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Rosetta 3 - General

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Normal topic Abinitio starts at the 27th amino acid
by JadAbbass » Thu, 2013-08-29 05:38
3
3,875 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic what option should I use if I want to use the dfire in 3.4
by Lindsay » Thu, 2012-04-12 05:19
3
3,867 by smlewis
Mon, 2014-04-21 06:47
Normal topic energy units
by jtmacd » Mon, 2009-07-06 10:39
1
3,864 by smlewis
Mon, 2014-04-21 06:47
Normal topic [dev] Using h-bonding values in new energy term
by ipetrik_ambry » Wed, 2017-03-01 11:33
4
3,857 by ipetrik_ambry
Thu, 2017-03-02 15:35
Normal topic ERROR: f.check_fold_tree
by sudhar » Mon, 2010-08-23 08:59
3
3,849 by smlewis
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,835 by smlewis
Mon, 2014-04-21 06:47
Normal topic Multi-state design with the error "unable to locate database file"
by yifeili1983 » Sun, 2019-03-31 18:30
1
3,831 by rmoretti
Wed, 2019-04-03 09:31
Normal topic Troubles using RigidBodyTransMover and RigidBodyPerturbMover
by alejandro » Thu, 2011-04-21 06:11
3
3,826 by alejandro
Mon, 2014-04-21 06:47
Normal topic I got the message "ERROR: Residue names must be unique!".
by monos_morpheus » Sun, 2011-02-06 03:55
2
3,819 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic Rosetta can't handle symmetric fold and dock for >10-subunit protein?
by myang » Mon, 2011-09-26 11:52
3
3,814 by IAndre
Mon, 2014-04-21 06:47
Normal topic Fix missing backbone residues
by Matthys » Mon, 2010-05-03 09:03
2
3,814 by Matthys
Mon, 2014-04-21 06:47
Normal topic Only 430 models are generated for membrane prediction
by justin » Wed, 2010-01-06 00:04
3
3,802 by smlewis
Mon, 2014-04-21 06:47
Normal topic Docking 2 proteins including ligands
by einew » Tue, 2011-03-08 13:33
3
3,795 by einew
Mon, 2014-04-21 06:47
Normal topic homo-oligomeric proteins.............folddock+symmetry+abinito
by anusmita_sahoo » Thu, 2010-04-29 02:59
2
3,792 by biofisikx
Mon, 2014-04-21 06:47
Normal topic Iterative local rebuilding vs automated structure refinement
by ahmadkhalifa » Fri, 2018-09-14 07:44
4
3,789 by rmoretti
Wed, 2018-11-21 14:11
Normal topic first run of abinitio in rosetta 3.2 produces an error right away
by burkheadlab » Fri, 2011-03-04 22:50
3
3,773 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop modeling FLAGS
by jklett » Fri, 2009-12-04 02:45
3
3,772 by jklett
Mon, 2014-04-21 06:47
Normal topic Negative design: Can a filter call a mover in rosetta scripts?
by jgans » Sat, 2012-09-08 21:28
2
3,766 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Is it CS-HM Rosetta restraint derivation i.e cm_scripts in Rosetta 3.3 bundles?
by nh_prt » Tue, 2013-03-26 12:22
3
3,748 by smlewis
Mon, 2014-04-21 06:47
Normal topic AnchoredPDBcreator
by spraha » Wed, 2012-03-14 23:34
3
3,742 by smlewis
Mon, 2014-04-21 06:47
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37
2
3,735 by smlewis
Mon, 2014-04-21 06:47
Normal topic error when running beta_strand_homodimer_design
by szypanther » Sun, 2014-05-25 20:22
2
3,735 by szypanther
Mon, 2014-05-26 22:03
Normal topic Parallel computing in RosettaDock3.1?
