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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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7,798 by admin
Fri, 2015-09-04 16:17
Normal topic charge grid in rosetta ligand docking using rosetta script
by syntekabio2019 » Mon, 2022-01-17 23:53
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10 by syntekabio2019
Mon, 2022-01-17 23:53
Normal topic Protein design: Ligand binding between two units of a homodimer
by chemotaxis_123 » Sun, 2022-01-02 16:01
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43 by chemotaxis_123
Sun, 2022-01-02 16:01
Normal topic I need help with cst file the paper: De Novo Computational Design of Retro-Aldol Enzymes
by Wenithor » Thu, 2022-01-06 12:20
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59 by Wenithor
Thu, 2022-01-06 12:20
Normal topic simple_cycpep_predict with N-term acetylation
by Ken » Fri, 2021-12-17 09:49
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67 by Ken
Fri, 2021-12-17 09:49
Normal topic Remodel's problem in treatment with non-protein residues
by Corvin » Mon, 2021-12-13 09:07
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70 by Corvin
Mon, 2021-12-13 09:07
Normal topic ERROR: APBS failed to generate the result file.
by bhavranek » Sat, 2021-12-18 11:01
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78 by bhavranek
Sun, 2021-12-26 21:05
Normal topic Segfault error while running MR Rosetta in Phenix
by memilton » Thu, 2021-12-16 09:09
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79 by memilton
Thu, 2021-12-16 09:09
Normal topic [LoopModelerMover] ERROR: Can't build a fold tree from a loop with an unspecified cut point.
by dgm3 » Sun, 2021-12-26 18:32
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82 by dgm3
Fri, 2021-12-31 17:42
Normal topic How to apply cartesian_ddg to multi-metric enzyme?
by Wang Zhe » Wed, 2021-12-08 10:07
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86 by Wang Zhe
Wed, 2021-12-08 10:07
Normal topic trRosetta - Nan occuring in Hbond calculation
by y_atsmonraz » Mon, 2021-10-04 09:16
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119 by y_atsmonraz
Mon, 2021-10-04 09:16
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
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123 by alonwenger
Sat, 2021-12-18 12:32
Normal topic connecting rna strands together
by y_atsmonraz » Tue, 2021-11-09 05:42
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125 by y_atsmonraz
Thu, 2021-11-11 04:51
Normal topic Rosetta DARc suboptimal dockings
by ddhoyo » Mon, 2021-10-11 06:18
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125 by ddhoyo
Mon, 2021-10-11 06:18
Normal topic Linker Building in scFv
by sam_dc » Sat, 2021-10-09 05:38
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135 by sam_dc
Sat, 2021-10-09 05:38
Normal topic Symmetry definition file versions
by Jeff Qu » Tue, 2021-09-28 09:53
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141 by Jeff Qu
Tue, 2021-09-28 09:53
Normal topic SecundaryStructure Filter
by Soler » Sun, 2021-11-21 22:20
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151 by Soler
Sun, 2021-11-21 22:20
Normal topic constraining different chains together in rosetta_cm
by y_atsmonraz » Thu, 2021-11-18 02:59
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163 by y_atsmonraz
Thu, 2021-11-18 03:01
Normal topic Problems with waters in CoupledMoves application
by Corvin » Tue, 2021-11-16 07:16
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165 by Corvin
Tue, 2021-11-16 07:22
Normal topic Repacker vs minimization
by Elijah_Hix » Fri, 2021-07-02 07:25
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167 by Elijah_Hix
Fri, 2021-07-02 07:25
Normal topic Error reading in/out glycosylated silent file - "Can't create a polymer bond after residue due to incompatible type"
by amorin » Mon, 2021-09-27 12:16
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167 by amorin
Mon, 2021-09-27 12:16
Normal topic FlexPepDock ab initio: behavior without fragment files
by nrollins » Mon, 2021-07-26 14:16
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169 by nrollins
Mon, 2021-07-26 14:16
Normal topic The energy terms in InterfaceAnalyzer
by Sunyp_IM » Tue, 2021-11-02 18:43
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175 by zivben
Sat, 2021-11-13 04:49
Normal topic C-termini remodelling of dimeric structure removes second chain
by LeonhardJS » Wed, 2021-10-13 06:23
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177 by LeonhardJS
Fri, 2021-11-12 01:20
Normal topic antibody - sequence position requested was 0
by jremmel » Mon, 2021-09-27 12:26
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178 by nannemdp
Mon, 2021-09-27 14:22
Normal topic FlexPepDock bug? Constraints do not appear in total_score?
