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Rosetta 3 - General

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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
2,530 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
1,834 by ahmadkhalifa
Wed, 2017-12-06 12:30
Normal topic Segfault with docking protocol
by almeida85 » Mon, 2021-02-08 06:39
2
1,007 by almeida85
Mon, 2021-02-08 09:50
Normal topic Checkpoints in Rosetta
by exchhattu » Mon, 2009-10-19 17:47
2
2,597 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Protein Docking Error
by ac.research » Thu, 2017-08-17 02:57
2
1,889 by ac.research
Fri, 2017-08-18 00:53
Normal topic Structure Prediction: Max Sequence Length?
by jcsaborio » Tue, 2009-07-14 12:10
2
3,547 by jcsaborio
Mon, 2014-04-21 06:47
Normal topic Rosetta ab initio with disordered regions
by smiruthi » Thu, 2011-12-15 14:37
2
2,602 by smiruthi
Mon, 2014-04-21 06:47
Normal topic constraints
by lah435 » Sun, 2017-03-12 03:25
2
1,949 by lah435
Mon, 2017-04-03 19:50
Normal topic MSDMover error in RECON protocol
by yifeili1983 » Mon, 2019-04-01 00:44
2
1,514 by yifeili1983
Mon, 2019-04-15 22:34
Normal topic mode=release compile on a mac-pro , seg faults and bus errors
by dnasmith » Thu, 2010-09-09 16:56
2
2,190 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
2,342 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
2,563 by DanielK
Mon, 2014-04-21 06:47
Normal topic What is a "silent file"?
by lanselibai » Mon, 2014-09-22 02:43
2
6,223 by lanselibai
Mon, 2014-09-22 08:13
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
1,848 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
562 by e3lm
Fri, 2022-05-06 16:10
Normal topic Extracting PDBs from a Silent file: "Can't find residue type for ARG"
by avsrivatsa » Sat, 2020-10-17 16:20
2
1,272 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
994 by diasmarieli
Fri, 2021-11-26 05:11
Normal topic rna_denovo and minize_rna
by frits » Wed, 2013-07-10 00:22
2
2,645 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
2,316 by MarkW
Fri, 2015-07-03 15:36
Normal topic ligand dock residue selection
by Silice » Wed, 2009-08-12 08:57
2
2,451 by frichter
Mon, 2014-04-21 06:47
Normal topic SnugDock equivalent in newer Rosetta code
by SenyorDrew » Tue, 2016-03-29 09:16
2
2,325 by SenyorDrew
Wed, 2016-04-06 10:52
Normal topic where is PyIgClassfiy.py ?
by mxp » Tue, 2020-07-07 23:57
2
1,275 by mxp
Wed, 2020-07-08 23:25
Normal topic Which rosetta for antibody modelling?
by oppopomoz » Wed, 2013-04-24 09:10
2
2,641 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Question about CartesianMD
by orionshih » Sun, 2018-04-29 21:07
2
1,664 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
998 by matteoferla
Mon, 2021-07-12 02:23
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
2,767 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
2,610 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
2,456 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
2,413 by jadolfbr
Sun, 2016-12-11 10:53
Normal topic clean_pdb.py
by duz » Wed, 2021-03-24 13:36
2
1,429 by duz
Thu, 2021-04-01 09:34
Normal topic AbInitioRelax.mpi Hangs - Waiting for Job Request
by nleroy » Thu, 2019-10-31 07:30
2
1,634 by nleroy
Fri, 2019-11-08 12:44
Normal topic Minimizing across jumps
by SenyorDrew » Thu, 2017-07-06 06:26
2
2,117 by SenyorDrew
Thu, 2017-07-06 07:48
Normal topic multi state protein design
by rohi » Fri, 2020-09-04 08:14
2
1,408 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
232 by Liviu Copoiu
Mon, 2022-10-31 16:03
Normal topic all-atom refinement with Relax application
by zwenthor » Mon, 2010-02-15 22:45
2
2,498 by zwenthor
Mon, 2014-04-21 06:47
Normal topic relax with restraints
by jtmacd » Mon, 2010-11-08 09:11
2
2,489 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
2,482 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
2,275 by smlewis
Sun, 2017-01-15 18:10
Normal topic Rescoring regions of structures
by erin_cutts » Mon, 2013-07-22 04:43
2
2,651 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
1,582 by rmoretti
Mon, 2018-08-20 11:51
Normal topic Performace Benchmarking
by Tushar Kush » Wed, 2019-12-04 02:50
2
1,829 by smlewis
Wed, 2019-12-04 13:07
Normal topic activation of filters in rosetta3.0 or later
by exchhattu » Thu, 2009-12-03 17:52
2
2,388 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Citing Rosetta3.0
by ctaylor » Fri, 2009-10-09 11:42
1
4,577 by smlewis
Mon, 2014-04-21 06:47
Normal topic rosetta@home in local PC farm
by jarod » Wed, 2010-05-05 18:31
1
1,910 by smlewis
Mon, 2014-04-21 06:47
Normal topic positive results in total_score by symmetry docking
by Jacob » Thu, 2011-06-16 05:18
1
3,133 by rmoretti
Mon, 2014-04-21 06:47
Normal topic error running rosetta3.0
by aschoenr » Wed, 2009-06-10 13:57
1
2,407 by jtmacd
Mon, 2014-04-21 06:47
Normal topic Building Rosetta PROBLEM
by nunesjulioc » Fri, 2010-02-26 06:03
1
1,722 by smlewis
Mon, 2014-04-21 06:47
Normal topic Pair potential
by jadolfbr » Thu, 2011-12-08 08:06
1
2,402 by smlewis
Mon, 2014-04-21 06:47
Normal topic Dumb question: Rosetta 3 vs Rosetta++, what's the difference?
