[phenixbb] h_bonds restraints
Maia Cherney
chern at ualberta.ca
Sat Mar 27 16:55:11 PDT 2010
Pavel,
I just want to restrain the distance between 2 particular waters. Is it
in the pdb_interpretation?
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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