[phenixbb] [EXTERNAL] Re: Phenix Real_Space_Refine and Torsion NCS restraints

Edward Berry berrye at upstate.edu
Tue Aug 4 11:04:29 PDT 2020

Sorry, I guess I didn't realize the reference restraints are by torsion
angles. I guess that would be the same as torsion angle restraint.

>>> "Edward Berry" <berrye at upstate.edu> 08/04/20 2:00 PM >>>
I guess the problem is that the model has to be somewhat flexible, so
tying them all to the same reference wouldn't work unless the restraints
are very loose.

You might try coordinate ncs, breaking it up into several individual
ncs_groups. If you don't know where the flexion is occurring, make a
large number of small groups along the chain - maybe 5 or ten residues
ar a time. After refining with this, superimpose using each group in
turn, and see what other groups are simultaneously superimposed well.
All those have the same operator, so can be combined into a single

>>> Oleg Sobolev <osobolev at lbl.gov> 08/04/20 1:47 PM >>>
Hi Mark,
You can try to achieve similar results using reference_model machinery.
If you assign the same reference model to your NCS copies (it could be
the same model you are refining) it will generate the same torsion angle
restraints for NCS copies effectively mimicking torsion NCS.

Best regards,
Oleg Sobolev.

On Sun, Aug 2, 2020 at 10:33 AM Mark A. White <mawhite at utmb.edu> wrote:


Are there plans to include Torsion Angle NCS restraints in the
Phenix.Real_Space_Refine module?  At low resolution (~ 3-4Å) I would
like to include NCS restraints, but my molecule is flexible and the
strict NCS constraints used in the Real_Space_Refine module are not

I am currently using phenix-1.18.2-3874.

Best regards,

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