by xhluo » Fri, 2010-09-03 02:31
3
3,728 by smlewis
Mon, 2014-04-21 06:47
Normal topic Models which are not recorded (Abinitio protocol)
by allan.ferrari » Fri, 2015-08-28 13:39
3
3,727 by rmoretti
Thu, 2015-09-17 12:42
Normal topic Rosetta numbering with missing occupancies
by ShaneOConnor » Fri, 2011-10-07 16:18
2
3,727 by ShaneOConnor
Mon, 2014-04-21 06:47
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31
3
3,722 by rmoretti
Mon, 2014-04-21 06:48
Normal topic what is 05.2009 ideal coordinates
by Lindsay » Tue, 2014-09-23 20:36
3
3,718 by rmoretti
Mon, 2014-09-29 13:45
Normal topic Question about run FLEXPEPDOCK with 3 chain
by phanvy » Wed, 2014-07-02 08:46
3
3,716 by phanvy
Wed, 2014-07-02 23:32
Normal topic NOE constraints with Rosetta 3.1
by mpiuzzi » Wed, 2010-02-24 02:40
3
3,714 by mpiuzzi
Mon, 2014-04-21 06:47
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50
2
3,713 by doranhen
Mon, 2014-04-21 06:47
Normal topic When does Rosetta switch from centroid to FA mode?
by MarkW » Fri, 2015-07-03 04:48
3
3,712 by rmoretti
Sun, 2015-07-05 14:28
Normal topic interpreting score values in silent output file after running abinitiorelax
by burkheadlab » Wed, 2011-03-09 15:42
3
3,709 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaDesign
by ac.research » Sun, 2019-07-21 01:20
2
3,701 by ac.research
Sat, 2019-08-03 08:12
Normal topic Loop Modelling: ERROR: switch_to_residue_type_set fails
by smiruthi » Wed, 2012-07-18 14:48
2
3,698 by smlewis
Mon, 2014-04-21 06:47
Normal topic rosettaScore.py has a typo, I think. Can I fix it in my own copy?
by mdeklotz » Thu, 2018-08-02 15:15
4
3,694 by rmoretti
Fri, 2018-08-03 11:39
Normal topic Silent Files
by ctaylor » Tue, 2009-12-22 09:22
3
3,691 by smlewis
Mon, 2014-04-21 06:47
Normal topic combine silent.out file
by venkatazb » Fri, 2016-07-22 05:22
1
3,691 by smlewis
Fri, 2016-07-22 07:31
Normal topic # decoys of silent
by fred » Wed, 2014-04-02 06:00
3
3,682 by fred
Fri, 2014-04-04 11:34
Normal topic Rosetta3.5 src/core/pack/dunbrack/RotamerLibrary.cc permission problem
by ytao » Fri, 2013-06-28 12:13
2
3,679 by ytao
Mon, 2014-04-21 06:48
Normal topic Can I compare binding affinity of different ligands using Rosetta?
by zg148119@ohio.edu » Sun, 2020-12-06 11:30
4
3,679 by nannemdp
Fri, 2021-02-05 06:49
Normal topic symmetric Docking- TRIMER in Rosetta 3.4 ?
by sdg_lab » Thu, 2012-04-12 04:22
1
3,671 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Rosetta CM round_thread.pdb doesn't exist and can't find pose (id = round)
by ahmadkhalifa » Wed, 2018-05-23 09:51
2
3,667 by rmoretti
Thu, 2018-06-28 14:09
Normal topic Abinitio Video
by ac.research » Tue, 2017-09-12 04:00
3
3,663 by ac.research
Sun, 2017-09-24 11:25
Normal topic Cluster gdtmm vs. rmsd
by brspurri » Thu, 2012-04-19 08:20
1
3,661 by rmoretti
Mon, 2014-04-21 06:47
Normal topic MET, MSE, and fMET Amino Acids
by ac.research » Sat, 2017-11-18 06:33
1
3,659 by smlewis
Sun, 2017-11-19 20:08
Normal topic Handling peptide with noncanonical aminoacids
by tigerous » Sat, 2013-12-28 17:16
1
3,658 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Loop Modeling
by ctaylor » Fri, 2009-12-18 11:42
3
3,657 by ctaylor
Mon, 2014-04-21 06:47
Normal topic ddG = dGmutant ‐ dGwildtype
by ela » Thu, 2018-07-26 09:17
3
3,654 by ela
Thu, 2018-08-09 08:04
Normal topic What is the difference between F and S labeled decoys?
by PaulaBanks » Tue, 2013-08-27 06:09
3
3,651 by PaulaBanks
Mon, 2014-04-21 06:48
Normal topic Error running design in 3.4
by inder » Thu, 2012-07-05 19:27
2
3,651 by inder
Mon, 2014-04-21 06:47
Normal topic why docking results are different?
