[phenixbb] Occupancy refinement

Pavel Afonine pafonine at lbl.gov
Wed Jun 1 05:59:27 PDT 2011

Hi Mark,

I'm pretty sure it is possible (and easy) to do in phenix.refine, but 
syntax to ask phenix.refine to do this may not be obvious... I should 
probably add more examples to the documentation. Meanwhile, if you send 
me the portion of your PDB file containing the residues in questions and 
HEME, then I will send you back a working example.


On 6/1/11 2:06 AM, Mark Roe wrote:
> Hi,
> I have a HEME covalently attached to an amino acid side chain. From 
> mass spec, the original sample was around 50/50 covalent attachment or 
> unlinked. I have created a new library file to deal with the 
> covalently linked HEME. Is there a way to refine the occupancy? I need 
> to constrain the new residue B167 to the original amino acid A167 AND 
> the original HEME A350. If I just do the normal occupancy refinement 
> the new B167 gets constrained only to the original side chain A167. Or 
> (since there isn't any large change in atom position) will the 
> occupancy refinement be meaningless anyway? It's not like different 
> orientations - just different bonding.

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