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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