Rigid bodies
By default, rigid bodies will be defined automatically based on
the specifications in the PDB files Input structures. If you want to define rigid bodies
differently to your PDB files, you can do it in a separate rigid_bodies
block at the top level of the JSON configuration file.
Warning
For rigid_bodies
to have an effect, you have to set add_rigid_bodies = False
in the Parameter file
The specification is the same as for PDB files:
{ "rigid_bodies": [ { "components": [ "list of selectors" ] }, { "components": [ "list of selectors" ] }, "and so on" ] }You can also use the
foreach_serie
andforeach_copy
keywords here:{ "rigid_bodies": [ { "foreach_serie": true, "foreach_copy": true, "components": [ "list of selectors" ] }, { "foreach_serie": true, "foreach_copy": true, "components": [ "list of selectors" ] }, "and so on" ] }An example:
{ "rigid_bodies": [ { "foreach_serie": true, "foreach_copy": true, "components": [ { "name": "Elp1_1", "subunit": "Elp1", "domain": "propeller1"} ] }, { "foreach_serie": true, "foreach_copy": true, "components": [ { "name": "Elp1_1", "subunit": "Elp1", "domain": "propeller2"} ] }, { "foreach_serie": true, "components": [ { "name": "Elp1_1", "subunit": "Elp1", "domain": "CTD", "copies": [0, 1]} ], "freeze": true }, { "foreach_serie": true, "foreach_copy": true, "components": [ { "name": "Elp2_1", "subunit": "Elp2", "resi_ranges": [ [1, 239], [257, 788] ] } ] }, { "foreach_serie": true, "foreach_copy": true, "components": [ { "name": "Elp3_4", "subunit": "Elp3", "domain": "helix4"} ] }, { "foreach_serie": true, "foreach_copy": true, "components": [ { "name": "Elp3_5", "subunit": "Elp3", "domain": "struct"} ] }, { "foreach_serie": true, "foreach_copy": true, "components": [ { "name": "Elp3_6", "subunit": "Elp3", "domain": "flex_helix"} ] } ] }