[phenixbb] Refinement problem in phenix

Muhammad Bashir Khan mbk at ualberta.ca
Fri May 22 18:13:07 PDT 2020


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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