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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
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5,003 by admin
Fri, 2015-09-04 16:17
Normal topic Mutations are ignored (fixbb) when using -auto_setup_metals option
by hdelrisco » Wed, 2019-06-19 15:43
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30 by hdelrisco
Wed, 2019-06-19 15:43
Normal topic File specification of binary part of silent file (especially PDB section)
by m.ebert » Wed, 2019-05-29 01:52
1
63 by smlewis
Wed, 2019-05-29 13:21
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06
3
65 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
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66 by weifulei
Sun, 2019-05-05 19:56
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
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70 by weifulei
Sun, 2019-05-05 19:56
Normal topic How to use the <CavityVolume> filter in the released version of Rosetta
by BioPython » Sun, 2019-05-12 20:07
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77 by BioPython
Sun, 2019-05-12 20:07
Normal topic How to define a theozyme from the .pdb crystal structure without ligand?
by weifulei » Mon, 2019-05-20 21:18
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81 by weifulei
Mon, 2019-05-20 21:18
Normal topic Hydrogen bond detection and shape complementarity
by sujigeorge1979 » Fri, 2019-06-14 02:39
2
81 by sujigeorge1979
Fri, 2019-06-14 21:11
Normal topic Error with simple_cycpep_predict protocol while using a native pdb file
by Florent Langenfeld » Tue, 2019-03-26 10:05
1
91 by vmulligan
Tue, 2019-03-26 11:23
Normal topic Denovo prediction from multiple fragment lengths
by ahmadkhalifa » Sun, 2019-03-24 03:55
1
100 by rmoretti
Sat, 2019-03-30 12:10
Normal topic The question about FavorNativeResidue
by asbelx » Fri, 2019-04-12 20:02
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102 by asbelx
Sat, 2019-04-13 01:13
Normal topic problems with implementing NOE constraints
by connyyu » Thu, 2019-04-11 12:37
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106 by connyyu
Thu, 2019-04-18 03:26
Normal topic Rosetta Antibody cuts off light chain?
by ziheng@mit.edu » Thu, 2019-05-02 15:17
1
106 by jeliazkov
Fri, 2019-05-03 07:00
Normal topic Rosetta params for taxol
by ahmadkhalifa » Sat, 2019-03-30 22:37
1
108 by rmoretti
Wed, 2019-04-03 10:03
Normal topic intrensic disrodered proteins
by ac.research » Thu, 2019-04-04 07:20
1
109 by vmulligan
Mon, 2019-04-08 14:49
Normal topic Multi-state design with the error "unable to locate database file"
by yifeili1983 » Sun, 2019-03-31 18:30
1
110 by rmoretti
Wed, 2019-04-03 09:31
Normal topic LHOC script problem in Rosetta Antibody
by ziheng@mit.edu » Thu, 2019-04-25 14:19
1
113 by ziheng@mit.edu
Thu, 2019-04-25 14:31
Normal topic alignblast.pl truncated file
by rlwoltz » Mon, 2019-03-11 18:32
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114 by rlwoltz
Mon, 2019-03-11 18:32
Normal topic How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?
by johnnytam100 » Wed, 2019-05-08 02:30
2
122 by johnnytam100
Wed, 2019-05-15 18:45
Normal topic Searching density map using real space correlation
by ahmadkhalifa » Fri, 2018-12-28 00:28
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125 by ahmadkhalifa
Fri, 2018-12-28 00:28
Normal topic MSDMover error in RECON protocol
by yifeili1983 » Mon, 2019-04-01 00:44
2
146 by yifeili1983
Mon, 2019-04-15 22:34
Normal topic Misleading error message
by renedominik » Tue, 2019-03-12 01:19
1
157 by vmulligan
Tue, 2019-03-26 11:30
Normal topic Relax output mmCIF file to a particular path
by AJVincelli » Sun, 2018-11-25 11:04
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158 by AJVincelli
Sun, 2018-11-25 11:09
Normal topic How to define the surface (???.surf) for surface_docking?
