[phenixbb] Bond to symmetry mate

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Thu Jan 26 14:29:43 PST 2012

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.


On Thu, Jan 26, 2012 at 11:28 AM, Eike Schulz <eike.schulz at embl.de> 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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
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