by albumns » Sat, 2010-12-18 23:53
3
3,651 by smlewis
Mon, 2014-04-21 06:47
Normal topic secondary structure prediction for generation of fragment libraries
by xpzhang » Sat, 2011-06-25 00:47
1
3,649 by smlewis
Mon, 2014-04-21 06:47
Normal topic CDR Cluster Constrained Relax Equivalent
by SenyorDrew » Wed, 2016-04-27 08:04
3
3,646 by SenyorDrew
Tue, 2016-06-14 06:43
Normal topic Comparative Modeling Tutorial Script not working
by Srinivas23 » Thu, 2017-09-21 12:00
4
3,645 by Srinivas23
Tue, 2017-10-24 10:58
Normal topic Can I thread a two chained structure in RosettaCM?
by ahmadkhalifa » Mon, 2018-01-08 09:41
3
3,643 by aaxx
Wed, 2019-11-06 01:44
Normal topic Pairwise decomposable terms in the Rosetta energy function
by pgainza » Wed, 2011-08-03 12:26
1
3,635 by rmoretti
Mon, 2014-04-21 06:47
Normal topic a question about protein-ligand docking in generating 1SW2 conformers
by Ryhon Wang » Wed, 2014-05-28 22:27
2
3,633 by rmoretti
Tue, 2014-06-03 11:45
Normal topic should rosetta3.1 do prepacking before docking?
by lqzhang » Thu, 2010-01-07 12:15
3
3,632 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rosetta remodel on intel Xeon Phi
by pablogalazdavison » Wed, 2016-09-14 15:35
3
3,629 by pablogalazdavison
Thu, 2016-09-15 16:36
Normal topic positive results in total_score by symmetry docking
by Jacob » Thu, 2011-06-16 05:18
1
3,613 by rmoretti
Mon, 2014-04-21 06:47
Normal topic sequence_tolerance optimize the binding to chemical compounds
by coomteng@gmail.com » Tue, 2015-05-05 07:32
3
3,610 by rmoretti
Mon, 2015-05-25 11:00
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
3,607 by rmoretti
Wed, 2014-12-03 18:52
Normal topic protein ligand docking
by patrickchirdon » Sun, 2018-12-30 15:07
4
3,606 by smlewis
Mon, 2018-12-31 08:58
Normal topic obtaing pdb files
by knutjbj » Fri, 2011-02-25 11:05
3
3,598 by scombs
Mon, 2014-04-21 06:47
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06
2
3,596 by vanita
Mon, 2014-04-21 06:47
Normal topic fixbb program
by Lindsay » Tue, 2012-05-08 13:56
3
3,595 by AndrewLeaver-Fay
Mon, 2014-04-21 06:47
Normal topic Molecular oxygen
by matteoferla » Sat, 2018-02-24 06:05
3
3,591 by matteoferla
Mon, 2018-02-26 02:05
Normal topic Rosetta Design Stalling
by Jhreed » Sun, 2016-03-06 14:38
3
3,578 by rmoretti
Mon, 2016-03-07 14:20
Normal topic Error score_scatter_plot.py
by jrcf » Wed, 2015-12-30 05:46
2
3,570 by jrcf
Fri, 2016-02-12 16:41
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56
3
3,569 by smlewis
Fri, 2016-07-29 07:43
Normal topic which make_fragments.pl
by renedominik » Mon, 2018-06-04 08:58
2
3,569 by renedominik
Sat, 2018-07-07 03:03
Normal topic Installing Rosetta Abinitio make_fragments.pl
by ctaylor » Thu, 2009-09-17 09:20
2
3,556 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Clustering and Protein Preparation for docking
by MRH » Sun, 2013-08-25 22:01
1
3,545 by rmoretti
Mon, 2014-04-21 06:48
Normal topic The concept of unsatisfied hydrogen bond
by asbelx » Wed, 2018-04-25 01:32
2
3,543 by asbelx
Thu, 2018-04-26 00:23
Normal topic Error when clustering the output from a docking study
by jos » Thu, 2011-09-08 03:26
2
3,539 by jos
Mon, 2014-04-21 06:47
Normal topic ERROR: Unable to open file: ./1brs_0001.pdb
by dkeidel » Tue, 2009-09-29 17:46
1
3,531 by smlewis
Mon, 2014-04-21 06:47
Normal topic rosettaremodel
by berk » Fri, 2013-06-07 00:42
3
3,524 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic how to use backrub in rosetta3.1
by lqzhang » Mon, 2010-01-11 14:43
3
3,523 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaCM density guided rebuilding methodology
by ahmadkhalifa » Thu, 2018-08-30 06:45
4
3,503 by ahmadkhalifa
Thu, 2018-08-30 23:09
Normal topic How do I add virtual atom to my cofactor (metal ion) in rosettadock?
