2.3 Calculate J‐matrix

This step will help you combine scaled coevolution scores in coevolution matrix -c and the rho scores for each residue pair -r and generate the J-matrix file -o using choice of lambda -l, we recommend 0.5 for equal weights on both matrices.

input options:

  -c COE, --coe COE     coevolution matrix file
  -r RHO, --rho RHO     File with RHO matrix
  -o OUT, --out OUT     J-matrix output file label
  -l DLAMBDA, --dlambda DLAMBDA Set Lambda value, default is 0.5. [FULL SCAN NOT IMPLEMENTED]
  --scalescore, --no-scalescore  Scale coevolution scores with average and set scores less then average to zero (default: True)
  --rhocutoff RHOCUTOFF Cut-off for absolute rho values; default is 0.5
  --lambdascan, --no-lambdascan  Scan lambda at dlambda intervals. (default: False)
  --scanall, --no-scanall Scan all J-Vectors. By default it is off. (default: False)

sample usage:

dyno_3_jmatrix.py -c coevolution.mat -r rho.mat -l 0.5 -o label