[phenixbb] Metal Coordination and symmetry operation
Pavel Afonine
pafonine at lbl.gov
Thu Oct 18 22:51:40 PDT 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 <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.
>>
>>
>>
>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>
>> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20121018/fdfc8d01/attachment.htm>
More information about the phenixbb
mailing list