by Anpu » Thu, 2018-09-27 07:34
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164 by Anpu
Thu, 2018-09-27 23:36
Normal topic perturb_temp flag
by Loki01 » Tue, 2018-11-27 05:06
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167 by rmoretti
Wed, 2019-04-03 09:58
Normal topic Errors in Interface_design_demo
by zhoubin » Fri, 2019-01-04 13:14
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178 by zhoubin
Fri, 2019-01-04 13:14
Normal topic Ab Initio large threshold for clustering
by Swillard » Mon, 2018-11-12 14:14
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180 by rmoretti
Wed, 2018-11-21 14:01
Normal topic crashed when loading RDC data
by yangshen12 » Fri, 2018-10-26 12:34
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184 by yangshen12
Fri, 2018-10-26 12:34
Normal topic Constraints use in RosettaCM
by a.book » Wed, 2018-10-03 12:11
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189 by a.book
Wed, 2018-10-03 15:56
Normal topic Memory leak when PDB preparation
by Jacky010 » Mon, 2019-05-06 01:28
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193 by Jacky010
Tue, 2019-05-14 01:24
Normal topic RosettaMatch Problem
by David » Tue, 2019-01-22 12:23
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197 by David
Tue, 2019-01-22 12:23
Normal topic Add hemes to cytochrome structures
by BuddySphinx » Sun, 2018-12-16 13:46
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197 by rmoretti
Fri, 2019-03-29 14:43
Normal topic make_fragments.pl
by rlwoltz » Fri, 2019-02-01 10:31
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201 by rlwoltz
Fri, 2019-02-01 10:31
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53
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201 by ela
Fri, 2018-08-31 02:53
Normal topic Params file for Methane
by dasdevashishdas » Sun, 2018-10-07 21:34
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203 by rmoretti
Mon, 2018-10-08 11:20
Normal topic Rosetta script to relax a neighborhood only
by matteoferla » Mon, 2018-10-29 03:34
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203 by jadolfbr
Fri, 2018-11-09 09:17
Normal topic env energy term
by bazzoli » Wed, 2018-10-10 01:59
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206 by bazzoli
Wed, 2018-10-10 01:59
Normal topic Consistent XYZvector length() zero failure in EnzDes
by mwfranklin » Thu, 2018-11-01 12:44
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214 by rmoretti
Wed, 2018-11-21 14:14
Normal topic RosettaDesign improvements
by ac.research » Mon, 2018-05-14 08:27
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215 by ac.research
Mon, 2018-05-14 08:27
Normal topic Denovo density excess map input and segmentation
by ahmadkhalifa » Mon, 2018-04-30 07:28
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218 by ahmadkhalifa
Fri, 2018-05-04 07:50
Normal topic restrict PackRotamersMover
by pmit » Thu, 2018-05-03 01:48
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221 by pmit
Thu, 2018-05-03 01:48
Normal topic Error in enzyme_design.default.linuxgccrelease: corrupted size vs. prev_size
by dasdevashishdas » Fri, 2018-10-12 00:55
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228 by dasdevashishdas
Fri, 2018-10-12 00:55
Normal topic Mutate multidomain protein
by frankfurter1 » Wed, 2018-05-09 04:40
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230 by frankfurter1
Wed, 2018-05-09 04:40
Normal topic Clarify ProteinInterfaceDesign “randomness”
by tsztain » Wed, 2019-02-27 09:41
3
230 by rmoretti
Sat, 2019-03-30 12:12
Normal topic De novo density assembly weights don't add up to a 100
by ahmadkhalifa » Fri, 2018-08-03 12:07
1
231 by rmoretti
Fri, 2018-08-03 12:37
Normal topic FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py
by obdulia » Wed, 2018-04-18 00:45
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231 by obdulia
Wed, 2018-04-18 00:45
Normal topic Calibur not listing cluster members
by Swillard » Sun, 2018-07-01 13:07
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237 by Swillard
Sun, 2018-07-01 13:07
Normal topic protocols.jd2.JobDistributor: [ ERROR ]
by johnnytam100 » Thu, 2019-04-11 09:30
5
242 by jadolfbr
Tue, 2019-04-16 09:15
Normal topic DockingProtocol mover ensemble error
by dfcoelho » Tue, 2018-10-16 08:32
1
244 by dfcoelho
Tue, 2018-10-16 08:35
Normal topic Question about FlexPepDock score
by aelatico » Thu, 2018-07-19 20:39
1
244 by rmoretti
Wed, 2018-08-01 16:04
Normal topic solution of the length of peptide candidates is larger than substrate with FlexPepDock and Flexpepbind
by ziqi1234 » Thu, 2018-05-24 02:18
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248 by ziqi1234
Thu, 2018-05-24 02:18
Normal topic What is the expected behaviour when minimizing a jump edge?
