[phenixbb] Solving a protein - ligand structure

Pavel Afonine pafonine at lbl.gov
Wed May 20 01:09:53 PDT 2020


One way of dealing with this is to place a (symmetry) unique copy of the 
ligand , which may be its part.
Alternatively it's possible to disable nonbonded repulsion forces for 
selected atoms.

Send me model and data files if still need help with this.


On 5/20/20 01:01, Tom Vanmarcke wrote:
> Dear,
> We are trying to solve a protein structure that contains a ligand 
> (polyoxometalate). We found the ligand in the electron density but 
> through the middle of the ligand goes a 2 fold axis. For this reason, 
> we placed the occupendency of the ligand on 0.50. When we try to 
> refine the structure using phenix.refine, the ligand breaks down even 
> when adding a cif restrain file.
> The cif restrain file contains information about atoms, angles and 
> bond lengths.
> Is there a way to fix this problem?
> Greetings

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