[phenixbb] magnesium

George Phillips phillips at biochem.wisc.edu
Sat Mar 13 16:28:42 PST 2010


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
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>> 
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