[phenixbb] magnesium

[Maia Cherney]

Hi Pavel,

does the program take into account that the Mg has 2+ charge (two 
electrons are missing)? I get negative density around Mg ion. Is it 
because of the lower occupancy or is it because the charge is not taken 
into account? Does the ion has a different name from neutral MG? like 
MG2+ ? I got the restraints for the coordination in the elbow.edits, but 
the Mg ion still has the same name MG.

Maia

Pavel Afonine wrote:
> Hi Maia,
>
> run
>
> phenix.metal_coordination model.pdb
>
> which will create elbow.edits file containing restraints definitions 
> for Mg - check them and edit if necessary to match your expectations.
>
> Then, next time you run phenix.refine, just give this elbow.edits file 
> at input:
>
> phenix.refine model.pdb data.mtz other_parameters elbow.edits
>
> I presume it can all be done from PHENIX GUI as well.
>
> Pavel.
>
>
> On 2/28/10 10:01 AM, Maia Cherney wrote:
>>
>> Hi,
>> I have a ligand (ADP) has a coordinated Mg2+ ion. The distance 
>> between Mg and each of the 6 ligands should be around 2.1 A. Does the 
>> program have the proper restraints for this distance (Mg2+-to-O) or I 
>> should manually make these restraints?
>>
>> Maia
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