[phenixbb] default bondlengths - metal
Engin Ozkan
eozkan at stanford.edu
Sat Feb 28 15:40:31 PST 2009
Thanks, Nigel. I had actually created the restraints manually with the
literature values (and that did match what I saw in density). I was
just testing this new tool, because it sure is bound to come handy. It
also gave me chance to point out the literature on this matter; this
work even suggests sigma values specifically for structure refinement.
Engin
Nigel W Moriarty wrote:
> 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
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
>>
>
>
More information about the phenixbb
mailing list