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Rosetta 3 - General

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Normal topic De Novo backbone generation vs Rosetta Match for enzdes and ligand binding.
by csvajda » Thu, 2022-06-30 09:55
2
1,050 by csvajda
Thu, 2022-06-30 16:26
Normal topic Error when using published constraints file
by Delfosse57 » Thu, 2023-08-17 11:22
2
644 by ikalvet
Mon, 2023-08-21 05:52
Normal topic Docking failure
by khanhbinh » Sun, 2012-09-23 22:19
2
3,225 by khanhbinh
Mon, 2014-04-21 06:47
Normal topic Multi-chain Modelling
by Sandy » Sun, 2015-08-09 14:41
2
4,482 by rmoretti
Tue, 2015-09-08 10:18
Normal topic Score function in protein-protein docking with constrains
by Zehui Zhou » Mon, 2023-02-06 03:31
2
1,190 by Zehui Zhou
Wed, 2023-02-15 05:40
Normal topic Why I have the different result with the same initial condition?
by mikelin » Sat, 2011-06-04 11:35
2
4,076 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
3,315 by zhisheng
Mon, 2014-04-21 06:47
Normal topic hydroxyproline patching problem
by aaj » Mon, 2016-02-22 07:33
2
3,075 by aaj
Mon, 2016-02-29 04:45
Normal topic Renumbering PDB
by jgustat » Wed, 2022-07-27 13:37
2
1,058 by jgustat
Thu, 2022-07-28 10:00
Normal topic abinitio demo is not progressing - new install
by jtpi6174 » Thu, 2022-03-24 03:49
2
1,205 by jtpi6174
Thu, 2022-03-24 09:43
Normal topic Where to find old version of Rosetta with git version number
by mao_x » Wed, 2019-08-07 01:22
2
2,525 by mao_x
Thu, 2019-08-08 01:37
Normal topic analyzing the protein protein docking without native structure
by rohi » Sun, 2020-10-11 20:42
2
1,842 by rohi
Tue, 2020-10-13 09:15
Normal topic ref2015: approx. kcal/mol or actually kJ/mol?
by matteoferla » Thu, 2021-10-07 04:04
2
2,230 by matteoferla
Thu, 2021-10-07 09:31
Normal topic redesign a enzyme by fixing the active site
by Lindsay » Wed, 2012-03-07 08:23
2
3,125 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Rosetta3.5 src/core/pack/dunbrack/RotamerLibrary.cc permission problem
by ytao » Fri, 2013-06-28 12:13
2
3,601 by ytao
Mon, 2014-04-21 06:48
Normal topic a question about protein-ligand docking in generating 1SW2 conformers
by Ryhon Wang » Wed, 2014-05-28 22:27
2
3,563 by rmoretti
Tue, 2014-06-03 11:45
Normal topic AtomPair and SPLINE
by attesor » Sat, 2015-06-20 11:42
2
3,945 by attesor
Thu, 2015-10-22 03:42
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51
2
3,155 by felipet
Sat, 2016-07-09 09:50
Normal topic Noncanonical amino acid HIP
by Victor » Fri, 2014-01-31 07:45
2
4,503 by Victor
Fri, 2014-01-31 10:41
Normal topic backbone-independent density
by SergeyP » Sun, 2016-03-20 04:57
2
2,678 by SergeyP
Thu, 2016-05-05 02:07
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36
2
2,717 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Why I_sc of Rosetta 2016.02 and 2018.21 are so different?
by eminegenetics » Mon, 2018-07-16 12:51
2
2,470 by eminegenetics
Wed, 2018-07-18 13:48
Normal topic Negative design: Can a filter call a mover in rosetta scripts?