by nrollins » Mon, 2021-07-26 14:29
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202 by nrollins
Mon, 2021-07-26 14:29
Normal topic clashes created with enzdes
by listofdina » Mon, 2021-08-02 06:51
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215 by listofdina
Mon, 2021-08-02 06:51
Normal topic Relaxed proteins show higher clash score in molprobity results.
by Wang Zhe » Fri, 2021-12-03 04:32
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235 by smlewis
Wed, 2021-12-08 13:02
Normal topic Issues with modifying dock.xml for multiple ligand docking
by DGR95 » Fri, 2021-05-14 12:51
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239 by DGR95
Fri, 2021-05-14 12:51
Normal topic FastRelax Refinement severe clashes
by Victor Tobiasson » Thu, 2021-05-20 06:55
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243 by Victor Tobiasson
Thu, 2021-05-20 06:55
Normal topic What is an SS0 predictor?
by ojmel » Fri, 2021-04-02 14:25
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250 by ojmel
Mon, 2021-04-12 07:50
Normal topic building a protein-dna homology model via cm_rosetta
by y_atsmonraz » Wed, 2021-10-20 23:11
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252 by y_atsmonraz
Tue, 2021-11-02 01:47
Normal topic Patch to impose tetrahedral geometry on backbone O atom
by georg » Thu, 2021-04-08 09:30
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253 by georg
Thu, 2021-04-08 09:31
Normal topic How to Perform point mutations with NCAA
by Subhrodeep Saha » Tue, 2021-06-22 02:05
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257 by vmulligan
Thu, 2021-06-24 13:23
Normal topic Writing down properties for new atom types
by Corvin » Tue, 2021-01-12 04:30
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262 by Corvin
Wed, 2021-01-13 04:00
Normal topic Segfault with Pepspec
by almeida85 » Thu, 2021-02-11 02:56
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271 by almeida85
Thu, 2021-02-11 02:56
Normal topic Python2 script in Rosetta3.13
by ddhoyo » Wed, 2021-09-15 04:05
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272 by matteoferla
Wed, 2021-09-15 06:04
Normal topic multi ligand docking using rosetta script
by syntekabio2019 » Tue, 2021-04-13 19:31
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272 by syntekabio2019
Tue, 2021-04-13 19:31
Normal topic Stepwise Monte Carlo - errors with ResidueTypeSet and Disulfides
by user42 » Wed, 2021-07-21 20:34
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273 by everyday847
Fri, 2021-07-30 13:26
Normal topic Blast error for rosetta antibody: No argument value given for Query file
by dngusdnr1 » Tue, 2021-06-08 17:30
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275 by taylorjones
Wed, 2021-06-09 16:38
Normal topic hpatch commands and how to identify patches
by Bianca Oliva » Thu, 2021-04-29 04:02
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276 by Bianca Oliva
Thu, 2021-04-29 04:02
Normal topic duplex RNA
by amir_tagh » Thu, 2021-08-05 06:34
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280 by everyday847
Mon, 2021-08-16 10:43
Normal topic PDB Clustering
by code_Monkey » Mon, 2021-04-05 10:40
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280 by code_Monkey
Mon, 2021-04-05 10:40
Normal topic Ab Initio folding with HEM ligand molecule
by jseco » Fri, 2021-03-05 06:49
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283 by jseco
Mon, 2021-03-08 03:40
Normal topic Question with rosetta AbPredict tutorial
by terabithia2011 » Mon, 2021-01-25 09:24
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292 by terabithia2011
Mon, 2021-01-25 09:24
Normal topic Topobuilder segmentation fault
by tatsiana.bylund » Mon, 2021-08-09 07:10
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296 by tatsiana.bylund
Mon, 2021-08-09 07:10
Normal topic flexpepdcok of lipid conjugated peptide with glyco protein.
