[phenixbb] phenix.refine with reference model

Oleg Sobolev osobolev at lbl.gov
Tue Dec 22 09:09:15 PST 2015

Dear Sebastian,

I hope you are using at least latest official release of Phenix.

One of the possible ways to proceed is to select only parts of your
reference structure that have more sequence identity and supply them along
with corresponding parts of your model via reference_model.reference_group
scope. I'm sure that there is a way to do so in Phenix GUI as well.

I'm happy to provide more specific advice, but I will need your files to do
so. You can send them directly to me (off-list). They will be kept in

Best regards,
Oleg Sobolev.

On Tue, Dec 22, 2015 at 2:28 AM, Falk, Sebastian <sfalk at biochem.mpg.de>

> Hi!
> I am currently building a 3.3 A structure of a large protein. I do have a
> reference model at much better resolution that has 58% sequence identity
> and 77% similarity.
> The structures are quite similar, there are only a few regions with
> insertions.
> However, phenix.refine does ‘accept’ the reference model and thus creates
> no torsion restraints.
> I also tried to run ProSmart in CCP4 but there the cut-off for the
> reference model is 75% sequence identity. I could not find any threshold
> for phenix.refine though.
> I am happy for any suggestion or tip how to include the reference model
> even though the sequence identity is not as high.
> Thank a lot.
> Sebastian
> Sebastian Falk
> Max-Planck-Institute for Biochemistry
> Structural Cell Biology
> Am Klopferspitz 18
> D-82152 Martinsried
> Germany
> sfalk at biochem.mpg.de
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