[phenixbb] Ligand refinement - geometry does not fit density

Dorothee Liebschner dcliebschner at lbl.gov
Mon May 4 13:33:16 PDT 2020


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?


On Mon, May 4, 2020 at 12:49 PM Schulz, Eike-Christian <
eike.schulz at 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
>    1. 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.
>    2. After refinement the ligand conformation cannot be changed in coot,
>    although I import the cif dictionary.
> Any advise ?
> Best,
> Eike
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