[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.
Pavel.
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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