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[any] abbaacognatadigadministratorakshephardaloshbauamelieamlerneramw579anandAndrewLeaverFayarubensteinAshafixasosa1964assaffaudavisaxelbazzolibborgobderbezubazzabiokharblivensbprattbrandon.frenzbrichetjbsbioBYachnincbohrsoncdbahlcesteveschantztchelsellcmgatescmilescolinDanielevorydanielzadannysahtoeDarwinyfudayekedelalamodelucaslDennisfeddimaiodrxduranamelantrianelazaraelizdongevanbaughfcchoufkammflofordasfrankwillmoreGabiPszollagerarddagkuzuglemmongrocklinGuestNuarfguffyslguxiao1990habibhajosephamoo6harinikharrelmHomoSapienhondahssnzdh2ihkimballimvjacobbalejacobbowman2015jadolfbrjaf18james.lucasjaumebonetjavierbqjecornJefferyCogjenlujgrayjianqingjklaijklemanjohnkaranicolasjonathawjrezendesjrporterjtapialjunzhou1988jwillis0720kalabharathkalekalngykkdrewkeleayonkeunwankhoulikimdnkisurbkmb413KouyakrishnakweikylebarlowLabontelah435langar2larrycchenglokitsadlukiMarvinNennymcclurejmedleyjmfooksamlajoiemlnancemmarlettmmravicmomearampacellampolsonmschmitzmtykamuellebkmurar0n.alexandsNaKengonannemdpnatteruwnawsadnivonnmarzenobuyasunornoconchusolangeorielgorlypoloparmefpattanspbradleypconerlypgreisenphysicsprgleasoptconwaypylesharleyralfordralford1rcachorenfrewrfalford12rhallettrmorettirobkleffnerronjroyUprpacheRusselsensacombssanbonsarelsberger8sboykenSergeysevyash-maximShaowepshashank.muchelishefflershekarashenh2shiraw1shirstsivleyrmsjbertolaniskudlaceksmlewisssrb.2012stoneinterstrnadjasumuduleelanandasvenskentamirhtelthomas.murarasutjacobs2tmaustin40tschiffnervmulligvyarovoy99walcobwallmlweitznerwendaowhbptwilsonctrXiaotongxingjiepanyhsiayumengwzhaobingchunzibochen

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[any] [none] abbaacognatadministratorakshephardaloshbauamelieamlerneramw579anandAndrewLeaverFayarubensteinasosa1964assaffaxelbborgobderbezubazzabiokharblivensbprattbrichetjBYachnincbohrsoncdbahlchelsellcmilescolindanielzadannysahtoeDarwinyfudelalamodelucasldimaiodrxduranamelantrianelizdongevanbaughfcchouflofordasGabiPszollagkuzuglemmongrocklinguffyslhabibhajosephamoo6harrelmhondahssnzdh2ihkimballimvjacobbalejadolfbrjaf18javierbqjecornjenlujgrayjianqingjklemanjohnkaranicolasjonathawjrporterjunzhou1988jwillis0720kdrewkeunwankhoulikimdnkrishnakweikylebarlowLabontelah435lukimedleyjmlnancemomearampacellampolsonmtykamuellebkNaKengonannemdpnawsadnivonnmarzenobuyasunornoconchusolangeorielgorlypoloparmefpbradleyprgleasoptconwayralfordrenfrewrfalford12rhallettrmorettirobkleffnerronjrpachesacombssanbonsarelsberger8sboykenSergeysh-maximshefflershirstsivleyrmsjbertolanismlewisstoneinterstrnadjasvenskentamirhtelthomas.murarasutjacobs2tmaustin40vmulligvyarovoy99wallmlweitznerwhbptXiaotongxingjiepanyhsiazibochen

[any] Bad CodingCrashDocumentationIncorrect ResultsInput HandlingMissing commit historyTransition scriptsWebsite error