by ravi.thakkkar369 » Fri, 2020-12-18 13:00
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302 by ravi.thakkkar369
Fri, 2020-12-18 13:00
Normal topic setup_RosettaCM.py
by browns02 » Mon, 2021-06-28 07:13
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303 by browns02
Tue, 2021-06-29 11:41
Normal topic Design of multimeric protein
by ldlamini » Mon, 2021-01-11 07:23
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303 by ldlamini
Mon, 2021-01-11 07:23
Normal topic Question about running scallo
by danbo » Mon, 2021-11-29 23:25
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309 by danbo
Wed, 2021-12-22 23:51
Normal topic Creating fragment files for proteins less than 27 aa in length
by Poladu » Tue, 2021-01-26 07:50
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309 by Poladu
Tue, 2021-01-26 07:50
Normal topic Modelling humanized camelid like antibody
by terabithia2011 » Tue, 2021-01-26 10:12
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319 by terabithia2011
Tue, 2021-01-26 10:12
Normal topic Bug Report - Encoding issue
by daniloboskovic » Tue, 2020-08-04 07:02
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327 by daniloboskovic
Tue, 2020-08-04 07:02
Normal topic RosettaCM/hybridize
by kywei » Wed, 2021-04-28 09:56
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328 by vmulligan
Wed, 2021-04-28 12:59
Normal topic Help with enzyme design files
by Wenithor » Thu, 2021-04-29 10:33
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328 by rmoretti
Thu, 2021-04-29 10:44
Normal topic metalloprotein ab initio with glutamic acid
by inorgchem » Tue, 2020-06-16 20:45
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330 by inorgchem
Tue, 2020-06-16 20:45
Normal topic Pepspec Anchor Dock
by Soler » Wed, 2020-09-16 19:08
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335 by Soler
Wed, 2020-09-16 19:08
Normal topic rosetta_cm segfault
by browns02 » Fri, 2021-07-09 13:35
2
335 by rmoretti
Fri, 2021-07-09 15:05
Normal topic RosettaAntibody - No matching templates for CDR1
by agctomer » Tue, 2021-01-19 22:45
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335 by agctomer
Tue, 2021-01-19 22:45
Normal topic residue_energy_breakdown of a protein-ligand complex.
by sam_dc » Tue, 2021-05-18 04:45
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344 by rmoretti
Tue, 2021-05-18 07:21
Normal topic RemodelMover and Input Pose
by ozyo » Tue, 2020-12-29 09:41
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350 by ozyo
Tue, 2020-12-29 09:41
Normal topic different value of score from rna_denovo and rna_score?
by yikanzhang » Wed, 2021-02-03 07:17
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355 by CameronJA
Tue, 2021-06-15 20:02
Normal topic clustering output file has few structures
by fabiotrovato » Mon, 2020-08-17 11:37
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357 by fabiotrovato
Mon, 2020-08-17 11:37
Normal topic Side-chain grafting at the fixed protein and position
by Kazu » Wed, 2020-05-20 08:49
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360 by Kazu
Wed, 2020-05-20 08:49
Normal topic core.optimization.LineMinimizer: [ ERROR ] Inaccurate G!
by aralz » Thu, 2021-02-11 00:46
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362 by aralz
Thu, 2021-02-11 00:46
Normal topic D-amino acids tripeptide docking.
by sam_dc » Sat, 2021-07-03 08:48
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362 by vmulligan
Tue, 2021-07-06 08:27
Normal topic RoseTTaFold
by ozsolomon » Thu, 2021-10-07 05:27
2
373 by ozsolomon
Thu, 2021-10-07 14:25
Normal topic Protonating all possible sites: the problem in MOL2 file format or the innate Rosetta feature(bug)?
by Corvin » Wed, 2020-12-16 04:58
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373 by Corvin
Wed, 2020-12-30 09:21
Normal topic Fewer than expected structures in clustering output
by fabiotrovato » Thu, 2020-08-20 00:59
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374 by fabiotrovato
Thu, 2020-08-20 00:59
Normal topic How to use base_pair_constraint for RNA as a constraint term?
by yels » Sat, 2021-04-03 01:19
1
377 by everyday847
Sun, 2021-04-04 12:48
Normal topic How many iterations of remodel is enough?
by daniloboskovic » Thu, 2020-07-16 08:07
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377 by daniloboskovic
Thu, 2020-07-16 08:14
Normal topic zero standard deviation of I_sc in protein-protein docking
by rohi » Fri, 2020-07-03 22:19
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378 by rohi
Fri, 2020-07-03 22:20
Normal topic Global Docking with carbohydrates
by ChiauShu » Sat, 2020-08-22 20:16
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381 by ChiauShu
Sat, 2020-08-22 20:16
Normal topic Should I be stripping water molecules from my input structure for Rosetta Design?