by jgans » Sat, 2012-09-08 21:28
2
3,712 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,778 by smlewis
Mon, 2014-04-21 06:47
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11
2
3,245 by Trentage
Mon, 2014-04-21 06:47
Normal topic restricting space in a design
by ast » Tue, 2012-01-17 06:31
2
2,810 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Number of conformations needed
by JadAbbass » Sun, 2014-02-16 13:21
2
2,870 by JadAbbass
Tue, 2014-02-18 07:27
Normal topic Problem with ClashCountCalculator
by masterofpuppets » Wed, 2015-01-07 04:47
2
2,823 by rmoretti
Fri, 2015-01-09 10:59
Normal topic Error using ddg_monomer application (Assertion `pose.residue(resnum).name1() == wt` failed)
by sgaray » Thu, 2021-06-24 14:47
2
2,612 by sgaray
Fri, 2021-06-25 11:26
Normal topic Bug in Loop Modeling
by dseelig » Thu, 2010-09-23 05:55
2
2,895 by smlewis
Mon, 2014-04-21 06:47
Normal topic Selecting Top Scoring Decoys
by kalabharath » Thu, 2011-10-20 22:08
2
2,968 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to minimize only a few key residues' orientation
by Ronghai Cheng » Mon, 2018-11-05 18:37
2
2,570 by Ronghai Cheng
Tue, 2018-11-13 21:56
Normal topic The hbond for REF2015
by asbelx » Mon, 2022-06-06 06:07
2
1,201 by asbelx
Mon, 2022-06-06 23:15
Normal topic Converting all residues to poly-Gly/Ala
by jtpi6174 » Tue, 2023-05-09 14:14
2
807 by jtpi6174
Tue, 2023-05-09 15:51
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37
2
3,662 by smlewis
Mon, 2014-04-21 06:47
Normal topic Add hemes to cytochrome structures
by BuddySphinx » Sun, 2018-12-16 13:46
2
2,184 by rmoretti
Fri, 2019-03-29 14:43
Normal topic different relaxed energy scores for one same protein structure
by ivareve125 » Sun, 2023-07-16 17:54
2
675 by ivareve125
Mon, 2023-07-17 17:37
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57
2
2,650 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to recover out files when run crashs
by samuelrpita » Tue, 2015-07-28 12:54
2
3,104 by samuelrpita
Thu, 2015-08-06 14:23
Normal topic Ddg calculation for a metalloprotein using APBS
by dfcoelho » Tue, 2019-11-19 10:06
2
1,903 by dfcoelho
Wed, 2019-11-20 05:39
Normal topic Should all input structures to energy_based_clustering have an output pdb file?
by Brian Wiley » Mon, 2023-01-30 20:42
2
880 by Brian Wiley
Tue, 2023-01-31 19:08
Normal topic RosettaDesign
by ac.research » Sun, 2019-07-21 01:20
2
3,533 by ac.research
Sat, 2019-08-03 08:12
Normal topic RosettaCM: adding constraints while keeping AUTO constraints
by Michele.Bonus » Sun, 2020-08-30 10:42
2
1,903 by Michele.Bonus
Sun, 2020-08-30 23:06
Normal topic clustering PDBs from docking
by jbujons » Wed, 2024-04-24 08:34
2
213 by jbujons
Wed, 2024-04-24 09:34
Normal topic Rosetta releases and revision numbers
by ShaneOConnor » Thu, 2011-11-17 13:55
2
4,718 by smlewis
Mon, 2014-04-21 06:47
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50
2
3,658 by doranhen
Mon, 2014-04-21 06:47
Normal topic RestrictToRepackingRLT and PreventRepackingRLT
by coomteng@gmail.com » Mon, 2018-03-05 11:19
2
2,657 by coomteng@gmail.com
Tue, 2018-03-06 02:31
Normal topic Basic help with Protein-DNA and Protein-Protein modeling and engineering
by Robert Evans » Sat, 2013-08-17 12:21
2
3,928 by Robert Evans
Mon, 2014-04-21 06:48
