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.
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