[phenixbb] h_bonds restraints

Pavel Afonine PAfonine at lbl.gov
Sat Mar 27 16:08:54 PDT 2010


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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