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 subunit

• The PDB file specification is added to data object in the JSON configuration file

• A 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 chains E and F, 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 in yourpath.pdb under chain F, and another part in yourpath2.pdb under chain B

• 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, chain X and Y of yourpath3.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"
                                  }
                              ]
                          }
                  ]
          }
      ]
  }