by mintseris » Tue, 2013-12-31 13:03
1
2,258 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Running the Matcher on multiple PDBs
by Jhreed » Thu, 2016-02-18 08:50
1
1,767 by rmoretti
Sun, 2016-02-21 06:38
Normal topic [dev] not seeing energy in pose row for new energy term in design
by ipetrik_ambry » Fri, 2017-03-03 13:16
1
1,681 by ipetrik_ambry
Tue, 2017-03-14 14:09
Normal topic Denovo prediction from multiple fragment lengths
by ahmadkhalifa » Sun, 2019-03-24 03:55
1
1,118 by rmoretti
Sat, 2019-03-30 12:10
Normal topic Ligand docking: how to generate the crystal_complex.pdb with hydrogens added
by nhinguyen26 » Wed, 2020-06-17 15:03
1
1,052 by matteoferla
Sat, 2020-06-20 03:56
Normal topic FastRelax Mover with symmetry, ligand and membrane
by Michele.Bonus » Wed, 2021-05-26 04:43
1
1,012 by matteoferla
Thu, 2021-06-03 08:24
Normal topic Ensemble Docking with RosettaDock 4.0 Protocol
by mb0261 » Wed, 2022-07-27 07:00
1
425 by mb0261
Mon, 2022-09-26 07:50
Normal topic Residue not found in pose
by lzx32 » Fri, 2011-09-09 03:42
1
2,427 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Symmetric Docking (Making Trimer from Monomerics Units)
by sdg_lab » Thu, 2012-04-12 09:21
1
1,964 by rmoretti
Mon, 2014-04-21 06:47
Normal topic AtomTree::torsion_angle() can't find dof! in match and enzdes
by petrikigor » Fri, 2012-10-19 09:49
1
2,269 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Clustering and Protein Preparation for docking
by MRH » Sun, 2013-08-25 22:01
1
3,006 by rmoretti
Mon, 2014-04-21 06:48
Normal topic dock & design
by sdh_h » Fri, 2016-09-02 03:07
1
1,931 by rmoretti
Mon, 2016-09-05 09:39
Normal topic Available of some protocals mentioned in publications
by SunH » Mon, 2013-09-09 20:47
1
1,829 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Error when using next-gen KIC (Signal 6)
by janwp » Tue, 2014-08-26 08:36
1
2,566 by amelie
Tue, 2014-09-30 14:29
Normal topic Can I use next generation KIC with fragments?
by Loki01 » Thu, 2017-12-07 06:19
1
1,286 by Loki01
Wed, 2017-12-13 05:27
Normal topic Params file for Methane
by dasdevashishdas » Sun, 2018-10-07 21:34
1
1,215 by rmoretti
Mon, 2018-10-08 11:20
Normal topic Are 100 structures the maximum generated when using homology_with_end_extension (broker protocol)?
by thaisarns » Fri, 2020-02-21 05:46
1
1,020 by sheehajh
Fri, 2020-02-21 12:41
Normal topic Residue outside res_map range
by amcallister » Fri, 2022-04-22 11:26
1
403 by aneeqh
Fri, 2022-09-02 13:36
Normal topic how to do ensemble docking using rosetta3.1
by lqzhang » Mon, 2010-01-11 10:31
1
1,872 by sid
Mon, 2014-04-21 06:47
Normal topic RosettaMatch in Rosetta3.2?
