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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
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