[phenixbb] h_bonds restraints

Maia Cherney chern at ualberta.ca
Sat Mar 27 17:23:12 PDT 2010

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)?


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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