[phenixbb] Metal Coordination and symmetry operation

[Pavel Afonine]

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 <pafonine at lbl.gov 
> <mailto:pafonine at lbl.gov>> 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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>
>

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