[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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