1. Global optimization
Enter the project directory
Prepare the JSON configuration file file, name it
X_config.json
for example.Add fit libraries to JSON configuration file as described in Adding precomputed fitting libraries to JSON
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
Run the modeling as described in Run the modelling