Hi Purity, You need to define the symmetry operation: For bonds to symmetry copies, specify the symmetry operation in xyz notation, for example: symmetry_operation = -x-1/2,y-1/2,-z+1/2 To obtain the symmetry_operation, either use Coot (turn on drawing on symmetry copies, then click on the copy and look for the symmetry operation in the status bar), or run this command: iotbx.show_distances your.pdb > all_distances This will produce a potentially long all_distances file, but if you search for sym= there will probably only be a few matches from which it is easy to pick the one you are interested in, based on the pdb atom labels. (taken from https://phenix-online.org/documentation/reference/refinement.html#definition... ) Best regards, Oleg Sobolev. On Mon, Jun 8, 2026 at 8:57 AM Ezennubia, Purity via phenixbb < [email protected]> wrote:
Hello everyone,
I am new to this forum and I am glad this exists for discussions between phenix users.
I have been trying to create a bond between two atoms belonging to different symmetry but when I create the bond restraints on phenix, I get an error message that says custom bonds with excessive length and I later realized the problem is not the bond length but the fact that the two atoms are in different symmetry.
Is there a way to make this work on phenix? I would love suggestions on this.
Thank you, Purity _______________________________________________ phenixbb mailing list -- [email protected] To unsubscribe send an email to [email protected] Unsubscribe: phenixbb-leave@%(host_name)s