Re: [phenixbb] Metal Coordination and symmetry operation

19 Oct 2012

      Hi Alex,

thanks for the file - I will have a closer look. Did you mean the 
restraint did not work or it worked but you wanted something else? (I'm 
just trying to understand if this is a Phenix problem that we need to fix).

Pavel

On 10/18/12 10:30 PM, Alex Theodossis wrote:
...
Hi Pavel,
thanks for the info. With it I was able to correctly define the 
symmetry-related links as per this example:
refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = name ZN   and chain C and resname ZN and resseq 
   1
    atom_selection_2 = name  NE2 and chain A and resname HIS and altid 
A and resseq   39
    symmetry_operation = -x+1,y+1/2,-z+1/2
    distance_ideal = 2.030000
    sigma = 0.050
  }
Unfortunately, this didn't have the desired result.  Instead, the 
addition of riding hydrogens fixed the problem.
I've also attached the relevant fragment of the refined model as 
requested.
Cheers,
Alex
On 17 October 2012 13:04, Pavel Afonine mailto:[email protected]> wrote:
Hi Alex,
Nigel is the best person to reply, so he may provide more
    comments. My understanding is that phenix.metal_coordination
    command (or whatever the equivalent click in the GUI is) should
    account for symmetry related atoms. If not you can fix it
    manually. First create edits file using phenix.metal_coordination
    and then add  symmetry related bonds as described here:
http://www.phenix-online.org/documentation/refinement.htm#anch353
Also, could you please send me the PDB file or its portion
    containing relevant to your question atoms and I will have a
    closer look?
Pavel
On 10/16/12 6:33 PM, Alex Theodossis wrote:
...
Dear bb,
I am trying to refine a Zn ion coordinated by symmetry
        related residues. To avoid groups being pushed away.  I have
        use phenix.metal_coordination to
        generate the necessary link edits. However only non-symmetry
        related interactions are accounted for. Is there a relevant
        option I can switch on?
        Alternatively, does anyone have an example of the syntax
        required to define the necessary symmetry operations in the
        elbow.edits file?
Thanks in advance.
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