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[any][none]-- ?? abinitio abinitio, probably more AbinitioRelax all all (at least all that use...scorefiles) all applications all applications that...CartBondedEnergy all applications ...ResidueConnections all jd2 all that design; fixbb is the big target all that use design + ...primarily all that use resfiles ...promeniently) all, presumably all; symmetric fixbb primarily antibody Antibody modeling suite - ...ROSIE any any jd2 any jd2 app any JD2 application any resfile reading ones any that use constraints, centroid...KIC any that use IAM, ...RosettaScripts any time membrane scoring is involved any using cartesian bonding any using patch files that ...properties any using PyMolMover or inheriting ...it Any which read PDBs any with executable-defined ...found anything supporting jd2 anything that uses dunbrack anything using CCD closure anything using sasa At least the score-app with -score_... backrub Backrub, any protocol with free ...angle BuildBindings.py cartesian minimization cart_bonded cartesian minimization cart_bonded energy function clean_pdb cluster cluster.cc cluster.default.linuxgccrelease cmake compare_sample_sources.R compilation bug compilation error compile error compiler error/issue, ...modules Confirmed to affect oop_dock_design ... Constraint use in PyRosetta constraints CstfileToTheozymePDB D060_Folding.py ddg_monomer demos/public/dock_ligand_and_...py Design with resfile development DNA & RNA applications? Docking docking in particular, ...constraints Docking via docking_...RosettaScripts docking, but really all docking, PyRosetta dockingprotocol docking_protocol email changelogs erraser erraser / rna_rosetta_ready_set.py erraser, rna in general everything exception handling EXIT_THROWS_EXCEPTION EXIT_THROWS_EXCEPTION, jd2 FeatureReporter Features database generation features_scientific_benchmark fixbb fixbb in particular, but ...exempt fixbb integration test fixbb most promeniently FloppyTail FloppyTail UBQ_E2_thioester FoldTree, so all format_converter, score_jd2, ...apps fragment picker fragment_picker fragment_picker in Rosetta 3.4 fragment_picker.linuxgccrelease get_rosetta.sh git git special hidden settings? homodimer_maker homology_modeling_threading_basic demo hotspot_hashing integration test hshash_utils ignore_zero_occupancy integration test integration test features_...schema integration test noe_assignment integration tests integration tests, integration3.py ...py integration.py integration.py enzdes integration.py loop_creation integration.py loop_hash InterfaceAnalyzer InterfaceAnalyzer (mover, but app too) InterfaceAnalyzer test InterfaceAnalyzer; its clients InterfaceAnalyzer; others that ...code InterfaceAnaylzerMover and its app JD2 JD2 applications kinematic loop_model ligand_docking loopmodel loopmodel.<binary> LoopModeling, anything else that ...KIC loop_model make_rot_lib Mantis manual many Many depending on context metalloprotein_abrelax minimize_with_cst minirosetta minirosetta - threading protocol minirosetta -protocol threading mm scoring, fa_standard_icoor molfile_to_params.py molfile_to_params.py; backrub Most N/A NA NMR / biological unit / multimodel PDBs none None at present none, git issue not an application not-at-application-level obey_ENDMDL oop_create, oop_dock_design oop_dock_design performance benchmark (email) pmut_scan_parallel, ?? pose.constraint_set() potentially anything that ...structures probably all profile.py PyRosetta pyrosetta primarily PyRosetta, Rosetta relax relax, others using constraints relax, score_jd2, others remodel ResourceManager using rosetta_scripts rna, swa, ...RMSDfilter Rosetta rosetta wiki Rosetta, PyRosetta rosettacommons RosettaRemodel RosettaScripts RosettaTests website rosetta_scripts Rosetta_scripts and anything ...manager rosetta_scripts FastRelax standard mover rosetta_scripts ReportToDB Mover rosetta_scripts, maybe others rosetta_scripts, rosettaDNA ROSIE ROSIE docking RS Features Output/ All ...databases Scientific BenchMarking scons scons compile time score score & minirosetta score_jd2, but likely any. score_jd2, LoopAnalyzer, loopmodel See above. startfrom_file SVN / git issue symmetric packing SymPackRotamersMover in RosettaScripts test/run.py those that use TorsionDOFMover UBQ_* UBQ_E2_thioester UBQ_E2_thioester, UBQ_Gp_* unknown VIP website

