[phenixbb] Mn - O distances

Jianghai Zhu jzhu at idi.harvard.edu
Mon Nov 28 16:16:23 PST 2011


Hi Nigel,

One thing I found out is that the slack keyword cannot be added into elbow.edits. After reading elbow.edits, phenix.refine will strip them off and replace them with slack=None.  I think this must be a bug.  

-- Jianghai




On Nov 23, 2011, at 11:32 AM, Nigel Moriarty wrote:

> Tim
> 
> I did a survey of the literature some time ago and used Harding, Acta
> Cryst. D62 (2006), 678-682 for the data used in
> phenix.metal_coordination. I recently added the data from Zheng et al.
> Journal of Inorganic Biochemistry 102 (2008) 1765-1776 and plan to
> include it soon.
> 
> You are quite correct that the coordination number affects the bond
> length. This is currently ignored in PHENIX but it may well be useful.
> I'll read Shannon and Prewitt with a view to improving the
> coordination code.
> 
> One thing you can do is add the slack option to the edits giving the
> bond potential a flat bottom. This allow complete freedom for the
> metal to use the electron density for fitting within the slack
> distance of the ideal.
> 
> refinement.geometry_restraints.edits {
>   bond {
>        action = *add
>        atom_selection_1 = chain F and resid 1 and name FE1
>        atom_selection_2 = chain A and resid 69 and name SG
>        distance_ideal = 2.35
>        sigma = 0.1
>        slack = 0.1
>   }
> }
> 
> I'm very interested in discussing your situation and making it better.
> If you send me your model (off line) we can investigate a better
> solution.
> 
> Nigel
> 
> NB. Any files sent to me will be held in strictest confidence.
> 
> 
> On Tue, Nov 22, 2011 at 2:48 PM, Timothy Springer
> <springer at idi.harvard.edu> wrote:
>> Hi, We are refining structures with Ca binding sites that are replaced by
>> Mn. Using the coordination restraints in Phenix (distance only) obtained
>> with phenix.metal_coordination, we wind up with the ligands coming somewhat
>> too close, so there is positive density on the opposite side of the ligating
>> residue from the metal. We may have a series of problems, including
>> incomplete replacement of Ca by Mn. However, the bigger issue I want to
>> address is coordination number.
>> In the work by Shannon and Prewitt, such as Acta Cryst. B25, 925, metal
>> oxides are examined, and the point is made that the Mn-O distance with a
>> coordination number of 6 is shorter than for 7. Ca commonly has either 6 or
>> 7 ligands, and with 7 ligands (most common) the O cannot squeeze as tightly
>> together and are farther away from Ca. Mn more commonly has 6 ligands, but
>> can have 7.
>> What are the distance restraints in Phenix based on? They seem similar to
>> those in Harding MM, Acta Cryst D62, 678 (2006). This paper lumps
>> measurements for different coordination numbers together for Mn-O and Ca-O
>> distances, but not for Co, Cu, and Zn.
>> It does seem to help to add metal ion restraints in Phenix. Things don't
>> seem to come out as well without them.
>> Would it be helpful to treat 6 and 7-coordinate metals differently? Or
>> should we just loosen the restraints?
>> How does Refmac treat metals? One does not need to add restraints in its
>> case.
>> With my best regards,
>> Tim
>> Timothy A. Springer, Ph.D.
>> Latham Family Professor of Biological Chemistry and Molecular Pharmacology
>> 
>> Harvard Medical School                   http://idi.harvard.edu/springer
>> Immune Disease Institute                 springer at idi.harvard.edu
>> Program in Cellular and Molecular Medicine, Dept. Medicine
>> Div. Hematology                                 Children's Hospital Boston
>> 3 Blackfan Circle, Rm 3103              phone:  617-713-8200
>> Boston MA 02115                               fax:        617-713-8232
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
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>> http://phenix-online.org/mailman/listinfo/phenixbb
>> 
>> 
> 
> 
> 
> -- 
> Nigel W. Moriarty
> Building 64R0246B, Physical Biosciences Division
> Lawrence Berkeley National Laboratory
> Berkeley, CA 94720-8235
> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
> Fax   : 510-486-5909       Web  : CCI.LBL.gov
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