Input structures
PDB files are defined by appropriately formatted objects (
{components: ...}
, see below) that define which chain of the given PDB file maps to which subunitThe PDB file specification is added to
data
object in the JSON configuration fileA PDB file can contain parts of different subunits, for example, in the example below,
yourpath.pdb
contains two subunits:<subunit_name1>
and< subunit_name2>
with chainsE
andF
, respectively.Different parts of subunits can be present in different PDB files and under different chain ids, for example, in the example below,
<subunit_name2>
has one part inyourpath.pdb
under chainF
, and another part inyourpath2.pdb
under chainB
by default, the rigid bodies are created based on this PDB file specification. All PDB fragments grouped into the same
components
list will be grouped into a rigid body. In the example below, chainX
andY
ofyourpath3.pdb
will be in the same rigid body and all other chains will be seperate rigid bodies.Specification:
{ "data": [ { "type": "pdb_files", "name": "pdb_files", "data": [ { "components": [ { "name": "<subunit_name1>", "subunit": "<subunit_name1>", "chain_id": "E", "filename": "yourpath.pdb" } ] }, { "components": [ { "name": "<subunit_name2>", "subunit": "<subunit_name2>", "chain_id": "F", "filename": "yourpath.pdb" } ] }, { "components": [ { "name": "<subunit_name2>", "subunit": "<subunit_name2>", "chain_id": "B", "filename": "yourpath2.pdb" } ] }, { "components": [ { "name": "<subunit_name3>", "subunit": "<subunit_name3>", "chain_id": "X", "filename": "yourpath3.pdb" }, { "name": "<subunit_name4>", "subunit": "<subunit_name4>", "chain_id": "Y", "filename": "yourpath3.pdb" } ] } ] } ] }