[phenixbb] default bondlengths - metal

Nigel W Moriarty NWMoriarty at lbl.gov
Sat Feb 28 15:25:46 PST 2009


Engin

Thanks for the posting.  You have discovered a hole in the coverage of 
the default bond lengths data.  Thanks for the link.  I'm sure it will 
be incorporated in the near future.

In the meantime, I'm sure you are aware that you can change the value in 
the "edits" file.

Nigel

On 2/28/09 9:44 AM, Engin Ozkan wrote:
> Hi, all,
>
> Recently following the phenixbb, I was made aware of 
> phenix.metal_coordination.  So I just gave it a try for a structure of 
> mine with sodium in it.  Specifically, I decided to turn the 
> use-default-bondlengths option on.  The result was surprising, because 
> the output file thinks that sodum to oxygen distances are supposed to be 
> 1.9 Angstroms.  Work done by Marjorie Harding and others have shown that 
> this distance should be about 2.4 (Acta Cryst. D62 (2006), 678-682; for 
> a summary of their numbers, 
> http://tanna.bch.ed.ac.uk/newtargs_06.html).  I wonder why 
> phenix.metal_coordination chose 1.9 A as the default Na-O distance, or 
> is the default option a different type of bond distance, I am not sure.
>
> Any clarification from the authors would be appreciated.
>
> Below is part of the output, showing the distance:
>
> refinement.geometry_restraints.edits {
>   bond {
>     action = *add
>     atom_selection_1 = name NA   and chain N and resname NA and resseq    1
>     atom_selection_2 = name  O   and chain A and resname PHE and resseq   76
>     distance_ideal = 1.920420
>     sigma = 0.01
>   }
> }
>
> Engin
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>
>   

-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
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Email : NWMoriarty at LBL.gov
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