[phenixbb] h_bonds restraints

[Pavel Afonine]

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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>>
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