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Rosetta 3 - Applications

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:18
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6,954 by admin
Fri, 2015-09-04 16:17
Normal topic Rosetta Remodel - Error in core::conformation::Conformation::residue(): The sequence position requested was 0.
by daniloboskovic » Fri, 2019-11-08 08:24
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52 by daniloboskovic
Fri, 2019-11-08 08:27
Normal topic running in MPI mode and multiple scores per output PDB file?
by dantimatter » Wed, 2019-10-30 09:42
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133 by dantimatter
Wed, 2019-11-06 09:51
Normal topic Alanine Scanning for 1 Protein (no interface)
by mags33 » Fri, 2019-10-25 10:08
2
86 by mags33
Wed, 2019-11-06 09:35
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
78 by allan.ferrari
Tue, 2019-11-05 16:52
Normal topic Warnings during relax
by cossio » Thu, 2018-10-11 14:42
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358 by rmoretti
Mon, 2019-11-04 13:56
Normal topic Symmetry mode in Remodel for N-terminal extension
by yvonne.chan2 » Mon, 2019-11-04 13:41
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45 by yvonne.chan2
Mon, 2019-11-04 13:41
Normal topic cryptic error "Got some signal... It is:15" -- an issue with 'fixbb', or something else?
by dantimatter » Wed, 2019-10-16 14:59
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119 by dantimatter
Wed, 2019-10-30 09:43
Normal topic An error with score app
by Genta » Tue, 2019-10-29 18:46
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36 by Genta
Tue, 2019-10-29 18:46
Normal topic antibody protocol fails
by hamedkhakzad » Mon, 2019-08-19 07:43
1
118 by smlewis
Tue, 2019-10-22 09:45
Normal topic Speed problem when running RosettaLigand ligand docking
by Nicole Deng » Tue, 2019-10-08 04:29
2
107 by Nicole Deng
Fri, 2019-10-18 19:09
Normal topic change number of output pose files written out (default=50) in ligand docking XML script
by hdelrisco » Fri, 2019-10-18 13:50
2
84 by hdelrisco
Fri, 2019-10-18 17:16
Normal topic denovo modelling on a virus-coat protein dimer
by aseem121 » Wed, 2019-10-16 06:55
1
99 by danpf
Wed, 2019-10-16 13:03
Normal topic Make error during installation of updated ncbi-blast-2.9.0+-src plus error with nr-database
by Corvin » Tue, 2019-10-01 02:04
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257 by Corvin
Tue, 2019-10-15 01:12
Normal topic "install_dependencies.pl" script: an optimization of HDD space during nr-pfilt data extracting and formatting stage
by Corvin » Thu, 2019-10-10 02:20
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70 by danpf
Thu, 2019-10-10 09:55
Normal topic "Make_fragments.pl" can't connect to dependencies links
by Corvin » Wed, 2019-09-04 23:54
2
189 by Corvin
Thu, 2019-10-10 01:12
Normal topic Segment File Gen - no ouput
by CATarr » Wed, 2019-10-09 19:05
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93 by CATarr
Wed, 2019-10-09 19:05
Normal topic how to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:40
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190 by xinmiaohe
Fri, 2019-10-04 08:54
Normal topic Energy function and iteration script files
by michelleqyh » Fri, 2019-09-27 09:06
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74 by smlewis
Fri, 2019-09-27 11:54
Normal topic Structure prediction using true distance and angle constraint
by maruhuang » Wed, 2019-08-21 02:29
4
146 by maruhuang
Thu, 2019-09-26 18:52
Normal topic how to "rescore" the models using lowest energy model from rosetta run as native, for RMSD vs Score plot?
by Danielsebas » Tue, 2019-09-24 03:51
1
86 by smlewis
Tue, 2019-09-24 12:43
Normal topic Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
by Danielsebas » Mon, 2019-09-23 03:24
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147 by smlewis
Mon, 2019-09-23 11:42
Normal topic antibody modeling error
by mxp » Mon, 2019-09-16 18:29
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115 by mxp
Mon, 2019-09-23 01:40
Normal topic Error with RosettaAntibodyDesign when running antibody_designer.linuxgccrelease
by bdzhh » Tue, 2019-09-17 17:02
1
99 by jadolfbr
Thu, 2019-09-19 08:53
Normal topic Can I use rosetta binaries built in one linux system to another linux system?
by Danielsebas » Wed, 2019-09-18 06:49
1
80 by rmoretti
Wed, 2019-09-18 10:36
Normal topic how to make "static" built binaries use multiple cpus like "mpi"?
