Re: [phenixbb] Refinement problem in phenix

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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov On Fri, May 22, 2020 at 6:13 PM Muhammad Bashir Khan 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 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 : [email protected] Fax : 510-486-5909 Web : CCI.LBL.gov

On Fri, May 22, 2020 at 1:27 PM Muhammad Bashir Khan 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

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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: [email protected]