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