[phenixbb] h_bonds restraints

Pavel Afonine PAfonine at lbl.gov
Sat Mar 27 16:57:55 PDT 2010

Hi Maia,

> I have done the things that you suggested, 


> 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;


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