by Danielsebas » Wed, 2019-09-18 06:41
3
109 by rmoretti
Wed, 2019-09-18 10:21
Normal topic Error with Formatdb of legacy blast when running "install_dependencies.pl"?
by Danielsebas » Mon, 2019-09-16 09:30
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82 by Danielsebas
Tue, 2019-09-17 01:03
Normal topic How to analyse multiple silent files from "Abinitiorelax" output to find best models?
by Danielsebas » Tue, 2019-09-10 10:01
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76 by smlewis
Mon, 2019-09-16 12:22
Normal topic "Install_dependencies.pl" gives "Aborted" when downloading "nr" database?
by Danielsebas » Sat, 2019-09-14 08:53
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106 by danpf
Mon, 2019-09-16 09:51
Normal topic How to make new VALL database?
by Danielsebas » Sun, 2019-09-08 02:16
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141 by Danielsebas
Wed, 2019-09-11 00:44
Normal topic Options "-out:prefix" didn't work
by maruhuang » Tue, 2019-09-10 05:42
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94 by maruhuang
Tue, 2019-09-10 20:03
Normal topic "make" error in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7"
by Danielsebas » Mon, 2019-09-02 08:14
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138 by Danielsebas
Sun, 2019-09-08 02:08
Normal topic extract docking pose from ligand docking silent file
by Ruska322 » Sat, 2019-09-07 05:21
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101 by Ruska322
Sat, 2019-09-07 05:21
Normal topic Unable to understand fragment picking tutorial points.
by Danielsebas » Thu, 2019-09-05 03:44
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142 by danpf
Fri, 2019-09-06 11:29
Normal topic ligand docking with MPI
by Ruska322 » Wed, 2019-09-04 03:47
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143 by Ruska322
Fri, 2019-09-06 07:13
Normal topic Rosetta make_fragments.pl error?
by Danielsebas » Mon, 2019-09-02 07:51
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155 by Danielsebas
Thu, 2019-09-05 03:35
Normal topic "sparks failed" error when running "make_fragments.pl"?
by Danielsebas » Tue, 2019-09-03 03:43
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187 by Danielsebas
Thu, 2019-09-05 03:09
Normal topic /database folder after running "install_dependencies.pl" size 657 GB?
by Danielsebas » Tue, 2019-09-03 03:32
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84 by danpf
Tue, 2019-09-03 10:15
Normal topic Rosetta fragment tools installation error
by Danielsebas » Thu, 2019-08-29 02:17
2
128 by Danielsebas
Sun, 2019-09-01 02:38
Normal topic how to find help informations on rosetta_scripts in rosetta3.10
by xinmiaohe » Mon, 2019-08-26 14:48
5
161 by xinmiaohe
Tue, 2019-08-27 08:37
Normal topic A problem with "make_fragments.pl" script dependencies
by Corvin » Fri, 2019-08-16 04:30
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182 by Corvin
Tue, 2019-08-27 00:46
Normal topic can anyone help me correct this script to do alanine scanning
by xinmiaohe » Mon, 2019-08-26 17:23
1
123 by xinmiaohe
Mon, 2019-08-26 18:16
Normal topic RosettaMatch
by xingqing326 » Mon, 2019-07-22 13:14
1
112 by rmoretti
Mon, 2019-08-26 12:57
Normal topic "Angle constraint: 0-length bonds" error
by purvi24 » Sun, 2019-07-28 10:09
1
122 by rmoretti
Mon, 2019-08-26 12:49
Normal topic PDB file name too long to be handled by file system
by dave » Thu, 2019-08-08 03:10
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95 by rmoretti
Mon, 2019-08-26 12:17
Normal topic Do partner1 and partner2 in mover BackrubDD mean chain1 and chain2 respectively?
by johnnytam100 » Fri, 2019-08-23 21:10
1
86 by rmoretti
Mon, 2019-08-26 12:03
Normal topic how to run ala_scan.xml
by xinmiaohe » Mon, 2019-08-26 09:38
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89 by xinmiaohe
Mon, 2019-08-26 09:38
Normal topic ProteinInterfaceDesign algorithm questions
by tsztain » Mon, 2019-02-18 14:10
1
289 by rmoretti
Sun, 2019-08-25 19:15
Normal topic Adding positional restraints to pure RNA system in DRRAFTER and rna_denovo
by zharmad » Fri, 2019-08-23 01:16
1
92 by everyday847
Fri, 2019-08-23 04:08
Normal topic debug rosetta_scripts FunFolDes run
by tatsiana.bylund » Sun, 2019-08-18 23:17
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110 by tatsiana.bylund
Sun, 2019-08-18 23:17
Normal topic RNP structure prediction flags
by daniloboskovic » Fri, 2019-08-16 11:10
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129 by daniloboskovic
Fri, 2019-08-16 11:17
Normal topic How does the label in pdb files looks like when using ResiduePDBInfoHasLabel?
