I am going through the PyRosetta Tutorial kindly written by the Gray Lab. I am going through it one chapter at a time sequencially and i have reached the folding tutorial: http://graylab.jhu.edu/pyrosetta/downloads/documentation/pyrosetta4_online_format/PyRosetta4_Workshop4_Folding.pdf
I am stuck in the point where the tutorial asks to set up my own Monte Carlo method (the first step of the tutorial), I do understand Monte Carlo, but i don't understand how to set it up for this particular tutorial, I have looking through the D060_Folding.py script: http://graylab.jhu.edu/pyrosetta/downloads/scripts/demo/D060_Folding.py but i could not isolate the monte carlo script (is it built into PyRosetta (the tutorial does not discuss it)? Do i have to write a new one? i don't understand).
Can anyone help? how should i start the tutorial? is there a written script i can see how the monte carlo is setup? the way the tutorial asks?
Excerpt from the tutorial that confuses me:
Now, write a program that implements a Monte Carlo algorithm to optimize the protein conformation. In the main program, create a loop with 100 iterations. Each iteration should call a subroutine to make a random trial move, score the protein, and then accept or reject the new conformation based on the Metropolis criterion
Is this supposed to be something very easy as to not discuss in detail? where can i read about it in detial?