by bio_james » Wed, 2017-12-13 09:13
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262 by bio_james
Wed, 2017-12-13 09:13
Normal topic Questions regarding fragmentation using Robetta
by ahmadkhalifa » Thu, 2018-06-28 13:24
1
263 by smlewis
Thu, 2018-06-28 13:34
Normal topic lDDT: local Distance Difference Test implemented?
by ipetrik_ambry » Wed, 2017-12-06 13:11
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273 by ipetrik_ambry
Wed, 2017-12-06 13:11
Normal topic How to minimize only a few key residues' orientation
by Ronghai Cheng » Mon, 2018-11-05 18:37
2
273 by Ronghai Cheng
Tue, 2018-11-13 21:56
Normal topic How did you begin to learn Rosetta?
by mdeklotz » Mon, 2018-07-30 10:08
1
284 by jkleman
Tue, 2018-07-31 13:19
Normal topic [dev] examples for implementing setup_for_packing, prepare_rotamers_for_packing?
by ipetrik_ambry » Mon, 2017-10-30 17:03
0
287 by ipetrik_ambry
Mon, 2017-10-30 17:03
Normal topic keep ATP in the kinase-peptide structure while docking
by ziqi1234 » Fri, 2017-11-10 04:04
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287 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic Method to keep ATP in the certain position in the prepack step
by ziqi1234 » Tue, 2017-11-21 05:55
0
289 by ziqi1234
Tue, 2017-11-21 05:55
Normal topic ab initio struction prediction
by Negarsardar » Mon, 2018-08-06 15:50
1
290 by smlewis
Tue, 2018-08-07 16:59
Normal topic Molfile to Params File Issue
by jferrie » Mon, 2018-04-23 15:25
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291 by jferrie
Mon, 2018-04-23 15:25
Normal topic Amino acid post-translational modifications
by aelatico » Tue, 2018-06-19 03:29
1
297 by smlewis
Tue, 2018-06-19 10:31
Normal topic Icouldnot find DDMI protocol for design protein
by ladimafakher » Mon, 2018-02-12 09:22
1
297 by rmoretti
Mon, 2018-02-12 09:39
Normal topic known disulfides in Remodel sequence
by matteoferla » Mon, 2018-09-10 06:43
1
300 by matteoferla
Thu, 2018-09-13 06:21
Normal topic Is it better to have smaller nstruct but many runs?
by Loki01 » Mon, 2018-11-19 11:50
3
307 by smlewis
Mon, 2018-11-19 13:20
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
317 by rmoretti
Mon, 2018-03-19 09:08
Normal topic Rosetta structure refinement alters bound ligand
by ahmadkhalifa » Mon, 2018-07-23 07:49
1
319 by rmoretti
Fri, 2018-08-03 08:59
Normal topic recommended function type for cross links data
by meravb » Sun, 2018-08-05 06:57
2
321 by rmoretti
Mon, 2018-08-20 11:51
Normal topic Docking a ligand to two movable domains of a protein
by brspurri » Wed, 2018-05-16 08:27
1
321 by rmoretti
Thu, 2018-06-28 14:22
Normal topic Reading chloride anions
by Martin Floor » Mon, 2018-08-27 14:29
2
339 by Martin Floor
Tue, 2018-08-28 13:21
Normal topic How to specify a specific rotamer
by Lior_UCSF » Wed, 2018-02-21 20:35
1
347 by rmoretti
Thu, 2018-02-22 09:29
Normal topic How to extract antibody from a set of pdb file may may contain antigen?