Normal topic Can't read constraint type
by allan.ferrari » Fri, 2015-08-28 12:33
2
2,952 by allan.ferrari
Mon, 2015-09-21 21:54
Normal topic Reading chloride anions
by Martin Floor » Mon, 2018-08-27 14:29
2
2,500 by Martin Floor
Tue, 2018-08-28 13:21
Normal topic Issues with angle Constraints during Docking
by LeonhardJS » Thu, 2021-01-28 04:40
2
1,820 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic Truncating a protein using rosetta
by Wexter300 » Mon, 2023-02-13 12:05
2
802 by Wexter300
Mon, 2023-02-13 13:04
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59
2
3,739 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Parametrisation problems
by DmitriiN » Tue, 2016-05-31 09:37
2
2,565 by DmitriiN
Wed, 2016-06-01 15:46
Normal topic Modelling Sheets
by monteirotorres » Thu, 2009-07-02 11:41
2
2,951 by monteirotorres
Mon, 2014-04-21 06:47
Normal topic runtime error
by exchhattu » Wed, 2010-03-03 02:54
2
2,630 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Protein Docking Error
by ac.research » Thu, 2017-08-17 02:57
2
2,391 by ac.research
Fri, 2017-08-18 00:53
Normal topic Rosetta ab initio with disordered regions
by smiruthi » Thu, 2011-12-15 14:37
2
3,027 by smiruthi
Mon, 2014-04-21 06:47
Normal topic constraints
by lah435 » Sun, 2017-03-12 03:25
2
2,461 by lah435
Mon, 2017-04-03 19:50
Normal topic MSDMover error in RECON protocol
by yifeili1983 » Mon, 2019-04-01 00:44
2
2,060 by yifeili1983
Mon, 2019-04-15 22:34
Normal topic Is there any significant improvement of model generation in rosetta3.4 comparing to rosetta3.3?
by jiongzhang » Fri, 2012-04-20 13:35
2
2,985 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Fitting a structure with an unrecognized residue to an EM density
by ahmadkhalifa » Tue, 2017-12-05 14:44
2
2,347 by ahmadkhalifa
Wed, 2017-12-06 12:30
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39
2
1,528 by almeida85
Mon, 2021-02-08 09:50
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44
2
2,651 by ndousis
Mon, 2014-04-21 06:47
Normal topic Extracting PDBs from a Silent file: "Can't find residue type for ARG"
by avsrivatsa » Sat, 2020-10-17 16:20
2
1,917 by avsrivatsa
Mon, 2020-10-19 18:16
Normal topic PIPER-FlexPepDock protocol file apply_ftresult.py missing
by diasmarieli » Thu, 2021-11-04 06:33
2
1,718 by diasmarieli
Fri, 2021-11-26 05:11
Normal topic rna_denovo and minize_rna
by frits » Wed, 2013-07-10 00:22
2
3,202 by frits
Mon, 2014-04-21 06:48
Normal topic Chi values for side chains when switching from centroid mode
by MarkW » Fri, 2015-07-03 04:43
2
2,783 by MarkW
Fri, 2015-07-03 15:36
Normal topic SnugDock equivalent in newer Rosetta code
by SenyorDrew » Tue, 2016-03-29 09:16
2
2,836 by SenyorDrew
Wed, 2016-04-06 10:52
Normal topic where is PyIgClassfiy.py ?
by mxp » Tue, 2020-07-07 23:57
2
1,821 by mxp
Wed, 2020-07-08 23:25
Normal topic mode=release compile on a mac-pro , seg faults and bus errors
by dnasmith » Thu, 2010-09-09 16:56
2
2,607 by dnasmith
Mon, 2014-04-21 06:47
Normal topic Energy updates in Rosetta 3.3
by gipsonb » Tue, 2011-10-11 09:58
2
2,757 by gipsonb
Mon, 2014-04-21 06:47
Normal topic possible error in make_fragments.pl and fix
by DanielK » Fri, 2012-04-27 02:23
2
3,042 by DanielK
Mon, 2014-04-21 06:47
Normal topic What is a "silent file"?
