as many custom bonds as you like between any pair of atoms. You can define custom angles too. Let me know if you have any questions or need any help with this. Pavel.