by chrisHKL » Wed, 2021-03-24 14:22
1
382 by smlewis
Wed, 2021-03-24 14:59
Normal topic Scoring after HBNet
by HHL_SIUC » Wed, 2020-07-01 10:49
0
383 by HHL_SIUC
Wed, 2020-07-01 10:49
Normal topic General question regarding ligand-docking
by Alison_Yajie » Thu, 2020-05-07 09:48
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388 by Alison_Yajie
Thu, 2020-05-07 09:48
Normal topic Filling the missing loops
by code_Monkey » Tue, 2021-04-27 07:44
2
392 by code_Monkey
Tue, 2021-04-27 12:11
Normal topic "Residue 7 was disulfide bonded but had no partner" with antibody.linuxgccrelease
by Sunyp_IM » Thu, 2020-06-04 05:53
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395 by Sunyp_IM
Thu, 2020-06-04 05:54
Normal topic Comparative Modeling Tutorial
by code_Monkey » Thu, 2021-03-04 12:35
1
397 by rmoretti
Fri, 2021-03-05 09:35
Normal topic Ligand docking with constraint
by Alison_Yajie » Wed, 2020-06-24 12:34
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399 by Alison_Yajie
Wed, 2020-06-24 12:34
Normal topic Residue selector
by Alison_Yajie » Wed, 2020-06-17 19:57
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403 by Alison_Yajie
Thu, 2020-06-18 09:47
Normal topic Error when using Remodel on a protein with a chemically bound ligand
by Pappmaschee » Wed, 2020-12-16 09:23
0
407 by Pappmaschee
Wed, 2020-12-16 09:23
Normal topic Does antibody_numbering_converter support camelid antibody?
by mxp » Tue, 2020-07-07 01:21
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407 by mxp
Tue, 2020-07-07 01:21
Normal topic Metal Ion in symmetric design
by tschiex » Wed, 2020-07-08 05:28
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412 by tschiex
Wed, 2020-07-08 05:28
Normal topic appropriate sampling for protein docking to a multi chain assembly
by SWM » Fri, 2020-01-24 11:22
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413 by SWM
Fri, 2020-01-24 11:22
Normal topic FlexPepDocking
by jlawrie » Tue, 2020-09-15 12:52
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413 by jlawrie
Tue, 2020-09-15 12:52
Normal topic RosettaAntibody3 - How can I model an extended H3?
by brspurri » Fri, 2020-08-28 09:11
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414 by brspurri
Fri, 2020-08-28 09:11
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-07-02 07:05
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415 by Alison_Yajie
Thu, 2020-07-02 07:10
Normal topic constraints in Rosetta ligand docking (AddorRemoveMatchCsts, Addconstraints Mover, and ConstraintSetMover)
by rohi » Mon, 2021-01-11 13:32
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416 by rohi
Mon, 2021-01-11 13:58
Normal topic Generalized KIC loop closure affects downstream residues without perturbations
by chenna » Mon, 2021-04-26 02:16
2
420 by chenna
Wed, 2021-04-28 07:18
Normal topic r_frag_quality
by ii_cnr » Mon, 2021-04-12 03:06
2
422 by ii_cnr
Mon, 2021-04-12 23:44
Normal topic ligand_docking: ligand preparation
by Alison_Yajie » Thu, 2020-05-21 09:42
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426 by Alison_Yajie
Thu, 2020-05-21 09:42
Normal topic protein relax
by Alison_Yajie » Tue, 2020-05-19 08:29
0
430 by Alison_Yajie
Tue, 2020-05-19 08:29
Normal topic Zero residues error in docking
by cjy318 » Tue, 2020-07-28 19:47
0
438 by cjy318
Tue, 2020-07-28 19:47
Normal topic NCAA attached at two points
by tsztain » Wed, 2021-06-16 15:20
3
438 by matteoferla
Sat, 2021-06-19 03:07
Normal topic Docking Analysis and Metrics in RosettaLigand.
by sam_dc » Tue, 2021-04-20 03:54
1
442 by rmoretti
Tue, 2021-04-20 13:27
Normal topic [Solved] Resetting a pose with RigidBodyTransMover
by bjharris » Wed, 2021-01-13 14:01
1
442 by bjharris
Fri, 2021-01-22 17:34
Normal topic Modelling of multi-component symmetrical structures
by LanMei » Wed, 2020-10-07 09:58
0
445 by LanMei
Wed, 2020-10-07 09:58
Normal topic Disulfide Bonds in Loop Modeling
by code_Monkey » Mon, 2021-05-03 08:27
2
449 by code_Monkey
Thu, 2021-05-06 07:14
Normal topic Element 'trRosettaProtocol': This element is not expected.
by csaylan » Tue, 2021-04-20 14:21
2
449 by csaylan
Tue, 2021-04-20 16:13

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