[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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