Pavel, I second Maia's 'request' to get proper scattering factors into Phenix for metal ions! Metallobiochemists need love, too. George George N. Phillips, Jr., Ph.D. Professor of Biochemistry and of Computer Sciences University of Wisconsin-Madison 433 Babcock Dr. Madison, Wi 53706 Phone/FAX (608) 263-6142 On Mar 13, 2010, at 6:24 PM, Maia Cherney wrote:
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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