[phenixbb] h_bonds restraints

Maia Cherney chern at ualberta.ca
Sun Mar 28 04:13:21 PDT 2010


Hi Pavel,

I have waters that are part of the Mg2+ coordination. They should be at 
~2.1A from Mg2+. At the same time, they should be at a hydrogen-bonding 
distance from each other (minimum 2.2A otherwise the validation at the 
PDB complains). The two waters after refinement without restraints had 
closer (2.12A) distance between them, so I managed to restrain the 
distance to 2.23A using pdb_interpretation. But my question was, should 
not the refinement automatically restrain close distances between any 
atoms, including waters? (By the way, I picked them manually).

Maia

Pavel Afonine wrote:
> Hi Maia,
>
> I'm not sure I understand the question. If you have that specific 
> water in your structure already (and you run phenix.refine with 
> "ordered_solvent=false"), then changing the h_bond_min_mac  or 
> h_bond_min_sol will not change anything since these parameters are 
> used in water update.
>
> However, if you are at the stage of water picking and the distance 
> between Mg2+ and prospective water peak is 2.2A then the water will be 
> placed there (providing that the corresponding peak satisfies the 
> other criteria).
>
> Could you please explain what exactly the problem is, and then I will 
> try my best to give you the solution?
>
> Thanks!
> Pavel.
>
>
> On 3/27/10 5:23 PM, Maia Cherney wrote:
>> Hi Pavel,
>> what is h_bond_min_mac  and h_bond_min_sol.
>>
>> which one should I change to 2.2 so that it will not affect the 
>> coordination distances of Mg2+ (around 2A)?
>>
>> Maia
>>
>> Pavel Afonine wrote:
>>> Hi Maia,
>>>
>>>> I have done the things that you suggested, 
>>>
>>> great!
>>>
>>>> and I have all the restraints for the Mg2+ and I see those 2 
>>>> waters, but they are at 2.12A distance.
>>>
>>> Are these two waters located in the centers of corresponding density 
>>> peaks? If this is the case then I don't see the subject of your 
>>> worries. If this is not the case (these waters are off the peaks) 
>>> then edit the file that defines restraints for water-Mg2+ interactions.
>>>
>>>> I think there should be some general restraints that should keep 
>>>> h_bonds at least at > 2.2A.
>>>
>>> Yes. You wrote it yourself in your previous email:
>>>
>>>   h_bond_min_mac = 1.8
>>>   h_bond_min_sol = 1.8
>>>   h_bond_max = 3.2
>>>
>>> Just change the values to what you like!
>>>
>>>> That is why I asked you about those defaults (1.8A etc). Why are 
>>>> they at 1.8A? Should not they be at least at 2.2A?  
>>>
>>> Honestly, I don't remember why I put these values (this is pretty 
>>> old code in phenix.refine that I wrote several years ago). All I 
>>> recall is that I had a reason for this. I probably need to run 
>>> through the whole PDB and see how the density peaks (actual, 
>>> residual, omit-residual) are distributed w.r.t. macromolecule, and 
>>> write it somewhere for the future reference. This could be a project 
>>> for a few weeks, but it will definitely yield a rock-solid 
>>> conclusion about "good" distances. Meanwhile feel free to edit the 
>>> available parameters.
>>>
>>> By the way, this is what CNS is using:
>>>
>>> {* minimum distance between water and any atom *}
>>> {===>} min=2.6;
>>> {* maximum distance between water and any atom *}
>>> {===>} max=4.0;
>>>
>>> {* minimum hydrogen bonding distance between water and O or N *}
>>> {===>} hmin=2.0;
>>> {* maximum hydrogen bonding distance between water and O or N *}
>>> {===>} hmax=3.2;
>>>
>>> Pavel.
>>>
>>> _______________________________________________
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>>> phenixbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>
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