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

Phone: 780-492-4577- e-mail: [email protected] _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

_______________________________________________ phenixbb mailing [email protected]http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]

-- ------------------------------------------------------ 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]

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 : [email protected] Fax   : 510-486-5909       Web  : CCI.LBL.gov http://CCI.LBL.gov

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

On Fri, May 22, 2020 at 1:27 PM Muhammad Bashir Khan mailto:[email protected]> 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: [email protected] mailto:[email protected] _______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected] mailto:[email protected]

_______________________________________________ phenixbb mailing list [email protected] mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe:[email protected] mailto:[email protected]

-- ------------------------------------------------------ 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] mailto:[email protected]