[phenixbb] Refinement

Pavel Afonine pafonine at lbl.gov
Tue Mar 31 11:12:15 PDT 2015

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?


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