[phenixbb] geometry_restraints between sym mates?

[Scott Classen]

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
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