[any][none] Line Used fixbb -database /...@options $mini/bin/rosetta_scripts....test %<path>/rosetta_source/bin/...options> (see description) * -in:file:obey_ENDMDL - -- -cst_file file_with_atompairconstraints -database <DATABASE> -s model0_raw...txt -nblist_autoupdate -out:levels all:warnings -out:levels core.chemical....hh:400 -resfile misnumbered.resfile -s <your.pdb> -s pdb_with_broken_loop.pdb -...closure . ../../../main/source/bin/...cst ./bin/fixbb.linuxgccrelease -help ./bin/relax.macosgccrelease -database... ./compare_sample_sources.R --...json ./fixbb.linux.gccrelease -...file ./integration.py ./integration.py -j20 -d /work/... ./integration.py tests.antib* ./rosetta/rosetta_source/bin/...database ./scons.py extrass=donothing ./SnugDock.c ./test/run.py -1 ImNotAValidTest /home/momeara/rosetta/rosetta...database /nas02/home/l/e/leaverfa/GIT/...flags /path/to/rosetta_scripts.default....xml /scratch/amw579/rosetta/rosetta_... /share/apps/mvapich2/1.7/...@options ? ?? all AnchoredPDBCreator -...pdb antibody- antibody_designer....@flags any any jd2 with ...10 Any remodel job with a trailing blank... Any that uses all_atom_rmsd any with backrub anything Anything that computes an hbond anything that scores a protein anything with a weights file ...plane backrub.<platofrm> backrub.default.macosclangrelease...pdb benchmark.linuxclangrelease -asdflkajsdf bin/loopmodel.macosgccrelease -d...loops bin/rosetta_scripts....@flags bsub -q week -o report.log -n 8...@flags cartesian minimization cart_bonded cartesian minimization cd rosetta_tests/integration && ./...py cluster -input_score_filter cluster.default....cluster cmake compilation bug compilation error compile error compiler issue constraints curl -O https://raw.github.com/...demos ddg_monomer -ddg::local_opt_only...true docking docking_protocol -cst_file $some_...REU docking_protocol -docking_local_...file docking_protocol....out:pdb dummy_command_line e.g. score_jd2 echo $PYROSETTA erraser erraser / rna_rosetta_ready_set....true erraser, rna in general ex: AnchoredDesign -thisisnotanoption exception handling executable -constraints::cst_fa_...cst EXIT_THROWS_EXCEPTION EXIT_THROWS_EXCEPTION, jd2 feature request FeatureReporter fixbb +/-linmem_ig fixbb -favor_native_res is ...useless fixbb -in:file:silent my_centroid_...out fixbb -I_want_this_reasonable_...hassle fixbb -linmem_ig ## fixbb -resfile resfile_that_...pdb fixbb.linuxgccrelease @flags_fixbb_...10 FloppyTail or UBQ_E2_thioester in mpi... FloppyTail; arguments irrelevant follow cmake build instructions fragment picker -s SPI.pdb fragment_picker.linuxgccrelease ...flags fragment_picker.linuxgccrelease ...flags get_rosetta.sh without curl installed git personal-tracked-branch test git special hidden settings? homodimer_maker....options homology_modeling_threading_basic demo http://www.rosettacommons.org/...html I wrote a unit test which will go in ... integration.py -j1 fixbb, ...fixbb integration.py enzdes integration.py features_database_schema integration.py fixbb integration.py fixbb is a fast example integration.py hotspot_hashing integration.py hshash_utils integration.py loop_creation integration.py loop_hash integration.py noe_assignment integration.py SnugDock integration.py startfrom_file integration.py this_test_has_no_...file integration.py zinc_heterodimer integration.py; integration.py -j1 integration3.py InterfaceAnalyzer -anything InterfaceAnalyzer -s a_pdb_with_...pdb InterfaceAnalyzer.default....database InterfaceAnalyzer....true InterfaceAnalyzer....true InterfaceAnalyzer....params InterfaceAnalzyer -pose_...calculator InterfaceAnaylzer -s 1s78....subcomplex) ipython irrelevant jd2memtest -l pdblist, where ...climb jd2_app -out:file:atom_tree_diff ...out loopmodel -loops:refine_repack_cycles loopmodel -loops:remodel perturb_kic... loopmodel.<binary> -kic_rama2b loopmodel.<binary> -loops:remodel ...kic loopmodel.<binary> -out:path sub_folder loopmodel.linuxgccrelease -...kic loopmodel.linuxgccrelease -...kic loopmodel.linuxgccrelease -...kic loop_model -perturb perturb_ccd make_rot_lib many minimize_with_cst.linuxgccrelease -... minirosetta -protocol threading minirosetta.linuxgccrelease @flags minirosetta.linuxgccrelease @options molfile_to_params.py molfile_to_params.py --mm-as-virt mypose = pose_from_pdb("test31....pdb") n/a N/A (See Steps To Reproduce above.) NA none none, git issue nope not accessible from command line not related to a command line not-at-application-level obey_ENDMDL oop_create, oop_dock_design -s any...pdb pdb reader, ignore_zero_occupancy pose.constraint_set() profile.py -c clang is broken; ...gcc ProteinResidueConformation Features python python clean_pdb.py python D060_folding.py --fasta_...200 python integration.py -j 48 python integration.py -j24 python TestBindings.py python ~/rosetta/tools/...ignorechain PyTracer Object refactoring relax.linuxgccrelease -s pdb....coords reported at top of forum thread required + -insert_...interpolation rosetta -l pdblist @options rosettaDNA.linuxgccrelease @design.flags RosettaScripts using...TaskAwareMinMover rosetta_app -s file.pdb -nstruct 100 rosetta_scripts rosetta_scripts -parser:protocol ...xml rosetta_scripts -s pdb.pdb -...1 rosetta_scripts @flags rosetta_scripts @flags.txt -...xml rosetta_scripts with ...pose rosetta_scripts.default.linuxgccdebug... rosetta_scripts.default....xml rosetta_scripts.default....database rosetta_scripts.linuxclangrelease -...s rosetta_scripts....score=$scor rosetta_scripts....score=$scor rosetta_scripts.linuxclangrelease...xml rosetta_scripts.linuxgccrelease...path> rosetta_scripts.linuxgccrelease -...out rosetta_scripts.linuxgccrelease @flags rosetta_scripts.mpimysql and rosetta_... rosetta_scripts.mpimysql....params rosetta_scripts....macosgccrelease rosetta_source/bin/fixbb....pdb rosetta_source/bin/format_...label rosetta_source/bin/rosetta_scripts....4 rosetta_source/bin/score....pdb rosetta_src_2015.05.57576_bundle/...3 ROSIE ROSIE antibody modeling ROSIE docking RotateJumpAxisMover; no command line run.sh which has --> cmd="time...@flags" scons bin mode=release extra=mpi scons mode=A,B vs. mode=B,A scons.py mode=release bin scons; run:version score.linuxgccrelease -...struct score.linuxgccrelease -in:file:native... score.macosgccrelease -database...params score_jd2 score_jd2 -s input.pdb score_jd2.default....score score_jd2.linuxclangdebug -...gz score_jd2.linuxgccdebug -s *.pdb score_jd2.linuxgccdebug -...gz score_jd2.linuxgccrelease -s ...res score_jd2.linuxgccrelease -...number score_jd2.linuxgccrelease -...false] score_jd2.linuxgccrelease -s ...A score_jd2.linuxgccrelease -...inputs See "steps to reproduce" see "Steps To Reproduce" above See "Steps To Reproduce" above. See "Steps To Reproduce" section...lines see above see above to reproduce See above. see additional information see features integration test...example see features_postgres integration test See Steps To Reproduce Above See steps to reproduce*** see, e.g. features integration test standard rosetta_scripts command line SVN / git issue test/run.py -1 AntibodyInfoTest... test/run.py -c clang --compiler_...4 this is rosettacommons.org ...report UBQ_E2_thioester -etc etc ...ubiquitins UBQ_E2_thioester -two_ubiquitins UBQ_E2_thioester -two_ubiquitins -...pdb UBQ_GP* series with ligand extra_bodies unknown various VIP -resfile does_nothing.resfile VIP -s pdb_with_ligands.pdb vip.linuxgccrelease -s mypdb -...reports website whatever.mysqlmpi....output with -kill_hairpins and standard ...file XMLs with any ...options [documentation] [in iPython] from rosetta....PointGraph ~/rosetta_source/bin/minirosetta....