by johnnytam100 » Fri, 2019-08-16 00:25
1
147 by JackMaguire
Fri, 2019-08-16 07:41
Normal topic Does it make sense if I do backrub after sequence design?
by johnnytam100 » Thu, 2019-08-15 05:15
3
162 by johnnytam100
Fri, 2019-08-16 00:20
Normal topic new BUNS for FunFolDes run
by tatsiana.bylund » Wed, 2019-08-14 20:57
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97 by tatsiana.bylund
Wed, 2019-08-14 20:57
Normal topic InterfaceAnalyzer:“too many tries in fill_missing_atoms!”
by mxp » Tue, 2019-08-06 00:41
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329 by mxp
Mon, 2019-08-12 18:42
Normal topic RosettaScripts LinkResidues
by Yero » Fri, 2019-05-17 05:26
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650 by Yero
Thu, 2019-07-18 01:39
Normal topic Usage of the TaskOperations "RestrictToCDRsAndNeighbors"
by johnnytam100 » Wed, 2019-04-10 02:58
1
203 by rmoretti
Wed, 2019-07-10 10:10
Normal topic is it necessary to always run relax before any Rosetta
by mainzer » Fri, 2019-04-12 01:35
1
253 by rmoretti
Wed, 2019-07-10 09:47
Normal topic protein interction design
by Negarsardar » Wed, 2019-05-15 12:01
1
189 by rmoretti
Wed, 2019-07-10 09:24
Normal topic Mutating phosphorylated residues to "canonical" residues and vice versa
by ValentinaSora » Mon, 2019-05-20 05:58
1
228 by rmoretti
Wed, 2019-07-10 09:22
Normal topic Error with talaris2014.wts, which leads to a garbade scorefunction in loop modelling for protein-protein docking
by Corvin » Wed, 2019-06-19 08:40
5
329 by rmoretti
Tue, 2019-07-09 10:13
Normal topic De novo structure building with medium resolution map
by BuddySphinx » Tue, 2019-07-02 09:07
2
145 by BuddySphinx
Tue, 2019-07-02 12:03
Normal topic kcenters_clustering_of_fragments
by bjharris » Mon, 2019-07-01 16:16
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128 by bjharris
Mon, 2019-07-01 16:16
Normal topic Rosetta_cm Segmentation Fault
by gszwabowski » Thu, 2019-06-20 12:55
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250 by gszwabowski
Wed, 2019-06-26 10:25
Normal topic Question about fastsaxs and saxs_score
by orionshih » Thu, 2019-06-13 02:30
2
215 by orionshih
Wed, 2019-06-26 03:54
Normal topic Relax with multiple small molecules
by jharamesh » Sun, 2019-05-26 19:34
1
173 by rmoretti
Mon, 2019-06-24 15:19
Normal topic The relax qustion of Rosetta VIP
by asbelx » Mon, 2019-06-10 07:52
1
158 by rmoretti
Mon, 2019-06-24 14:42
Normal topic Membrane ab-initio modelling of a beta-strand
by hzhekova » Mon, 2019-06-10 14:22
1
187 by rmoretti
Mon, 2019-06-24 14:39
Normal topic Enzyme Design FlexBB Protocol Bug: DNA/RNA handling
by kettner » Fri, 2019-06-14 14:16
1
490 by rmoretti
Mon, 2019-06-24 13:46
Normal topic Rosetta_cm Partial Threading Removing Parts of Sequence
by gszwabowski » Thu, 2019-06-20 12:30
1
149 by rmoretti
Mon, 2019-06-24 13:43
Normal topic VH-VL Orientation in antibody
by sujigeorge1979 » Mon, 2019-06-17 01:23
1
172 by jeliazkov
Mon, 2019-06-17 06:03
Normal topic AddHelixSequenceConstraints Mover2
by Negarsardar » Sat, 2019-06-01 01:54
1
168 by vmulligan
Thu, 2019-06-13 15:01
Normal topic AddHelixSequenceConstraints Mover
by Negarsardar » Thu, 2019-05-30 03:17
2
184 by vmulligan
Thu, 2019-06-13 14:59
Normal topic RosettaAntibody core.pose.util error
by rishibedi » Fri, 2018-10-05 01:31
2
463 by esozdemir
Thu, 2019-06-13 12:19
Normal topic Write error during saving of PDB-file after working with it in the Rosetta through Unix terminal
by Corvin » Thu, 2019-04-25 01:20
2
275 by Corvin
Wed, 2019-06-12 00:04
Normal topic How can I set ref2015 and ligand.wts(-restore_pre_talaris_2013_behavior )
by asbelx » Sat, 2019-06-08 00:07
2
199 by asbelx
Sat, 2019-06-08 17:03
Normal topic SEWING and motif file generation
by rbjacob » Thu, 2018-07-12 07:28
10
1,288 by zhangying1990
Tue, 2019-06-04 18:04
Normal topic Rosetta_CM error unrecognized atom 'CS' this atom is not in PDB
by rlwoltz » Thu, 2019-01-24 19:43
2
495 by karenjgonzalez
Fri, 2019-05-31 07:18
Normal topic protein interface design
by Negarsardar » Tue, 2019-05-28 07:04
2
271 by Negarsardar
Thu, 2019-05-30 23:46
Normal topic Sampling a wider range of RMSD of poses by Rosetta Dock
by johnnytam100 » Tue, 2019-05-21 22:28
1
197 by johnnytam100
Thu, 2019-05-23 20:52
Normal topic Choosing weight file for interface design?
