1. Global optimization

  1. Enter the project directory

  2. Prepare the JSON configuration file file, name it X_config.json for example.

  3. Add fit libraries to JSON configuration file as described in Adding precomputed fitting libraries to JSON

  4. Create Parameter file, name it params.py for example.

    For the global optimization, the following parameters are important:

    • protocol

      protocol = 'denovo_MC-SA'

      or, if you have flexible beads and want to optimize them using Conjugate Gradient:

      protocol = 'denovo_MC-SA-CG'

      Note

      The protocol parameter takes as argument keywords specifying the Assembline modelling mode to be used as described in Parameter file.

    • in scoring_functions, discrete_restraints must be added to all scoring functions to indicate restraints from fit libraries.

      Warning

      Do not run global optimization without discrete restraints as it will completely ruin the transformation matrices for the fit libraries

    • discrete_restraints_weight

  5. Run the modeling as described in Run the modelling