1,328
edits
Phenix: Difference between revisions
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(→NCS: try to correct) |
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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 ==== | ||
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* Automatic detection of NCS groups: | * Automatic detection of NCS groups: | ||
phenix.refine data.hkl model.pdb | phenix.refine data.hkl model.pdb ncs=True ncs_search.enabled=True | ||
* Manual specification of NCS groups: | * Manual specification of NCS groups: | ||
phenix.refine data.hkl model.pdb ncs_groups.params | phenix.refine data.hkl model.pdb ncs_groups.params | ||
where ncs_groups.params contains e.g.: | where ncs_groups.params contains e.g.: | ||
refinement.ncs.restraint_group { | refinement.ncs.restraint_group { | ||