[phenixbb] Metal Coordination and symmetry operation

Pavel Afonine pafonine at lbl.gov
Tue Oct 16 19:04:22 PDT 2012

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:


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?


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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