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@LBL.gov Fax : 510-486-5909 Web : CCI.LBL.gov
On Fri, May 22, 2020 at 6:13 PM Muhammad Bashir Khan <mbk@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@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@LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
On Fri, May 22, 2020 at 1:27
PM Muhammad Bashir Khan <mbk@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?