On 13/07/2026 17:02, Eleanor Dodson wrote:
This is more or less the right answer. AFAICS, Coot is doing the right
thing and giving you clashes where you have missing links.
Make the links (the menu item is in the Ligand module).
Paul.
--
You need to add a link record to the refinement. (Or ask refmac at to
do it for you.. )
The command is MAKE LINK YES and that would adds links to your Ca etc..
On Mon, 13 Jul 2026 at 14:03, amit gaur
<[email protected]> wrote:
Hi All,
I am currently trying to model calcium and sodium ions in Coot,
but I am encountering atomic clashes after placing them. Based on
the electron density, I am confident that these sites are occupied.
Has anyone experienced this before or have any suggestions on how
to handle these clashes? I would appreciate any advice.
Thank you!
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