[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)?
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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