Here is an example: refinement.geometry_restraints.edits { bond { action = *add delete change atom_selection_1 = chain A and resname HEM and resid 154 and name FE atom_selection_2 = chain A and resname MTO and resid 155 and name O symmetry_operation = -x,y,-z distance_ideal = 2.2 sigma = 0.01 } } To get the symmetry_operation, you can 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 give you a long all_distances file, but if you look for "sym=" hopefully there will only be a few matches. Ralf On Thu, Jan 26, 2012 at 11:28 AM, Eike Schulz wrote:

Dear phenixbb,

I am sure this is a trivial problem encountered before and that there is a solution to it – however, I was unfortunately not able to solve it myself or with the help of the online documentation.

The problem: In one of my structures a nucleic acid chain extends over several symmetry mates. How can I create and refine a bond (in my case 5'-phosphate to 3'-end ) to that symmetry mate?

Many thanks in advance

Eike

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