by johnnytam100 » Tue, 2019-05-07 00:47
2
231 by johnnytam100
Tue, 2019-05-21 22:33
Normal topic Behavior of nstruct
by johnnytam100 » Wed, 2019-05-15 22:22
3
293 by johnnytam100
Tue, 2019-05-21 20:48
Normal topic protein protein interaction design
by Negarsardar » Wed, 2019-05-15 06:13
3
326 by ajasja
Wed, 2019-05-15 15:40
Normal topic loop design for Conformational bias
by dhirajks » Thu, 2019-05-09 21:22
1
175 by jadolfbr
Fri, 2019-05-10 07:53
Normal topic Protein Protein Docking with Constraints
by ajaniharesh » Wed, 2019-04-10 07:26
1
210 by rmoretti
Thu, 2019-05-09 15:40
Normal topic missing atom number 5 atom name CB
by ajaniharesh » Fri, 2019-04-26 12:08
1
198 by rmoretti
Fri, 2019-04-26 12:13
Normal topic Coverage of sequence space?
by johnnytam100 » Sun, 2019-04-21 23:25
4
406 by johnnytam100
Thu, 2019-04-25 19:28
Normal topic Highly negative total score
by Ruchi_P_Jain » Wed, 2019-04-24 19:55
1
221 by nannemdp
Thu, 2019-04-25 07:58
Normal topic input file for loop modeling
by Negarsardar » Tue, 2019-04-16 10:21
1
215 by rmoretti
Tue, 2019-04-16 11:07
Normal topic How to specify only design surface residues and loops by RosettaScripts?
by johnnytam100 » Sun, 2019-04-07 21:47
4
381 by johnnytam100
Wed, 2019-04-10 02:48
Normal topic ERROR: Specified chain does not exist.
by ajaniharesh » Fri, 2019-04-05 11:14
2
326 by ajaniharesh
Tue, 2019-04-09 06:53
Normal topic Abinitio the Broker protocol
by ac.research » Sun, 2019-03-24 03:56
1
233 by rmoretti
Fri, 2019-04-05 00:18
Normal topic Segmentation Fault
by ajaniharesh » Fri, 2019-03-29 11:21
4
692 by ajaniharesh
Thu, 2019-04-04 07:07
Normal topic Threading a sequence onto a template with ligands/metal ions included
by ajkal » Wed, 2017-04-19 11:53
3
1,256 by ahmadkhalifa
Sun, 2019-03-31 23:27
Normal topic Threading with Ligand
by ekwan » Thu, 2018-12-06 15:10
1
281 by rmoretti
Fri, 2019-03-29 13:21
Normal topic reporting bugs? (erraser in rosetta 3.10)
by meyer » Fri, 2018-12-14 09:40
2
322 by everyday847
Fri, 2019-03-29 13:13
Normal topic Missing atoms and cannot find atom pose when refining ligand position with EM density
by BuddySphinx » Mon, 2018-12-31 16:22
1
339 by rmoretti
Fri, 2019-03-29 13:06
Normal topic Unexpected Error with RosettaCM -
by terry » Fri, 2019-02-22 14:26
1
472 by rmoretti
Fri, 2019-03-29 12:25
Normal topic Docking to TM protein plus lipid bilayer
by renedominik » Tue, 2019-03-12 06:58
1
280 by rmoretti
Fri, 2019-03-29 10:11
Normal topic Two questions on the RosettaScripts flexbb-interfacedesign.xml
by johnnytam100 » Fri, 2019-03-15 04:54
1
265 by rmoretti
Fri, 2019-03-29 09:58

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