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Rosetta 3 - General

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Normal topic Fragment file viewers
by MajorID » Fri, 2012-02-24 20:57 		2
 2,876 by smlewis
Mon, 2014-04-21 06:47
Normal topic Cluster application, How does it sort decoys by energy?
by Apiwat » Wed, 2014-04-16 01:52 		2
 3,039 by Apiwat
Thu, 2014-04-17 09:56
Normal topic "caught exception" for PDB with membrane "DUM" residues
by nitroamos » Wed, 2018-05-30 08:35 		2
 3,967 by Awagner7
Tue, 2020-04-28 10:51
Normal topic Creation of core.* file in current running directory
by alejandro » Tue, 2011-12-06 06:19 		2
 3,222 by alejandro
Mon, 2014-04-21 06:47
Normal topic Multigraft
by bo » Tue, 2013-12-24 18:06 		2
 3,316 by Sergey Menis
Mon, 2014-04-21 06:48
Normal topic Meaning of a couple terms?
by aloshbau » Sun, 2016-02-07 16:48 		2
 2,659 by aloshbau
Sun, 2016-02-14 20:14
Normal topic Rosetta Double changing mmCIF chain ID
by Victor Tobiasson » Thu, 2021-05-13 07:57 		2
 1,618 by Victor Tobiasson
Thu, 2021-05-13 08:33
Normal topic weird prolines with hydroxyls from fixbb.linuxgccrelease
by louisclark » Wed, 2010-08-25 15:01 		2
 2,918 by louisclark
Mon, 2014-04-21 06:47
Normal topic Having trouble producing a .pdb file from a silent output file after running abinitio relax
by burkheadlab » Wed, 2011-03-09 12:48 		2
 3,149 by burkheadlab
Mon, 2014-04-21 06:47
Normal topic Adding noncanonical amino acid (PCA) to Rosetta 3
by JuliusSu » Fri, 2014-08-01 11:23 		2
 4,176 by JuliusSu
Fri, 2014-08-08 02:07
Normal topic Intermediate file insertion
by exchhattu » Wed, 2009-09-02 18:44 		2
 2,828 by exchhattu
Mon, 2014-04-21 06:47
Normal topic error--rosetta fragment‐based refinement protocol for refinement against EM density
by gsuchunli » Thu, 2016-06-30 11:06 		2
 4,277 by rmoretti
Tue, 2016-07-12 08:18
Normal topic RosettaDOM
by ndousis » Sun, 2010-12-12 01:08 		2
 3,415 by ndousis
Mon, 2014-04-21 06:47
Normal topic is there a preferred way to enforce an hydrogen bond ?
by logandonaldson » Wed, 2013-03-20 13:14 		2
 2,925 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Fragment picker
by phanvy » Mon, 2014-12-08 04:25 		2
 3,406 by phanvy
Wed, 2014-12-10 00:17
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41 		2
 2,914 by rmoretti
Mon, 2016-03-14 07:58
Normal topic Data Check for a newb
by ac.research » Sun, 2017-03-12 23:42 		2
 2,485 by ac.research
Fri, 2017-03-31 07:36
Normal topic ERROR: Unable to open weights/patch file
by almeida85 » Tue, 2022-08-09 05:33 		2
 1,187 by almeida85
Thu, 2022-08-11 00:32
Normal topic RosettaCM: "Ligands must be added to all templates"
by lanselibai » Tue, 2021-06-22 10:42 		2
 1,403 by lanselibai
Wed, 2021-06-23 13:21
Normal topic double mutations scan
by Lindsay » Fri, 2012-04-27 12:51 		2
 3,108 by Lindsay
Mon, 2014-04-21 06:47
Normal topic Using a broker file with relax
by Al52 » Mon, 2015-11-30 20:24 		2
 2,780 by Al52
Tue, 2015-12-01 18:22
Normal topic RNA update library
by Anne Klein » Mon, 2022-05-16 16:04 		2
 1,188 by Anne Klein
Tue, 2022-05-24 21:38
Normal topic question about scoring silent output files and their contents
by burkheadlab » Wed, 2011-07-27 16:28 		2
 3,427 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Documentation missing in MultiGraft
by aroop » Thu, 2012-03-15 07:39 		2
 3,108 by aroop
Mon, 2014-04-21 06:47
Normal topic RosettaRemodel
by berk » Wed, 2013-07-10 11:21 		2
 2,926 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic Does RNA parses checkpoint matrix as well as protein
by qlj » Wed, 2014-03-05 06:03 		2
 2,998 by qlj
Thu, 2014-03-06 22:20
Normal topic metal_ions formal charge question
by lah435 » Tue, 2015-02-03 09:35 		2
 3,083 by lah435
Thu, 2015-02-12 09:16
Normal topic Can I use the relax mode application for removing clashes in a membrane protein homology model?
