Phenix: Difference between revisions

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740 bytes added ,  3 June 2020
→‎Special positions: Bond across symmetry axis
(→‎Special positions: Bond across symmetry axis)
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Single atoms on (or close enough to) a special position (i.e. on one or more 2-,3-,4- or 6-fold rotation axis/axes) are automatically restrained to stay on that special position. For anything else (like a ligand crossing a symmetry element) the trick is: reducing occupancy to 1/n for a n-fold rotation axis, and excluding atoms from non-bonded repulsions with their symmetry mates - see [[Phenix#Switching_off_specific_interactions]] .
Single atoms on (or close enough to) a special position (i.e. on one or more 2-,3-,4- or 6-fold rotation axis/axes) are automatically restrained to stay on that special position. For anything else (like a ligand crossing a symmetry element) the trick is: reducing occupancy to 1/n for a n-fold rotation axis, and excluding atoms from non-bonded repulsions with their symmetry mates - see [[Phenix#Switching_off_specific_interactions]] .
==== Bond across symmetry axis ====
There is a small hint at
[https://www.phenix-online.org/documentation/reference/refinement.html#definition-of-custom-bonds-and-angles]
For bonds to symmetry copies, specify the symmetry operation in xyz notation, for example:
symmetry_operation = -x-1/2,y-1/2,-z+1/2
The whole .eff file might look like:
refinement.geometry_restraints.edits {
    bond {
      action = *add delete change
      atom_selection_1 = chain A and resid 1199 and name O4
      atom_selection_2 = chain A and resid 1196 and name C1
      symmetry_operation = X-1/2,-Y+1/2,-Z
      distance_ideal = 1.439
      sigma = 0.020
    }
}
(this is from a posting of Oleg Sobolev to PHENIXBB on  Wed, 27 May 2020 15:55:27 -0700)


==== NCS ====
==== NCS ====
1,330

edits

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