[any][none]- 00000 ...(c859ecaf652ec006e09b3ad2dc687d4442e1c247) 04/01/2014 06b47ca 1691dfed3fb982744aa0c7c71baf03fad73acccf 30259bba8f 36c2c81b7794e1f70a9520da778b3239dc3757a5 48527 49536 49544 49555 49569 49586 49607 49633 49635 49645 49759 49861; 50044 49998 4e55781 50040 50051 50181 50204 50232 50279 50383 50606 50659 50678 50679 50745 50765 50879 50949 50960 50962 51160 + 51165 51170 51175 51236 51265 51417 51461 51537 51539 51547 51751 51768 52000 52266 52418 52642 52735; 52812 53112 53486 53570 53575 53871 53872 53892 53903 53948 53989 54040 54161 54253 54268 54296 54313 54322 54328 54387 54418 54428 54502 54533 54609 (this is a "disappeared ...number) 54635 54637 54660 54684 54685 54768 54830 55030 55062 55074 55248 55496 56176 56977 56978 56982 57131 57188 57867 58057 68a25f6cf54d946afe86786bdab4c81dd9cfd0a8 72b2597ee4599e6553bb448b9b13b8025f8bb776 736e60e 88623c0f028e62133994b10c3eb7ec3542e5e93d 9456691412c6900df7e71dda50518aa0c1e7cf30 ??? a9caa5d244fd677aabcdb6d63252236131e522b2 aa7b53799ffbe6b All bd4f744e3d3f8991df09cff9528de41e4dd04542 d16b60c9d6d dup e5a8135 head n/a NA PR 2448 r49576 r53947 releases after 02/29/16 TBD trunk xxxxxx

[any][none]Feature Request Confirmed As Bug

[any][none]FILE->SetupPDBsForRosetta-...analyze Load PDB, Show in Pymol; Load ...window

[any][none]CleanPDB window main, Advanced PyMol ...window

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