Adding precomputed fitting libraries to JSON

1. Fit every structure using our Efitter pipeline, calculate solutions_pvalues.csv files using genpval, as described in the previous steps.

2. For each structure, add the following “positions” lines to the pdb_files (if add_rigid_bodies_from_pdb set to True) or rigid_bodies specifications (see Input structures and Rigid bodies)

   {
       "components": [
           {
           "name": "required, keep same as subunit name",
           "subunit": "required, keep same as subunit name",
           "chain_id": "required, which chain from the PDB file should be read as input for this subunit",
           "filename": "yourpath.pdb"
           }
       ],
       "positions": "<path>/solutions_pvalues.csv",
       "positions_type": "chimera - optional, chimera is default",
       "max_positions": "optional, by default all fits are read",
       "positions_score": "log_BH_adjusted_pvalues_one_tailed is default",
   }
   

   For example:

   {
       "components": [
           {
           "name": "<subunit_name1>",
           "subunit": "<subunit_name1>",
           "chain_id": "E",
           "filename": "yourpath.pdb"
           }
       ],
       "positions": "<path>/solutions_pvalues.csv",
       "positions_type": "chimera",
       "max_positions": 10000,
       "positions_score": "log_BH_adjusted_pvalues_one_tailed"
   }
   

   Warning

   If you do have the rigid_body block specification and add_rigid_bodies_from_pdb set to False in params.py, the positions MUST be added there, not in pdb_files, otherwise they won’t have an effect.

3. If there is 1-to-1 mapping between PDB files and rigid bodies AND you want to take the same number of fits for every structure:

   1. Fit every structure using our fitting pipeline, calculate solutions_pvalues.csv files (as above)

   2. Add the following “alternative_positions” definition to the JSON in the data section:

      {
          "active": true,
          "type": "alternative_positions",
          "positions_type": "chimera",
          "add_from_dir": "<fitting master dir>/<parameter set fitting dir>/<map dir>",
          "max": 10000,
          "score": "log_BH_adjusted_pvalues_one_tailed"
      }