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Error about using BuildDeNovoBackboneMover

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Error about using BuildDeNovoBackboneMover

Hi! I am sorry for asking about the segementation fault problems because this be caused by many things. It is the first time I wrote a Rosetta scripts and I really stuck on the script.

I tried to use BuildDeNovoBackboneMover to generate backbones based on the antibody structure I got, I wrote the xml file but it shows:

[LINE]: 11

Segmentation Fault


This is my XML file:

                <ScoreFunction name="sfxn_16" weights="beta_nov16"/>
                <ScoreFunction name="sfxn" weights="beta_nov16"/>
                <AntibodyRegion name="Abselect" region="cdr_region" cdr_definition="Chothia"/>
                <AddCDRProfileSetsOperation name="AddCDRs" cdrs="all cdrs" include_native_restype="true" picking_rounds="3"/>
                <ScoreType name="score_filter" score_type="sfxn_16" threshold="0" confidence="0"/>
                <ResidueCount name="res_count_all" max_residue_count="9999" confidence="0"/>
                <BuildDeNovoBackboneMover name="dn_backbone" dump_pdbs="false" >
                        <BlueprintArchitect name="bp_arch" blueprint="template1.bp"/>
                        <RemodelLoopMoverPoseFolder scorefxn="sfxn_16"/>
                <Add mover="dn_backbone"/>
        <OUTPUT />

My input is :rosetta313/main/source/bin/rosetta_scripts.hdf5.linuxgccrelease -parser:protocol blueprint_build.xml -corrections::beta_nov16 -s model-0.relaxed_0003.pdb -out:prefix test_

The model-0.relaxed_0003.pdb file is attached, I think it is because my input pdb or the blueprint file? But I do not know how to modify it based on my purpose. Could anyone please help me solve the problem? Thank you!

This is blueprint file.1.16 KB
model-0.relaxed_0003.pdb308.96 KB
Post Situation: 
Wed, 2024-05-29 01:47

The standard recommendation in figuring out segfaults is to recompile and run with mode=debug versus mode=release -- this enables additional checking which should point out issues which might not be apparent in the regular run. Additionally, even if it still crashes, the ROSETTA_CRASH.log file output will have additional information about where, exactly, in the code the segfault is coming from.


P.S. We're updating the site, and as part of that we're moving the forums to Github Discussions.

If you have additional questions or are still having issues, please feel free to open up a thread over there.

Thu, 2024-06-20 13:22