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Rosetta 3 - General

Topic / Topic starter Repliessort ascending Views Last post
Normal topic Cluster gdtmm vs. rmsd
by brspurri » Thu, 2012-04-19 08:19 		2
 4,055 by rmoretti
Mon, 2014-04-21 06:47
Normal topic The following options have been set but have not yet been used
by jrcf » Fri, 2015-10-09 10:48 		2
 3,953 by jrcf
Fri, 2015-10-16 10:57
Normal topic RifDock building error on Ubuntu 20.04，please help！
by guowuchen » Mon, 2022-03-28 03:53 		2
 1,966 by guowuchen
Wed, 2022-03-30 04:20
Normal topic -fake_native Error - not found in command line of rosetta 3.2.1
by vsjasion » Wed, 2011-10-05 12:01 		2
 3,441 by vsjasion
Mon, 2014-04-21 06:47
Normal topic mutate residue at termini
by jarek » Fri, 2013-09-13 09:24 		2
 3,865 by jarek
Mon, 2014-04-21 06:48
Normal topic Cannot create cst files from upl files
by road runner » Wed, 2015-11-11 22:07 		2
 2,883 by road runner
Tue, 2015-12-01 10:08
Normal topic keep crystal structure hydrogens
by gw » Wed, 2011-07-20 03:54 		2
 3,374 by gw
Mon, 2014-04-21 06:47
Normal topic How to remove clashes in peptide bonds and proline residue?
by Anatol » Fri, 2012-08-31 09:26 		2
 3,197 by Anatol
Mon, 2014-04-21 06:47
Normal topic Interface energy vs binding energy
by Apiwat » Wed, 2014-02-05 00:47 		2
 6,434 by Apiwat
Sat, 2014-02-08 01:41
Normal topic Checkpoints in Rosetta
by exchhattu » Mon, 2009-10-19 17:47 		2
 3,184 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Explanation of constraint functions?
by aloshbau » Mon, 2015-12-14 22:38 		2
 2,595 by aloshbau
Mon, 2015-12-14 23:30
Normal topic error in mol2 to params conversion for GAliganddocking
by jalan » Wed, 2020-04-22 06:08 		2
 1,996 by jalan
Thu, 2020-04-23 05:19
Normal topic Chain name being read as residue
by MarkusAurelius » Mon, 2021-03-22 11:19 		2
 1,502 by MarkusAurelius
Mon, 2021-03-29 09:06
Normal topic score.sc only shows total_score and with all zeros
by johnnytam100 » Mon, 2022-06-06 20:04 		2
 1,069 by johnnytam100
Tue, 2022-06-07 19:18
Normal topic Calculating SAP score using RosettaScripts
by varunmc99 » Fri, 2023-05-12 11:03 		2
 1,054 by varunmc99
Fri, 2023-05-12 11:49
Normal topic Structure Prediction: Max Sequence Length?
by jcsaborio » Tue, 2009-07-14 12:10 		2
 4,152 by jcsaborio
Mon, 2014-04-21 06:47
Normal topic constrain files tutorial
by knutjbj » Fri, 2011-02-18 23:57 		2
 2,829 by smlewis
Mon, 2014-04-21 06:47
Normal topic ERROR: filtered_alignments.size() > 0
by jhbrown » Tue, 2012-01-17 13:28 		2
 2,613 by jhbrown
Mon, 2014-04-21 06:47
Normal topic Fix missing backbone residues
by Matthys » Mon, 2010-05-03 09:03 		2
 3,778 by Matthys
Mon, 2014-04-21 06:47
Normal topic Error running design in 3.4
by inder » Thu, 2012-07-05 19:27 		2
 3,629 by inder
Mon, 2014-04-21 06:47
Normal topic smoothly kill a mpirun process
by fred » Tue, 2014-02-18 06:06 		2
 5,441 by Ashafix
Wed, 2014-02-19 06:53
Normal topic Good baseline settings for side chain packing
by pachecoj » Tue, 2015-01-13 19:25 		2
 4,434 by rmoretti
Wed, 2015-01-21 10:05
Normal topic rosetta compile
by MA » Wed, 2017-04-26 00:46 		2
 2,377 by MA
Thu, 2017-04-27 18:53
Normal topic Fold tree error
by mansi » Tue, 2010-05-18 07:43 		2
 4,020 by mansi
Mon, 2014-04-21 06:47
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34 		2
 4,255 by Jeffrey_Chen
Tue, 2014-03-25 23:06
Normal topic Free FSC score for validating refinement
by ahmadkhalifa » Thu, 2018-05-10 05:53 		2
 2,563 by ahmadkhalifa
Fri, 2018-06-29 07:54
Normal topic Predict the N-terminal of a protein
by aliaselin » Mon, 2010-11-08 03:23 		2
 2,691 by smlewis
Mon, 2014-04-21 06:47
Normal topic No structure mods allowed during scoring! error
by jadolfbr » Wed, 2013-12-04 14:06 		2
 3,340 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic ligand dock residue selection
by Silice » Wed, 2009-08-12 08:57 		2
 3,006 by frichter
Mon, 2014-04-21 06:47
Normal topic Peptide building
by berk » Thu, 2015-07-30 06:53 		2
 3,087 by rmoretti
Thu, 2015-08-06 09:21
Normal topic disulfide bridges in loop modeling
by pledor » Fri, 2010-08-06 06:49 		2
 3,322 by pledor
Mon, 2014-04-21 06:47
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
 2,661 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 Connecting 2 Domains Via Non-Flexible Linker
by jurkm » Mon, 2011-09-05 06:10 		2
 5,948 by kbuhr
Tue, 2015-07-14 04:30
Normal topic Symmetric Processing for evaluating side-chain of chi angle
by qlj » Wed, 2012-10-10 04:08 		2
 3,077 by smlewis
Mon, 2014-04-21 06:47
Normal topic minimum number of nstruct to build at 65% homolgy
by MRH » Thu, 2013-08-22 07:29 		2
 3,141 by MRH
Mon, 2014-04-21 06:48
Normal topic Working through tutorials: expected output scorces differ from calculated results
by j.schmue » Sat, 2020-01-18 13:16 		2
 1,933 by j.schmue
Tue, 2020-01-28 13:31
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 activation of filters in rosetta3.0 or later
by exchhattu » Thu, 2009-12-03 17:52 		2
 2,897 by exchhattu
Mon, 2014-04-21 06:47
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
 2,916 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 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 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
 2,782 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 Cluster Error
by justin » Mon, 2010-04-26 00:06 		2
 3,017 by justin
Mon, 2014-04-21 06:47
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 Building Rosetta 3.1 for cs-Rosetta
by zdn3023 » Fri, 2010-02-26 14:31 		2
 3,127 by zdn3023
Mon, 2014-04-21 06:47
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 what is the relationship and difference between Rosetta 3.0 and miniRosetta
by jarod » Thu, 2010-05-06 20:57 		2
 3,002 by jarod
Mon, 2014-04-21 06:47
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 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 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 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
 3,104 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 make_fragments
by ctaylor » Mon, 2009-09-21 12:41 		2
 3,057 by ctaylor
Mon, 2014-04-21 06:47
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 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 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
 3,186 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
 2,710 by SergeyP
Thu, 2016-05-05 02:07
Normal topic Problems in Loop Modeling
by jklett » Mon, 2009-10-19 07:26 		2
 3,394 by jklett
Mon, 2014-04-21 06:47
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 restricting space in a design
by ast » Tue, 2012-01-17 06:31 		2
 2,836 by rmoretti
Mon, 2014-04-21 06:47