[phenixbb] Refinement problem in phenix

[Nigel Moriarty]

It's place_ions at the CLI or "Place elemental ions" in the GUI on the
"Refinement settings" tab. As Pavel said, UNX is an unknown ion so you
can't really refine it. You could make it HOH to see what happens but you
should know something about what it may be.

Cheers

Nigel

---
Nigel W. Moriarty
Building 33R0349, Molecular Biophysics and Integrated Bioimaging
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov


On Fri, May 22, 2020 at 6:13 PM Muhammad Bashir Khan <mbk at ualberta.ca>
wrote:

> Hi Nigel;
> I tried to find that option, but I can not find it. Could you please give
> some more hints where is that option is hidden.
>
> Thanks
>
> Bashir
>
> On Fri, May 22, 2020 at 4:11 PM Pavel Afonine <pafonine at lbl.gov> wrote:
>
>> Hi,
>>
>> please define "refinement still not working". I think phenix.refine wont
>> accept UNX because it has undefined scattering type.
>>
>> Pavel
>>
>> On 5/22/20 13:41, Nigel Moriarty wrote:
>>
>> Muhammad
>>
>> There is an option in refinement that will determine the ion that best
>> fits a density blob. You should try that after removing the UNX.
>>
>> Cheers
>>
>> Nigel
>>
>> ---
>> Nigel W. Moriarty
>> Building 33R0349, Molecular Biophysics and Integrated Bioimaging
>> Lawrence Berkeley National Laboratory
>> Berkeley, CA 94720-8235
>> Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
>> Fax   : 510-486-5909       Web  : CCI.LBL.gov
>>
>>
>> On Fri, May 22, 2020 at 1:27 PM Muhammad Bashir Khan <mbk at ualberta.ca>
>> wrote:
>>
>>> Hi there;
>>>
>>> I find some unknown density in my map, where I put SO4 and in some UNX.
>>> I merged and save all in one PDB. I run ReadySet to make cif. file, but
>>> refinement still not working. Can anybody explain what else I should
>>> provide?
>>>
>>> Thanks in advance
>>>
>>> Bashir
>>>
>>> --
>>> ------------------------------------------------------
>>> Muhammad Bashir Khan, Ph.D.
>>> Research Associate
>>> Department of Biochemistry
>>> Medical Science Bldg.
>>> Lab 3-27
>>> University of Alberta
>>> Edmonton AB, T6G 2H7
>>>
>>> Phone: 780-492-4577-
>>> e-mail: mbk at ualberta.ca <cbrooks1 at ualberta.ca>
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>>
>>
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>>
>
> --
> ------------------------------------------------------
> Muhammad Bashir Khan, Ph.D.
> Research Associate
> Department of Biochemistry
> Medical Science Bldg.
> Lab 3-27
> University of Alberta
> Edmonton AB, T6G 2H7
>
> Phone: 780-492-4577-
> e-mail: mbk at ualberta.ca <cbrooks1 at ualberta.ca>
>
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