# Libmini crashes after protocol run

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Libmini crashes after protocol run
#1

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")

Category:
Post Situation:
Tue, 2017-01-31 09:48
whooper

Will, when you saying "...message saying that libmini.so has stopped working": - what is exactly the error message?

Tue, 2017-01-31 13:42
Sergey