Dear Amit Gaur,
You can have a look on our work on the MetalCoord program:
https://github.com/Lekaveh/MetalCoordAnalysis
https://journals.iucr.org/d/issues/2024/12/00/von5002/index.html
It can also give you external distance and angle restraints which can be
used in refmac, servalcat, phenix.refine or Coot. In Coot 0.9, select
Calculate -> Modules -> Restraints, and then Restraints -> Read Extra
Refmac Restraints... In Coot 1, click on the + with arrow in the right
top corner and select Restraints, and then Restraints -> Import
Restraints...
Good luck! Please keep us updated how it goes.
Cheers,
Martin
On 13/07/2026 14:02, amit gaur 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!
*Amit Gaur, *
*Department of Biomedical Science,*
*College of Medicine,*
*Florida State University,*
*1115 W Call St, Tallahassee, FL,32304*
*
*
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