Libmini crashes after protocol run

[Anonymous]

Hi, 

I’m currently working on a loop modeling script in PyRosetta, for inclusion as a protocol in InteractiveRosetta. Essentially, the script takes a collection of protein fragments, attempts to insert them into a scaffold using AnchoredGraftMover, and scores each pose.  The script works fine, but some time after it finishes running I’ll get a message saying that libmini.so has stopped working. Does anyone have any idea why this could be happening? I’ve included the script below. I’m using PyRosetta 3. 

Thanks,

Will

# If we got results, try to build models with them

if (num_results > 0):

try:

initializeRosetta()

import rosetta.protocols.grafting as graft



# Set some parameters



scorefxn = create_score_function("talaris2013")

start_residue = int(loop_params[1])

stop_residue = int(loop_params[2])





except:

raise Exception("ERROR: Couldn't initialize Rosetta!")

writeError("ERROR: Couldn't initialize Rosetta!")



i = 1

models  = []

scores  = []

lengths = []



# Try to make models from all the loops, or up to the max number specified

while i < min((num_results + 1), (int(loop_params[6]) + 1)):



try:

# Make a copy of the scaffold, load the loop

temp_pose = pose_from_pdb(pdbfile)

loopfile = "loopout_" + str(i) + ".pdb"

loop = pose_from_pdb(loopfile)



graftmover = graft.AnchoredGraftMover(start_residue, stop_residue, loop, 1, 1)

graftmover.set_cycles(500)

graftmover.apply(temp_pose)



#Add the model and its score to their respective lists, as well as the length of     each insertion

temp_score = scorefxn(temp_pose)

scores.append(temp_score)

models.append(temp_pose)

lengths.append(loop.total_residue())









# Sort models by energy and write them out so we can look at them

# Write out a file with info about each loop



i = 1

f = open("INDELoutputtemp", "w")

for score, model, length in sorted(zip(scores, models, lengths)):

outname = "INDELmodel_" + str(i) + ".pdb"

model.dump_pdb(outname)

f.write(outname + "t" + str(score) + "t" + str(length) + "n")

i += 1



f.close()

os.rename("INDELoutputtemp", "INDELoutput")

 

[Anonymous]

Will, when you saying “…message saying that libmini.so has stopped working”: – what is exactly the error message?

[Anonymous]

Will, when you saying “…message saying that libmini.so has stopped working”: – what is exactly the error message?

[Anonymous]

Will, when you saying “…message saying that libmini.so has stopped working”: – what is exactly the error message?

[Author]

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