Similar orientation restraints
These restraints promote similar orientation between pairs of identical subunits, domains or residues.
They can be defined in the JSON configuration file like this:
{
"type": "similar_orientation",
"active": true,
"name": "Ely5-Nup120_similar_orientation",
"comment": "We assume Ely5 interacts in the same way with all copies of Nup120",
"data": [
[
[
{"subunit": "Nup120", "serie": "NR_1", "copies": [0]}, {"subunit": "Ely5", "serie": "NR_1", "copies": [0]}
],
[
{"subunit": "Nup120", "serie": "NR_2", "copies": [0]}, {"subunit": "Ely5", "serie": "NR_2", "copies": [0]}
]
]
],
"weight": 10,
"k": 1,
"first_copy_only": true,
"repr_resolution": 10
}
Parameters
- type
Must be “similar_orientation”
- active
true or false, whether the restraint should be created, you can set to false to save on loading time if you don’t need this restraint (even if it’s true, you still need to add it to a scoring function to have it an effect)
- name
whatever name. Use this name to refer to this restraint in Parameter file when defining the scoring functions
- comment
Optional comment, useful for documenting
- data
A pair of pairs of Selectors between which the interaction restraints should be defined
- weight
Weight of this restraint
- first_copy_only
true or false, Apply only to the first molecule copy of each series?
- repr_resolution
The resolution of representation to which this restraint should be applied
- k
Spring constant for the harmonic potential, redundant to weight, ignore