by SenyorDrew » Fri, 2010-08-13 07:47
1
2,490 by smlewis
Mon, 2014-04-21 06:47
Normal topic idealization error
by albumns » Mon, 2011-02-07 01:28
1
1,866 by smlewis
Mon, 2014-04-21 06:47
Normal topic Interpreting decoy ensemble
by lah435 » Wed, 2015-06-10 10:25
1
1,689 by rmoretti
Fri, 2015-07-03 13:51
Normal topic general question about protein docking
by albumns » Mon, 2010-12-13 23:26
1
2,206 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic Generate full symmetric assembly from subsystem
by lj269 » Thu, 2011-04-28 20:04
1
2,130 by IAndre
Mon, 2014-04-21 06:47
Normal topic ratio of conformers and docking output
by pramod » Fri, 2014-12-12 12:54
1
2,001 by rmoretti
Mon, 2014-12-15 02:37
Normal topic setup_run error with multiple resonance lists
by aep » Fri, 2016-03-18 13:36
1
1,795 by rmoretti
Thu, 2016-04-28 15:49
Normal topic problems with implementing NOE constraints
by connyyu » Thu, 2019-04-11 12:37
1
1,149 by connyyu
Thu, 2019-04-18 03:26
Normal topic simple_cycpep_predict issue modifying terminal residue
by JEaston » Thu, 2020-06-25 13:15
1
1,029 by vmulligan
Mon, 2020-06-29 13:09
Normal topic Internal error while running AbinitioRelax
by Subhrodeep Saha » Sun, 2021-06-13 03:44
1
805 by rmoretti
Wed, 2021-06-23 02:17
Normal topic null rosetta energy/score
by fred » Tue, 2011-10-18 10:31
1
1,897 by fred
Mon, 2014-04-21 06:47
Normal topic which modules support MPI now?
by albumns » Fri, 2013-11-08 01:32
1
1,885 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Consistent XYZvector length() zero failure in EnzDes
by mwfranklin » Thu, 2018-11-01 12:44
1
1,320 by rmoretti
Wed, 2018-11-21 14:14
Normal topic ShapeSimilarity, ElectrostaticSimilarity (RosettaSurf)
by Ken » Mon, 2022-05-23 07:16
1
427 by ajasja
Mon, 2022-05-23 07:19
Normal topic location of define_interface.py
by rohi » Mon, 2020-10-26 19:42
1
1,038 by rmoretti
Mon, 2020-10-26 19:52
Normal topic Error in RMSD calculation when native sequence deviates
by abdullah » Tue, 2009-11-10 08:56
1
2,314 by smlewis
Mon, 2014-04-21 06:47
Normal topic Non-ideal residue detected
by cnelson » Thu, 2010-07-01 12:20
1
1,960 by smlewis
Mon, 2014-04-21 06:47
Normal topic Pairwise decomposable terms in the Rosetta energy function
by pgainza » Wed, 2011-08-03 12:26
1
3,183 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Problems in installing Rosetta3 in Red Hat Linux
by jjz2009 » Mon, 2009-08-24 19:16
1
1,895 by smlewis
Mon, 2014-04-21 06:47
Normal topic Could the Relax step be used separately ? (solved)
by wszjzhang » Tue, 2010-03-30 15:00
1
1,849 by smlewis
Mon, 2014-04-21 06:47
Normal topic ERROR: Unable to open weights.
by libai2098 » Thu, 2010-12-30 17:54
1
1,893 by smlewis
Mon, 2014-04-21 06:47
Normal topic Need help with compilation (How to test if compilation is sucessful)
by greenfur » Fri, 2012-06-29 12:29
1
2,742 by smlewis
Mon, 2014-04-21 06:47
Normal topic pdb 2 silent with ss information
by kalabharath » Sun, 2013-04-14 20:59
1
2,133 by smlewis
Mon, 2014-04-21 06:47
Normal topic non-canonical residues parametrisation
by DmitriiN » Tue, 2016-04-05 02:37
1
1,724 by rmoretti
Fri, 2016-04-08 08:43
Normal topic Library of unnatural amino acid parameters
by saxen » Mon, 2017-04-17 11:08
1
3,321 by smlewis
Tue, 2017-04-18 08:33
Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06
1
683 by lanselibai
Wed, 2021-06-23 14:53
Normal topic PDB weird to PDB rosetta friendly
by jpfuenzalidawx » Fri, 2022-09-02 04:43
1
234 by rmoretti
Tue, 2022-09-06 08:13
Normal topic Model Extraction
by mdweirna » Tue, 2010-04-13 15:28
1
1,728 by smlewis
Mon, 2014-04-21 06:47
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44
1
1,812 by rmoretti
Wed, 2015-02-18 09:19
Normal topic Some problems with the "advanced protein-protein docking" tutorial
by Sunyp_IM » Tue, 2017-06-27 09:33
1
1,556 by smlewis
Wed, 2017-06-28 06:59
Normal topic IS there any source code about protein structure prediction with only sequences information?
by ylwang » Mon, 2019-07-08 02:36
1
1,255 by rmoretti
Mon, 2019-07-08 08:05
Normal topic Extracting a part of a silent file as another silent file
by almeida85 » Wed, 2021-07-28 23:53
1
788 by zivben
Sat, 2021-07-31 08:16
Normal topic About Rosetta Scoring Function
by wszjzhang » Wed, 2010-02-03 09:22
1
2,140 by smlewis
Mon, 2014-04-21 06:47
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