pafonine at lbl.gov
Tue Mar 31 11:12:15 PDT 2015
> 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?
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