Hi,

Update to a newer Phenix version, 1.14 is pretty old.

Does the atom that leaves the density have otherwise correct geometry, i.e. are bond lengths and angles according to your restraints file (you can see it in .geo file)? Does this atom have correct ideal values (check cif restraints file or use Reel)?

I don't know what could be the issue with coot. Does the terminal window give some message when you load the cif file?

Dorothee

On Mon, May 4, 2020 at 12:49 PM Schulz, Eike-Christian <eike.schulz@mpsd.mpg.de> wrote:

Dear all,

I am refining a structure with a simple ligand in phenix 1.14. The ligand is present in 2 conformations at approx. equal occupancy. Refinement of the 2 conformations runs smoothly, but 2 problems occur

One of the ligand atoms is placed out of the electron density after refinement. The geometry file (via elbow) is present during refinement. The atom is not in an extreme position or clashes with anything else.
After refinement the ligand conformation cannot be changed in coot, although I import the cif dictionary.

Any advise ?

Best,

Eike

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