[phenixbb] Refinement using a homolog as a reference

Jeff Headd jjheadd at lbl.gov
Thu Jul 25 07:55:44 PDT 2013

Hi Amar,

Yes, can use the homolog as a reference model. The method will do a
secondary structure-based alignment, so the sequence differences shouldn't
matter. You don't need to prune the model, as this will be handled
automatically. The differing numbering schemes should be handled
automatically, and you can check the log file to see which residues are
matched to assure that you are seeing the behavior you expect.

If you find that it is not matching the residues correctly, let me know and
I would be happy to help you offline.


On Thu, Jul 25, 2013 at 4:44 AM, Joshi, Amar (Dr.) <aj180 at leicester.ac.uk>wrote:

> Hi,
> I am refining ligand-protein complexes at 3.2Å dataset with a human
> protein. My Rfree is ~0.34 but my ramachandran stats are concerning me: 85%
> favoured, 4.5% disallowed.
> The structure of a yeast homolog has been deposited at 2.4Å resolution.
> The yeast structure contains additional loops but is ~55% identical to the
> human protein. The overall conformation between the homologs is very
> similar.
> Can I use this as a reference model? Should I prune the reference model?
> Will different numbering schemes affect the refinement?
> Many thanks,
> Amar
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