[phenixbb] real_space_refine questions

Oleg Sobolev osobolev at lbl.gov
Mon Jun 12 12:30:25 PDT 2017

Dear Daniel,

- Is it possible to restrain the position of certain parts of the model
> (i.e. "freeze" them so that they move at all) to do focused refinement of
> subdomains or loops?
Although it is not currently possible to completely "freeze" some atoms
(exclude them from coordinate refinement) in phenix.real_space_refine, you
can try reference coordinate restraints described in #14 in documentation
to restrain certain atoms to their initial position. Depending on sigma you
provide these restraints could be more or less strict (use smaller sigma to
make them stronger).

> - In the instructions it says that you can do both NCS constraints and
> restraints. How you do the latter? I can only do the former by default or
> by defining ncs_constraints=True and give a NCS definition file.
I'm afraid it is mistake in the instructions. I believe that presently NCS
torsion restraints are not available in phenix.real_space_refine.

> - When I do a run with run=rigid_body, some rigid body groups move in to
> each other and overlap. Is there no collision detection using this
> algorithm? If I do a run=minimization_global, things work a bit better in
> this regard, but is not really what I want (at this stage). Am I doing
> something wrong? Here is the run command and the rigid body definition file:
Hopefully, Pavel will be able to answer this question.

Best regards,
Oleg Sobolev.
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