[phenixbb] default bondlengths - water

Engin Ozkan eozkan at stanford.edu
Sat Feb 28 18:38:31 PST 2009


While we are on the matter, I needed a clarification in default H-bond 
distances in for water picking. The default parameters are:
    h_bond_min_mac = 1.8
    h_bond_min_sol = 1.8
    h_bond_max = 3.2
These values do work well, actually.

Are these numbers the distance between the H-bond acceptor and the 
hydrogen itself? More commonly, people speak of acceptor to donor 
distances, but these values are too small for that (which are usually 
~2.3-3.5 A)?

Engin

Engin Ozkan wrote:
> 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
>>>
>>>   
>>>     
>>>       
>>   
>>     
>
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