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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
5,396 by admin
Fri, 2015-09-04 16:17
Normal topic ​​B​3​-protein design using rosettaScript movers
by straore » Mon, 2015-03-16 05:05
2
1,553 by straore
Fri, 2015-04-17 01:54
Normal topic [Mover] is not known to the MoverFactory
by Jhreed » Fri, 2016-08-05 12:23
4
2,172 by msardejani
Sun, 2016-08-07 17:49
Normal topic [dev] Using h-bonding values in new energy term
by ipetrik_ambry » Wed, 2017-03-01 11:33
4
1,681 by ipetrik_ambry
Thu, 2017-03-02 15:35
Normal topic [dev] quickest way to determine bond distance between polymeric-bonded residues in Pose/Conformation
by ipetrik_ambry » Thu, 2018-01-18 12:26
1
749 by rmoretti
Tue, 2018-01-30 08:29
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
1,018 by ipetrik_ambry
Tue, 2017-03-14 14:09
Normal topic [dev] examples for implementing setup_for_packing, prepare_rotamers_for_packing?
by ipetrik_ambry » Mon, 2017-10-30 17:03
0
468 by ipetrik_ambry
Mon, 2017-10-30 17:03
Normal topic [dev] determine which score_type's enabled in create_energy_method?
by ipetrik_ambry » Fri, 2017-10-27 15:37
3
1,079 by rmoretti
Mon, 2017-10-30 12:02
Normal topic Write PDB with multiple side-chain configurations
by pachecoj » Tue, 2014-09-30 21:42
2
1,688 by pachecoj
Thu, 2014-10-09 18:15
Normal topic Working through tutorials: expected output scorces differ from calculated results
by j.schmue » Sat, 2020-01-18 13:16
2
301 by j.schmue
Tue, 2020-01-28 13:31
Normal topic Will Rosetta Flexpepdock be adequate for this for now.?
by monos_morpheus » Wed, 2011-04-27 19:10
1
1,704 by londonir
Mon, 2014-04-21 06:47
Normal topic why not scoring function in loop model?
by albumns » Thu, 2011-01-06 00:13
1
1,449 by smlewis
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
895 by eminegenetics
Wed, 2018-07-18 13:48
Normal topic Why is it called Rosetta?
by cossio » Sun, 2016-03-13 14:28
1
978 by smlewis
Sun, 2016-03-13 15:25
Normal topic Why I have the different result with the same initial condition?
by mikelin » Sat, 2011-06-04 11:35
2
2,826 by JeffreyGray
Mon, 2014-04-21 06:47
Normal topic why energy is positive?
by albumns » Tue, 2014-12-23 00:05
3
2,342 by rmoretti
Mon, 2015-02-09 11:21
Normal topic why docking results are different?
by albumns » Sat, 2010-12-18 23:53
3
2,012 by smlewis
Mon, 2014-04-21 06:47
Normal topic Why are all source codes .gz and not .tgz
by jasnyderjr » Tue, 2016-12-20 21:23
12
4,857 by smlewis
Thu, 2016-12-22 13:11
Normal topic Which rosetta for antibody modelling?
by oppopomoz » Wed, 2013-04-24 09:10
2
1,724 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic which modules support MPI now?
by albumns » Fri, 2013-11-08 01:32
1
1,229 by rmoretti
Mon, 2014-04-21 06:48
Normal topic which make_fragments.pl
by renedominik » Mon, 2018-06-04 08:58
2
1,271 by renedominik
Sat, 2018-07-07 03:03
Normal topic Where to find old version of Rosetta with git version number
by mao_x » Wed, 2019-08-07 01:22
2
591 by mao_x
Thu, 2019-08-08 01:37
Normal topic Where is the flag -preserve_input_cb?
by mdyini » Wed, 2011-03-09 14:40
1
1,193 by smlewis
Mon, 2014-04-21 06:47
Normal topic where is PyIgClassfiy.py ?
