[phenixbb] Refinement problem in phenix

[Pavel Afonine]

Also, have a look at

https://journals.iucr.org/d/issues/2014/04/00/lv5059/lv5059.pdf

to know what to expect from "Place elemental ions" option. Briefly, it 
won't place anything and it relies on meaningful inputs!

Pavel

On 5/22/20 18:19, Nigel Moriarty wrote:
> 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 <http://CCI.LBL.gov>
>
>
> On Fri, May 22, 2020 at 6:13 PM Muhammad Bashir Khan <mbk at ualberta.ca 
> <mailto: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
>     <mailto: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
>>         <mailto:NWMoriarty at LBL.gov>
>>         Fax   : 510-486-5909       Web  : CCI.LBL.gov
>>         <http://CCI.LBL.gov>
>>
>>
>>         On Fri, May 22, 2020 at 1:27 PM Muhammad Bashir Khan
>>         <mbk at ualberta.ca <mailto: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 <mailto:cbrooks1 at ualberta.ca>
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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 <mailto:cbrooks1 at ualberta.ca>
>

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