by Sunyp_IM » Mon, 2017-11-13 17:11
1
359 by ac.research
Sat, 2017-11-18 06:54
Normal topic protein ligand docking
by patrickchirdon » Sun, 2018-12-30 15:07
4
361 by smlewis
Mon, 2018-12-31 08:58
Normal topic Undocumented changes in BackrubDD
by abhi_pe_acharya » Mon, 2018-07-16 00:24
2
365 by abhi_pe_acharya
Sun, 2018-08-05 22:03
Normal topic ERROR: FragmentIO: could not open file
by ahmadkhalifa » Wed, 2018-01-31 13:30
1
366 by rmoretti
Wed, 2018-01-31 14:57
Normal topic Rosetta lack of necessary application
by ylwang » Wed, 2018-11-07 01:13
3
369 by rmoretti
Wed, 2018-11-21 13:50
Normal topic Question about CartesianMD
by orionshih » Sun, 2018-04-29 21:07
2
379 by orionshih
Tue, 2018-05-01 21:16
Normal topic Issue with Loop Analyzer Mover ouput
by abhi_pe_acharya » Mon, 2018-04-30 09:55
2
380 by abhi_pe_acharya
Mon, 2018-04-30 22:54
Normal topic Rosetta matching error
by purvi24 » Mon, 2018-03-12 02:38
1
380 by smlewis
Mon, 2018-03-12 09:57
Normal topic Modeling transmembrane and intracellular domain
by Sunyp_IM » Sun, 2018-04-08 06:44
1
385 by jkleman
Sat, 2018-04-14 10:55
Normal topic Propagating the same mutation over "different" chains
by mdeklotz » Thu, 2018-07-26 09:27
3
385 by rmoretti
Fri, 2018-08-03 08:42
Normal topic Peripheral membrane protein modeling
by Fukiishi » Tue, 2018-10-02 02:09
3
385 by matteoferla
Thu, 2018-10-04 01:30
Normal topic Do Rosetta support hydroxide(OH-) and oxide(O2-) params?
by dasdevashishdas » Thu, 2018-08-16 21:15
2
392 by dasdevashishdas
Thu, 2018-08-23 18:02
Normal topic Incorporating Rosetta Binary and Database to a Web Server Pipeline
by smkim » Fri, 2018-09-28 20:35
1
393 by rmoretti
Fri, 2018-11-09 12:22
Normal topic Expanding the silent file
by jharamesh » Fri, 2018-01-12 09:15
2
395 by rmoretti
Mon, 2018-01-15 14:35
Normal topic Total Rama Score
by jcminerlanl » Thu, 2018-05-10 07:19
1
395 by rmoretti
Thu, 2018-06-28 14:28
Normal topic Calculate ddG in mutation scan of a homodimer
by zachdebruine » Thu, 2018-02-01 10:02
1
399 by rmoretti
Mon, 2018-02-05 15:44
Normal topic Docking Local Refine Not Moving Input
by SenyorDrew » Sat, 2017-10-21 08:26
1
400 by SenyorDrew
Mon, 2017-11-20 13:27
Normal topic Can I use next generation KIC with fragments?
by Loki01 » Thu, 2017-12-07 06:19
1
401 by Loki01
Wed, 2017-12-13 05:27
Normal topic Is CST_Design required for enzdes protocol?
by dasdevashishdas » Mon, 2018-09-03 00:51
2
403 by dasdevashishdas
Thu, 2018-09-27 03:35
Normal topic Error using FilterScan with rosettascripts
by SenyorDrew » Tue, 2016-12-13 14:29
0
403 by SenyorDrew
Tue, 2016-12-13 14:29
Normal topic Rosetta-based projects using and licensing
by SergeyP » Fri, 2018-10-26 15:45
3
407 by SergeyP
Mon, 2018-11-12 09:19
Normal topic Docking individual residue ussing RosettaDock
by a-eatemadi@razi... » Wed, 2017-09-06 05:50
1
409 by rmoretti
Wed, 2017-09-06 08:47
Normal topic Why I_sc of Rosetta 2016.02 and 2018.21 are so different?
by eminegenetics » Mon, 2018-07-16 12:51
2
412 by eminegenetics
Wed, 2018-07-18 13:48
Normal topic Problem with the top 25 fragments used in the library of 200 nine-residue fragments in AbinitioRelax
by MA » Wed, 2017-07-26 01:12
1
419 by rmoretti
Mon, 2017-08-21 09:55
Normal topic The algorithm of adding missing Hydrogen to a backbone
by ac.research » Tue, 2018-03-06 03:48
1
419 by rmoretti
Sat, 2018-03-17 10:43
Normal topic Segmentation fault (core dumped) denovo_density.linuxgccrelease
by ahmadkhalifa » Sun, 2018-04-15 17:52
1
427 by smlewis
Mon, 2018-04-16 16:32
Normal topic SNUGDOCK
by adva » Sun, 2017-07-16 00:49
1
432 by jeliazkov
Tue, 2017-07-18 09:51
Normal topic Error running GenericMonteCarlo mover within MultipleOutputWrapper mover
by abhi_pe_acharya » Mon, 2018-04-16 04:58
1
433 by abhi_pe_acharya
Thu, 2018-04-19 03:49

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