I was able to get PyRosetta up and running on my mac under OS X 10.6.6 . I am working on what I think is a simpler version of the ddG script (we don't need the docking feature). What I am trying to do is bring in a pdb file, score it using the ddG paramters, and then mutate each residue (basically cycle through all the possible combinations)to see what happens to the ddG values are. The start of the script is here: (The loop is a mess at the moment)
from rosetta import *
pose = Pose()
pose_from_pdb( pose , "2O2X_clean.pdb" )
pymover = PyMOL_Mover()
ddG_scorefxn = ScoreFunction()
ddG_scorefxn.set_weight( fa_atr , 0.44 )
ddG_scorefxn.set_weight( fa_rep , 0.07 )
ddG_scorefxn.set_weight( fa_sol , 1.0 )
ddG_scorefxn.set_weight( hbond_bb_sc , 0.5 )
ddG_scorefxn.set_weight( hbond_sc , 1.0 )
print"ddG = "
for i in range(1,pose.total_residue()+1):
I run this script using ipython in the same folder with the .py file and PyRosetta. When I run the script in ipython using run code.py the ddG_scorefxn(pose) comes up blank. But when I type ddG_scorefxn(pose) on the ipython command line it spits out the answer. I've noticed this for a few other things as well.
I was wondering if there was a work around for this? Thanks!