[phenixbb] positional restraints in real_space_refine?

Oleg Sobolev osobolev at lbl.gov
Fri Oct 4 12:48:18 PDT 2019

Hi Daniel,

>  Now I'm thinking of cutting out these helices and manually position them
> approximately where I want them. But I fear that this will case headache at
> the "joint".

This is very likely. If the distance would be too big, there will be no
connection. If you will specify links manually, for long distances this may
cause instability in "joint" region during refinement.

> Is it possible to use the manual positions as a reference for positional
> restraints,

No. Unfortunately, the reference_coordinate_restraints are not designed to
take other model.

> Or is there a better way of refining this structure?
Maybe you can try "Real space refine zone" in Coot and drag the piece of
model into the density there maintaining the reasonable geometry during the

Best regards,
Oleg Sobolev.

> Regards,
> Daniel
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