Selectors
Selectors are collections of keywords used to “select” parts of the system and act on them. For example, you can select a part of the system and define as rigid body, add to an EM restraint, or other restraints.
Syntax / list of allowed keywords:
{
"subunit": "....",
"state": "....",
"states": "....",
"domain": "....",
"serie": "....",
"copies": "....",
"chain_id": "....",
"chainIds": "....",
"filename": "....",
"resi_ranges": "....",
}
Additionally, Input structures and Rigid bodies specifications allow using the special foreach_serie
and foreach_copie
modifiers.
They allow to apply selectors to all series in the sytem and/or to all copies within the matching series.
Examples:
Residue 925 of the Nup120 subunit in the series named NR_1
{"subunit": "Nup120", "serie": "NR_1", "resi_ranges": [925]}
The membrane_binding domain of the Copy 0 of the Nup155 subunit in the IR_cyt_outer ring (one of the four sub-rings of the inner ring of the nuclear pore complex)
{
"name": "Nup155",
"subunit": "Nup155",
"domain": "membrane_binding",
"copies": [
0
],
"serie": "IR_cyt_outer"
}
All copies of Nup107 subunit in the CR series
{
"name": "Nup107",
"subunit": "Nup107",
"serie": "CR"
}
Define the same PDB file for each copy of Elp1 in all series
{
"foreach_serie": true,
"foreach_copy": true,
"components": [
{ "name": "Elp1",
"subunit": "Elp1",
"domain": "propeller1",
"filename": "in_pdbs/Elp1_NTD_1st_propeller.pdb"
}
]
}
Define a rigid body for propeller1 domain for each copy of Elp1 in all series
{
"rigid_bodies": [
{
"foreach_serie": true,
"foreach_copy": true,
"components": [
{ "name": "Elp1_1", "subunit": "Elp1", "domain": "propeller1"}
]
}
]
}