phillips at biochem.wisc.edu
Sat Mar 13 16:28:42 PST 2010
I second Maia's 'request' to get proper scattering factors into Phenix for metal ions! Metallobiochemists need love, too.
George N. Phillips, Jr., Ph.D.
Professor of Biochemistry and of
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.
> 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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