[phenixbb] default bondlengths - water

[Pavel Afonine]

Hi Engin,

these are the distances between non-hydrogen atoms (even if H atoms are 
present in the model).

The soft low limit cutoff allows to account for map imperfections due to 
data and model quality.

I did not systematically investigate this. If I recall correctly, I put 
these numbers in based on 1) looking "what others do"; 2) PDB survey; 3) 
tests with a few models.

Pavel.



On 2/28/09 6:38 PM, Engin Ozkan wrote:
> 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
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>>>>
>>>>   
>>>>     
>>>>       
>>>>         
>>>   
>>>     
>>>       
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