MantisBT - Rosetta
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0000039Rosetta[All Projects] Input Handlingpublic2012-07-05 10:032014-07-19 13:50
tjacobs2 
rmoretti 
normalcrashalways
resolvedfixed 
 
 
Docking
rosetta_source/bin/rosetta_scripts.mpipostgres.linuxgccrelease -s single_chain.pdb -docking:dock_pert 2 4
68a25f6cf54d946afe86786bdab4c81dd9cfd0a8
0000039: Running docking on a single-chain PDB causes a segfault
Running docking on a single-chain PDB causes a segfault
Run the docking script (pasted in additional information) on a PDB with only a single chain. Await segfault
RosettaScripts protocol:

<ROSETTASCRIPTS>
        <SCOREFXNS>
      <s12_prime weights="score12prime"/>
        </SCOREFXNS>
    <TASKOPERATIONS>
      <RestrictToInterfaceVector name=vectorTask chain1_num=1 chain2_num=2 CB_dist_cutoff=10.0 nearby_atom_cutoff=5.5 vector_angle_cutoff=65.0 vector_dist_cutoff=8.0/>
      <RestrictChainToRepacking name=repack1 chain=1/>
      <RestrictChainToRepacking name=repack2 chain=2/>
      <RestrictToRepacking name=repackonly/>
      <InitializeFromCommandline name=cmdTask/>
      <IncludeCurrent name=currentTask/>
        </TASKOPERATIONS>
        <FILTERS>
      <Rmsd name=rms threshold=50.0 confidence=1/>
    </FILTERS>
        <MOVERS>
      <Prepack name=prepack scorefxn=s12_prime jump_number=1 min_bb=0 task_operations=vectorTask,repackonly,cmdTask,currentTask/>
      <DockingProtocol name=dockprotocol docking_local_refine=1 docking_score_high=s12_prime ignore_default_docking_task=1 task_operations=vectorTask,repack1,repack2,cmdTask,currentTask/>
      <TaskAwareMinMover name=minmover scorefxn=s12_prime chi=1 bb=1 jump=1 task_operations=vectorTask,cmdTask,currentTask/>
      <InterfaceAnalyzerMover name=fullanalyze scorefxn=s12_prime packstat=1 pack_input=0 jump=1 tracer=0 use_jobname=1 resfile=0 />
        </MOVERS>
        <APPLY_TO_POSE>
        </APPLY_TO_POSE>
        <PROTOCOLS>
      <Add mover_name=prepack/>
      <Add mover_name=dockprotocol filter_name=rms/>
      <Add mover_name=minmover filter_name=rms/>
      <Add mover_name=fullanalyze/>
        </PROTOCOLS>
</ROSETTASCRIPTS>
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Issue History
2012-07-05 10:03tjacobs2New Issue
2014-07-19 13:50rmorettiFixed in SVN Version => 68a25f6cf54d946afe86786bdab4c81dd9cfd0a8
2014-07-19 13:50rmorettiNote Added: 0000351
2014-07-19 13:50rmorettiStatusnew => resolved
2014-07-19 13:50rmorettiResolutionopen => fixed
2014-07-19 13:50rmorettiAssigned To => rmoretti

Notes
(0000351)
rmoretti   
2014-07-19 13:50   
Segfault was due to attempting to find an interface between two chains that don't exist. Catch and utility exit instead.