chern at ualberta.ca
Sat Mar 13 16:24:06 PST 2010
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.
Pavel Afonine wrote:
> Hi Maia,
> 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.
> On 2/28/10 10:01 AM, Maia Cherney wrote:
>> 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?
>> phenixbb mailing list
>> phenixbb at phenix-online.org
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> phenixbb at phenix-online.org
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