Running MutInf (and options)

Quick Start: run the program like this:

python ~/trajtools/dihedral_mutent.py -x ~/IL2_Flex/${pdb}_62GLU_SS/ -a "yes" -o 6 -w 30 -p 0 -c "yes" -n 6 test_new3_adaptive.reslist > test_new3_adaptive_out.txt

For this example, the directory structure would look like:

~/IL2_Flex/${pdb}_62GLU_SS/

run1/

dihedrals/g_chi/*.xvg.gz

run2/

dihedrals/g_chi/*.xvg.gz

run3/

dihedrals/g_chi/*.xvg.gz

Usage (with basic options):

python ~/trajtools/dihedral_mutent.py \

-x <base_directory>

-a <yes/no; adaptive partitioning>

-n <number of blocks total>

-o <number of blocks to take together>

-w <number; 360 divided by this number is the number of bins used per degree of freedom>

-p < permutations; required when “-a no” is used>

-c <yes/no; correct for undersampling bias>

Most commonly, we will just aggregate all the data together as per McClendon, Friedland, et. al. 2009.

To do this, the -o option (number of runs to take at a time) needs to be the same as the -n option (the number of runs)