by monos_morpheus » Sat, 2011-02-05 21:24
2
3,499 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic No RMS and IRMS values in protein/nucleic acid docking
by rbeier1 » Wed, 2016-01-13 12:41
2
3,493 by smlewis
Thu, 2016-01-14 08:19
Normal topic sequence_tolerance is very slow when -ms:num_packs > 1
by coomteng@gmail.com » Thu, 2016-08-25 13:17
3
3,492 by coomteng@gmail.com
Fri, 2016-08-26 00:01
Normal topic rama vs p_aa_pp vs ref score terms
by jharamesh » Thu, 2015-12-03 14:24
1
3,490 by rmoretti
Thu, 2015-12-03 15:14
Normal topic ddG from backrub
by jte » Tue, 2010-10-05 14:09
3
3,480 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaDesign Server, reproducing optimized interface conformation
by AlexanderMetz » Thu, 2012-02-09 10:41
1
3,480 by smlewis
Mon, 2014-04-21 06:47
Normal topic about the option -constraints:cst_fa_file & -constraints:cst_fa_weight
by jiongzhang » Sat, 2010-12-25 12:55
1
3,479 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problem with protein and ligand preparation before ligand docking.
by zg148119@ohio.edu » Fri, 2021-02-05 06:47
3
3,471 by rmoretti
Tue, 2021-02-09 09:22
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06
3
3,469 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic relax NOT CONVERGED
by albumns » Thu, 2010-06-24 21:25
3
3,466 by smlewis
Mon, 2014-04-21 06:47
Normal topic Unknow atom_name: LYS 1HZ in enzdes after match
by petrikigor » Fri, 2012-10-19 09:35
1
3,466 by rmoretti
Mon, 2014-04-21 06:47
Normal topic -fake_native Error - not found in command line of rosetta 3.2.1
by vsjasion » Wed, 2011-10-05 12:01
2
3,465 by vsjasion
Mon, 2014-04-21 06:47
Normal topic question about scoring silent output files and their contents
by burkheadlab » Wed, 2011-07-27 16:28
2
3,452 by rmoretti
Mon, 2014-04-21 06:47
Normal topic RosettaDOM
by ndousis » Sun, 2010-12-12 01:08
2
3,448 by ndousis
Mon, 2014-04-21 06:47
Normal topic Fragment picker
by phanvy » Mon, 2014-12-08 04:25
2
3,442 by phanvy
Wed, 2014-12-10 00:17
Normal topic Design constraints on pairs of residues
by SenyorDrew » Mon, 2017-10-02 07:25
3
3,439 by SenyorDrew
Mon, 2017-11-13 11:44
Normal topic Creating new residue type for pyridoxal phosphate bound to lysine (LLP) [Solved]
by franfdez » Sat, 2012-01-28 11:39
1
3,438 by franfdez
Mon, 2014-04-21 06:47
Normal topic Ca-RMSD
by jrcf » Mon, 2016-02-29 16:39
2
3,435 by jrcf
Tue, 2016-05-03 17:40
Normal topic Homology Model gives output - but completely wrong!
by Julix » Wed, 2012-10-31 10:10
1
3,429 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Combine flags file with command line arguments?
by cossio » Mon, 2014-12-22 13:52
1
3,427 by smlewis
Tue, 2014-12-23 13:58
Normal topic Explanations to membrane_abinitio options
by justin » Wed, 2010-02-10 01:14
3
3,427 by justin
Mon, 2014-04-21 06:47
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