by doranhen » Thu, 2012-12-20 05:45 		2
 3,097 by doranhen
Mon, 2014-04-21 06:47
Normal topic force hydrogen rebuild on input
by jtmacd » Mon, 2013-11-18 08:28 		2
 3,149 by jtmacd
Mon, 2014-04-21 06:48
Normal topic Why are 'fa_rep' and 'fa_intra_rep' higher in 'ref2015_soft.wts' than in 'ref2015.wts'?
by JW_24 » Tue, 2023-01-24 04:40 		2
 991 by JW_24
Tue, 2023-01-24 14:52
Normal topic cluster input_score_filter
by lj269 » Thu, 2011-09-01 15:29 		2
 3,147 by attesor
Fri, 2014-10-31 04:23
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36 		2
 2,736 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Why I have the different result with the same initial condition?
by mikelin » Sat, 2011-06-04 11:35 		2
 4,102 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic De Novo backbone generation vs Rosetta Match for enzdes and ligand binding.
by csvajda » Thu, 2022-06-30 09:55 		2
 1,081 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
 684 by ikalvet
Mon, 2023-08-21 05:52
Normal topic Docking failure
by khanhbinh » Sun, 2012-09-23 22:19 		2
 3,250 by khanhbinh
Mon, 2014-04-21 06:47
Normal topic Multi-chain Modelling
by Sandy » Sun, 2015-08-09 14:41 		2
 4,525 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
 1,234 by Zehui Zhou
Wed, 2023-02-15 05:40
Normal topic abinitio demo is not progressing - new install
by jtpi6174 » Thu, 2022-03-24 03:49 		2
 1,236 by jtpi6174
Thu, 2022-03-24 09:43
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37 		2
 3,697 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04 		2
 3,806 by smlewis
Mon, 2014-04-21 06:47
Normal topic Where to find old version of Rosetta with git version number
by mao_x » Wed, 2019-08-07 01:22 		2
 2,571 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
 1,885 by rohi
Tue, 2020-10-13 09:15
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11 		2
 3,264 by Trentage
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
 3,336 by zhisheng
Mon, 2014-04-21 06:47
Normal topic hydroxyproline patching problem
by aaj » Mon, 2016-02-22 07:33 		2
 3,102 by aaj
Mon, 2016-02-29 04:45
Normal topic Renumbering PDB
by jgustat » Wed, 2022-07-27 13:37 		2
 1,087 by jgustat
Thu, 2022-07-28 10:00
Normal topic ref2015: approx. kcal/mol or actually kJ/mol?
by matteoferla » Thu, 2021-10-07 04:04 		2
 2,279 by matteoferla
Thu, 2021-10-07 09:31
Normal topic FARFAR2 error: no edge found that contains seqpos!
by mandar » Tue, 2024-06-18 18:39 		2
 27 by rmoretti
Thu, 2024-06-20 13:13
Normal topic harmonic_Calphas in RosettaLigand flags.txt
by cpkuntz » Wed, 2010-07-14 08:57 		2
 2,669 by smlewis
Mon, 2014-04-21 06:47
Normal topic redesign a enzyme by fixing the active site
by Lindsay » Wed, 2012-03-07 08:23 		2
 3,148 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
 3,632 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
 3,593 by rmoretti
Tue, 2014-06-03 11:45
Normal topic AtomPair and SPLINE
by attesor » Sat, 2015-06-20 11:42 		2
 3,971 by attesor
Thu, 2015-10-22 03:42
Normal topic Histidine phosphorylation by a patch
by felipet » Sat, 2016-07-09 06:51 		2
 3,184 by felipet
Sat, 2016-07-09 09:50
Normal topic Noncanonical amino acid HIP
by Victor » Fri, 2014-01-31 07:45 		2
 4,535 by Victor
Fri, 2014-01-31 10:41
Normal topic backbone-independent density
by SergeyP » Sun, 2016-03-20 04:57 		2
 2,708 by SergeyP
Thu, 2016-05-05 02:07
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59 		2
 3,759 by biofisikx
Mon, 2014-04-21 06:47
Normal topic restricting space in a design
by ast » Tue, 2012-01-17 06:31 		2
 2,836 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Number of conformations needed
by JadAbbass » Sun, 2014-02-16 13:21 		2
 2,894 by JadAbbass
Tue, 2014-02-18 07:27
Normal topic Problem with ClashCountCalculator
by masterofpuppets » Wed, 2015-01-07 04:47 		2
 2,846 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
 2,660 by sgaray
Fri, 2021-06-25 11:26
Normal topic Bug in Loop Modeling
by dseelig » Thu, 2010-09-23 05:55 		2
 2,916 by smlewis
Mon, 2014-04-21 06:47
Normal topic Selecting Top Scoring Decoys
by kalabharath » Thu, 2011-10-20 22:08 		2
 2,996 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
 2,601 by Ronghai Cheng
Tue, 2018-11-13 21:56
Normal topic The hbond for REF2015
by asbelx » Mon, 2022-06-06 06:07 		2
 1,239 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
 848 by jtpi6174
Tue, 2023-05-09 15:51
Normal topic Why I_sc of Rosetta 2016.02 and 2018.21 are so different?
