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2024-12-04 02:41 CST
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[any]
parent of
child of
duplicate of
has duplicate
related to
Application(s) Affected
Command Line Used
Fixed in SVN Version
Developer Options
GUI Interaction Seqeunce
GUI Window Used
[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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server
silent files
user_support
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