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

[Pavel Afonine]

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.