Hi Mohamed,
How do tell phenix.refine to not move my HEM ligand around?
yes, you can exclude selected atoms from refinement of coordinates in Phenix refinement GUI: Refinement settings -> Modify selection for: XYZ coordinates -> Edit -> type atom selection in "Edit selected" field (under XYZ refinement) like "chain A and resseq 1" or "chain A and resname ATP" However, I would rather find why correct geometry is not preserved.
I have a cif file describing the ligand but in my case, I can see clear density of it not following the ideal geometry.
If you send me files (off mailing list of course!) I will see if I can explain it.. You can copy to Nigel too as chances are that if you choose to send files I will be talking to him anyway.
As an example, I have attached a screenshot from Coot.
It's hard to infer what's going on from a static image..
In fact, the C atom is covalently linked to the nearest Cys, so the HEM side chain should be 'moved' into the density and the green blob shouldn't be there.
Is this link defined anywhere in restraints used in refinement? Pavel