Check the logs

The assembline.py script prints various logs to the screen or to the log files indicated in the cluster submission template.

The log includes:

  • the list of final parameter values

  • summary of the molecular system created: molecules, series, chain IDs, rigid bodies, etc.

  • restraints that are being created

  • optimization logs:

    • restraint values used for optimization, before and after optimization, and between each simulated annealing temperature change

At this point you need to inspect the logs and determine whether the diagnostic messages in logs directory are matching what you intended:

  • Are all mappable crosslinks added properly as restraints?

  • Do the created rigid bodies match what you expected?

  • Is the number of connectivity restraints ok?

  • Are the Monte Carlo moves as expected from the configuration file?

  • The log displays how many times each rigid body moved, is the number reasonable?

    • E.g. if you ask for 10,000 steps at each simulated annealing temperature and have 5 rigid bodies and 500 flexible beads,

      each rigid body only a small number of moves (each step is a single move) and you may need to increase the number of steps. For flexible beads it is not a problem if the “denovo_MC-SA-CG” protocol has been specified in params.py - they would move substantially with additional Conjugate gradient steps

  • Are the Monte Carlo acceptance rates reasonable?

    • at high Simulated Annealing temperatures the fraction of upward moves should be high, and decrease with lower temperature

    • the number of downward movements should be non-zero and decrease with temperature