by lanselibai » Mon, 2014-09-22 02:43
2
7,170 by lanselibai
Mon, 2014-09-22 08:13
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
2,344 by aneamtu
Mon, 2018-01-08 23:49
Normal topic -ignore_unrecognized_res doesn't work
by e3lm » Fri, 2022-05-06 14:47
2
1,337 by e3lm
Fri, 2022-05-06 16:10
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06
2
3,541 by vanita
Mon, 2014-04-21 06:47
Normal topic rosetta run error
by isengupta13 » Thu, 2010-06-03 19:00
2
3,213 by aminzia
Fri, 2019-07-26 13:14
Normal topic AbInitioRelax.mpi Hangs - Waiting for Job Request
by nleroy » Thu, 2019-10-31 07:30
2
2,269 by nleroy
Fri, 2019-11-08 12:44
Normal topic Which rosetta for antibody modelling?
by oppopomoz » Wed, 2013-04-24 09:10
2
3,112 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Question about CartesianMD
by orionshih » Sun, 2018-04-29 21:07
2
2,176 by orionshih
Tue, 2018-05-01 21:16
Normal topic Why does the sum of the per-residue total energy not match the whole score?
by matteoferla » Fri, 2021-07-09 08:36
2
1,746 by matteoferla
Mon, 2021-07-12 02:23
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
3,218 by einew
Mon, 2014-04-21 06:47
Normal topic ERROR:: Exit from: src/core/fragment/ConstantLengthFragSet.cc line: 116
by phanvy » Wed, 2014-10-08 22:28
2
3,147 by phanvy
Wed, 2014-10-15 21:41
Normal topic rama energy term and explicit zero
by SergeyP » Sat, 2015-12-19 05:25
2
2,977 by SergeyP
Sun, 2015-12-20 01:44
Normal topic Calibur-linux binary or source code availability?
by jasnyderjr » Sat, 2016-12-10 23:36
2
2,936 by jadolfbr
Sun, 2016-12-11 10:53
Normal topic clean_pdb.py
by duz » Wed, 2021-03-24 13:36
2
2,443 by duz
Thu, 2021-04-01 09:34
Normal topic relax with restraints
by jtmacd » Mon, 2010-11-08 09:11
2
2,934 by jtmacd
Mon, 2014-04-21 06:47
Normal topic filter score by I_sc and keep top 1000
by aaj » Tue, 2016-01-19 07:13
2
2,972 by aaj
Mon, 2016-02-22 07:43
Normal topic Different weights in the constraints for each stage of AbinitioRelax
by allan.ferrari » Sun, 2017-01-15 04:35
2
2,787 by smlewis
Sun, 2017-01-15 18:10
Normal topic Rescoring regions of structures
by erin_cutts » Mon, 2013-07-22 04:43
2
3,189 by erin_cutts
Mon, 2014-04-21 06:48
Normal topic recommended function type for cross links data
by meravb » Sun, 2018-08-05 06:57
2
2,139 by rmoretti
Mon, 2018-08-20 11:51
Normal topic Performace Benchmarking
by Tushar Kush » Wed, 2019-12-04 02:50
2
2,672 by smlewis
Wed, 2019-12-04 13:07
Normal topic Minimizing across jumps
by SenyorDrew » Thu, 2017-07-06 06:26
2
2,621 by SenyorDrew
Thu, 2017-07-06 07:48
Normal topic multi state protein design
by rohi » Fri, 2020-09-04 08:14
2
2,001 by rmoretti
Tue, 2021-02-09 13:45
Normal topic total_score changes when decomposing bb hbonds ref2015
by Liviu Copoiu » Mon, 2022-10-31 15:40
2
975 by Liviu Copoiu
Mon, 2022-10-31 16:03
Normal topic jd2 time out error
by ytao » Mon, 2013-03-04 20:47
2
2,812 by ytao
Mon, 2014-04-21 06:47
Normal topic Unable to download Rosetta
by Yair Tenorio » Mon, 2023-10-23 11:48
2
557 by Yair Tenorio
Mon, 2023-10-23 12:29
Normal topic Is CST_Design required for enzdes protocol?
by dasdevashishdas » Mon, 2018-09-03 00:51
2
2,422 by dasdevashishdas
Thu, 2018-09-27 03:35
Normal topic What is the best way to make a residue-specific SASA constraint?
by jmaly » Thu, 2020-01-23 16:40
2
2,483 by matteoferla
Wed, 2020-01-29 12:18
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