[phenixbb] h_bonds restraints

[Maia Cherney]

Hi Pavel,
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. I 
think there should be some general restraints that should keep h_bonds 
at least at > 2.2A.
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?
Maia

Pavel Afonine wrote:
> Hi Maia,
>
> I assume that these waters are already present in your structure.
>
> Then run
> phenix.phenix.metal_coordination model.pdb
>
> That will create a restraints file for you Mg2+. Edit it, if 
> necessary, to satisfy your expectations. These two waters should be 
> there.
>
> Run phenix.refine and give it that restraints file. If you run 
> phenix.refine with "ordered_solvent=true" option, then phenix.refine 
> may or may not remove these two waters. If you absolutely need to keep 
> these waters, run phenix.refine with "ordered_solvent=true" untill the 
> last moment, then add two waters and run it again with 
> "ordered_solvent=false". Something like this...
>
> Pavel.
>
>
> On 3/27/10 3:50 PM, Maia Cherney wrote:
>> Hi Pavel,
>>
>> I have 2 important waters at 2.12 A distance after refinement. They 
>> are ligands of Mg2+. How can I restrain this distance to 2.3A (to 
>> pass pdb validation)? Is it in the ordered solvent that I need to 
>> change the default
>>    h_bond_min_mac = 1.8
>>    h_bond_min_sol = 1.8
>>    h_bond_max = 3.2
>>
>> Maia
>>
>> Pavel Afonine wrote:
>>> Hi,
>>>
>>> phenix.refine removes F-obs outliers for refinement. See .log file 
>>> for the number of such reflections. Also, it automatically removes 
>>> Fobs=0.
>>> Do phenix.mtz.dump data.mtz to see the content of your MTZ file.
>>>
>>> Pavel.
>>>
>>>
>>> On 3/27/10 1:26 PM, r n wrote:
>>>>
>>>> Hi all
>>>> I observed that for the same data set and resolution, number of 
>>>> reflections for the refinement is different
>>>> values both in phenix (9488), refmac5 (9423) and refmac using coot 
>>>> interface (9530).
>>>>
>>>> Please anyone can let me know why the differences between the 
>>>> programs for same resolution and data.
>>>>
>>>> Thanks
>>>> ram
>>>>
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