MantisBT - Rosetta
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IDProjectCategoryView StatusDate SubmittedLast Update
0000361Rosetta[All Projects] Bad Codingpublic2015-09-28 12:262015-09-28 12:26
Reporternannemdp 
Assigned To 
PrioritynormalSeverityminorReproducibilityalways
StatusnewResolutionopen 
PlatformMacBook ProOSOSXOS Version10.10.3
Product VersionTrunk 
Fixed in Version 
Application(s) Affectedrosetta_scripts, maybe others
Command Line Usedrosetta_src_2015.05.57576_bundle/main/source/bin/rosetta_scripts.default.macosclangrelease @bug_example.flags -parser:protocol bug_example.xml -s 1UBQ_clean.pdb -nstruct 3
Developer Options
Fixed in SVN Version
Summary0000361: accumulation of REMARK output in packRotamersMover when nstruct>1
DescriptionThe PackRotamersMover tracks and writes to the output pdb the residues which are packed or designed using REMARK lines.
When nstruct > 1 the REMARK lines which track packable and designable residues and write out to the output pdb accumulate. So, if you use the PackRotamersMover 3 times then the number of REMARK lines is 3 times the number of decoys generated by the currently running process.

The issue tracks to PackRotamersMover::note_packertask_settings. Bug identified in 2015.05.57576 but code has not changed since 2011.
Steps To Reproduceissue identified while using RosettaScripts. Files attached to reproduce.
Additional InformationApparently you can only upload 1 file.....

FLAGS FILE
-database rosetta_src_2015.05.57576_bundle/main/database

-ndruns 2
-jd2:ntrials 100
-run:timer

-ex1
-ex2
-use_input_sc
-talaris2014

-options:user
-run:version

-chemical:exclude_patches LowerDNA UpperDNA Cterm_amidation SpecialRotamer protein_cutpoint_upper protein_cutpoint_lower VirtualBB ShoveBB VirtualDNAPhosphate VirtualNTerm CTermConnect sc_orbitals pro_hydroxylated_case1 pro_hydroxylated_case2 ser_phosphorylated thr_phosphorylated tyr_phosphorylated tyr_sulfated lys_dimethylated lys_monomethylated lys_trimethylated lys_acetylated glu_carboxylated cys_acetylated tyr_diiodinated N_acetylated C_methylamidated MethylatedProteinCterm

-out:pdb_gz
#-mute all

-run:multiple_processes_writing_to_one_directory


RS XML FILE
<ROSETTASCRIPTS>
    <SCOREFXNS>
        <talaris2014 weights=talaris2014.wts />
    </SCOREFXNS>
    <TASKOPERATIONS>
        <RestrictToRepacking name=repackonly />
        <InitializeFromCommandline name=ifcl />
        <IncludeCurrent name=ic />
        <ReadResfile name=rrf filename="bug_example.resfile" />
    </TASKOPERATIONS>
    <FILTERS>
    </FILTERS>
    <MOVERS>
        <PackRotamersMover name=rp scorefxn=talaris2014 task_operations=rrf,ifcl,ic />
        
        <ParsedProtocol name=multi_rp >
            <Add mover=rp />
            <Add mover=rp />
            <Add mover=rp />
        </ParsedProtocol>
        
    </MOVERS>
    <APPLY_TO_POSE>
    </APPLY_TO_POSE>
    <OUTPUT scorefxn=talaris2014 />
    <PROTOCOLS>
        <Add mover_name=multi_rp />
    </PROTOCOLS>
</ROSETTASCRIPTS>

RESFILE bug_example.resfile
NATRO
start
1 A NATAA
2 A NATAA
3 A NATAA
4 A NATAA
5 A NATAA
6 A NATAA
7 A NATAA
8 A NATAA
9 A NATAA
10 A ALLAAxc
11 A ALLAAxc
12 A ALLAAxc
13 A ALLAAxc
14 A ALLAAxc
15 A ALLAAxc
16 A ALLAAxc
17 A ALLAAxc
TagsNo tags attached.
Relationships
Attached Files? 1UBQ_clean.pdb (48,762) 2015-09-28 12:26
https://carbon.structbio.vanderbilt.edu/mantisbt/file_download.php?file_id=48&type=bug
Issue History
Date ModifiedUsernameFieldChange
2015-09-28 12:26nannemdpNew Issue
2015-09-28 12:26nannemdpFile Added: 1UBQ_clean.pdb

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