[phenixbb] geometry_restraints between sym mates?

Scott Classen SClassen at lbl.gov
Mon May 17 17:13:25 PDT 2010

That did the trick.
On May 17, 2010, at 4:32 PM, Ralf W. Grosse-Kunstleve wrote:

> Hi Scott,
>> So in my example below the SM atom is ~2.5? from OE1 of GLU313, but
>> it is also ~2.5? from OE1 of GLU285 of a symmetry related protein. The
>> problem is that in my particular choice of symmetry equivalent atoms
>> GLU285 is really more like 20-30? away, and phenix.refine does NOT
>> like that.
> You can fix the problem like this:
>  bond {
>    atom_selection_1 = "name SM and chain M and resname SM and resseq 1"
>    atom_selection_2 = "name OE1 and chain A and resname GLU and resseq 285"
>    symmetry_operation = -x,y,-z+.5
>    distance_ideal = 2.5
>    sigma = 0.2
>  }
> The symmetry operation above is just an example and most likely
> not the one you need. The find out the proper one, use Coot to draw
> the symmetry copy of your molecule (near the SM), then click on the
> symmetry-equivalent OE1. Coot should show you the symmetry operation
> that was used to draw the atom. Simply copy it into the phenix.refine
> parameter file.
> Ralf

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