I'm sorry. Let me explain further. I have one molecule per ASU. I have a metal ion located between two proteins. There are coordinating oxygens coming from both protein molecules and I would like to add explicit bond length restraints. So in my example below the SM atom is ~2.5Å from OE1 of GLU313, but it is also ~2.5Å 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 20-30Å away, and phenix.refine does NOT like that. BTW I am adding bonds to the "geometry_restraints.edits" section On May 17, 2010, at 2:05 PM, Ralf W. Grosse-Kunstleve wrote:

Hi Scott,

...

Is this possible?

# on working model 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 313" distance_ideal = 2.5 sigma = 0.2 } # on SYM mol 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" distance_ideal = 2.5 sigma = 0.2 }

Sorry, I'm not certain where you see the potential problem. Could you explain some more? Just in case: phenix.refine support bonds to symmetry copies, via e.g. symmetry_operation=-x,y,-z inside the bond scope. I can explain more if that's what you are looking for.

Ralf _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

That did the trick. Thanks, Scott 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