by eminegenetics » Mon, 2018-07-16 12:51 		2
 2,498 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
 3,733 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Modelling Sheets
by monteirotorres » Thu, 2009-07-02 11:41 		2
 2,977 by monteirotorres
Mon, 2014-04-21 06:47
Normal topic generating 10 lowest energy structures from abinitio
by isengupta13 » Fri, 2010-05-07 11:44 		2
 2,667 by ndousis
Mon, 2014-04-21 06:47
Normal topic RosettaDesign
by ac.research » Sun, 2019-07-21 01:20 		2
 3,582 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
 1,933 by Michele.Bonus
Sun, 2020-08-30 23:06
Normal topic runtime error
by exchhattu » Wed, 2010-03-03 02:54 		2
 2,648 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Rosetta releases and revision numbers
by ShaneOConnor » Thu, 2011-11-17 13:55 		2
 4,746 by smlewis
Mon, 2014-04-21 06:47
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50 		2
 3,685 by doranhen
Mon, 2014-04-21 06:47
Normal topic Add hemes to cytochrome structures
by BuddySphinx » Sun, 2018-12-16 13:46 		2
 2,214 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
 715 by ivareve125
Mon, 2023-07-17 17:37
Normal topic How to recover out files when run crashs
by samuelrpita » Tue, 2015-07-28 12:54 		2
 3,129 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
 1,932 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
 927 by Brian Wiley
Tue, 2023-01-31 19:08
Normal topic Basic help with Protein-DNA and Protein-Protein modeling and engineering
by Robert Evans » Sat, 2013-08-17 12:21 		2
 3,961 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
 2,979 by allan.ferrari
Mon, 2015-09-21 21:54
Normal topic Reading chloride anions
by Martin Floor » Mon, 2018-08-27 14:29 		2
 2,529 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
 1,849 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic Truncating a protein using rosetta
by Wexter300 » Mon, 2023-02-13 12:05 		2
 844 by Wexter300
Mon, 2023-02-13 13:04
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06 		2
 3,564 by vanita
Mon, 2014-04-21 06:47
Normal topic rosetta run error
by isengupta13 » Thu, 2010-06-03 19:00 		2
 3,244 by aminzia
Fri, 2019-07-26 13:14
Normal topic Parametrisation problems
by DmitriiN » Tue, 2016-05-31 09:37 		2
 2,589 by DmitriiN
Wed, 2016-06-01 15:46
Normal topic RestrictToRepackingRLT and PreventRepackingRLT
by coomteng@gmail.com » Mon, 2018-03-05 11:19 		2
 2,685 by coomteng@gmail.com
Tue, 2018-03-06 02:31
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
 3,007 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
 2,372 by ahmadkhalifa
Wed, 2017-12-06 12:30
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39 		2
 1,561 by almeida85
Mon, 2021-02-08 09:50
Normal topic Protein Docking Error
by ac.research » Thu, 2017-08-17 02:57 		2
 2,420 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
 3,051 by smiruthi
Mon, 2014-04-21 06:47
Normal topic constraints
by lah435 » Sun, 2017-03-12 03:25 		2
 2,492 by lah435
Mon, 2017-04-03 19:50
Normal topic MSDMover error in RECON protocol
by yifeili1983 » Mon, 2019-04-01 00:44 		2
 2,088 by yifeili1983
Mon, 2019-04-15 22:34
Normal topic SnugDock equivalent in newer Rosetta code
by SenyorDrew » Tue, 2016-03-29 09:16 		2
 2,860 by SenyorDrew
Wed, 2016-04-06 10:52
Normal topic where is PyIgClassfiy.py ?
by mxp » Tue, 2020-07-07 23:57 		2
 1,851 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
 2,622 by dnasmith
Mon, 2014-04-21 06:47