[phenixbb] default bondlengths - water

[Engin Ozkan]

Thanks Pavel,

If my memory from grad school serves me well, short or high-energy 
hydrogen bonds are between 2.2 to 2.5 A.  They are observed in protein 
structures (and did generate a few nice review papers and controversy at 
the time, if I remember correctly), but any distance smaller than ~2.1 A 
(say, a 1.8 A hydrogen bond as phenix.refine is allowed to pick) does 
not sound likely given my limited understanding of the subject (The 
distances are between H-acceptor to H-donor). Any recent biophysical 
chemistry graduates with fresh minds in the audience?

I did check my pdb files that were refined with phenix.refine defaults, 
and asked coot to "Check/Delete Waters". Happily enough, coot found no 
waters nearer than 2.3 A to protein (which is the coot default: 2.3 to 
3.5).  That was the reason that made me think the phenix default 
distances of 1.8 to 3.2 might be something else.  At the end of the day, 
the defaults work, so that's good.

Engin

Pavel Afonine wrote:
> 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
>>>>> _______________________________________________
>>>>> phenixbb mailing list
>>>>> phenixbb at phenix-online.org
>>>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>>>
>>>>>   
>>>>>     
>>>>>       
>>>>>         
>>>>   
>>>>     
>>>>       
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>>
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