[phenixbb] default bondlengths - metal

[Engin Ozkan]

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
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>>   
>>     
>
>