by mxp » Tue, 2020-07-07 23:57
2
164 by mxp
Wed, 2020-07-08 23:25
Normal topic where do new .params files go?
by einew » Wed, 2011-01-05 12:09
1
1,597 by smlewis
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
1,977 by rmoretti
Sun, 2015-07-05 14:28
Normal topic What's the unit of Rosetta energy function?
by Run » Tue, 2014-06-24 00:44
1
4,130 by rmoretti
Tue, 2014-07-01 12:45
Normal topic what's the difference between recovery and sequence identity
by Lindsay » Thu, 2012-04-26 05:46
3
2,667 by smlewis
Mon, 2014-04-21 06:47
Normal topic What's a good application to thread a sequence over a peptide (of a peptide-protein complex) and minimize?
by brspurri » Tue, 2013-02-12 08:19
6
4,577 by smlewis
Mon, 2014-04-21 06:47
Normal topic what rotamer lib is used in rosetta3.5?
by Lindsay » Thu, 2014-02-06 16:11
6
3,507 by rmoretti
Fri, 2014-03-28 09:03
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
2,194 by smlewis
Mon, 2014-04-21 06:47
Normal topic what kind of focefield does Rosetta based on?
by albumns » Tue, 2010-07-06 11:08
1
1,248 by smlewis
Mon, 2014-04-21 06:47
Normal topic what is the xxx.static.linuxgccrelease?
by syoifczeri » Sat, 2015-10-31 04:09
2
3,842 by syoifczeri
Mon, 2015-11-02 03:59
Normal topic What is the total_score that relax outputs?
by cossio » Tue, 2014-12-02 13:50
4
2,774 by cossio
Thu, 2014-12-04 05:41
Normal topic what is the relationship and difference between Rosetta 3.0 and miniRosetta
by jarod » Thu, 2010-05-06 20:57
2
1,676 by jarod
Mon, 2014-04-21 06:47
Normal topic What is the general protocol for antibody-antigen docking without the native antibody-antigen structures?
by Sunyp_IM » Sun, 2017-08-13 05:42
11
3,561 by smlewis
Tue, 2017-08-29 08:56
Normal topic What is the expected behaviour when minimizing a jump edge?
by bio_james » Wed, 2017-12-13 09:13
0
444 by bio_james
Wed, 2017-12-13 09:13
Normal topic What is the different between dun08 and default dunbrack library?
by SunH » Mon, 2010-11-08 06:14
1
1,552 by smlewis
Mon, 2014-04-21 06:47
Normal topic What is the difference between F and S labeled decoys?
by PaulaBanks » Tue, 2013-08-27 06:09
3
1,872 by PaulaBanks
Mon, 2014-04-21 06:48
Normal topic What is the best way to make a residue-specific SASA constraint?
by jmaly » Thu, 2020-01-23 16:40
2
377 by matteoferla
Wed, 2020-01-29 12:18
Normal topic What is the best protocol to predict the missing residues in X-ray crystallisation?
by lanselibai » Sun, 2019-12-29 04:44
1
302 by matteoferla
Wed, 2020-01-01 04:30
Normal topic what is minirosetta
by Lindsay » Tue, 2012-04-10 07:48
2
7,697 by Lindsay
Mon, 2014-04-21 06:47
Normal topic What is a "silent file"?
by lanselibai » Mon, 2014-09-22 02:43
2
4,564 by lanselibai
Mon, 2014-09-22 08:13
Normal topic what is 05.2009 ideal coordinates
by Lindsay » Tue, 2014-09-23 20:36
3
1,864 by rmoretti
Mon, 2014-09-29 13:45
Normal topic What is "residue packing", "repacking", and so on?
by cossio » Wed, 2014-12-03 08:49
2
1,779 by cossio
Wed, 2014-12-03 14:51
Normal topic What is "repack", "prepack"?
by cossio » Wed, 2015-11-04 17:59
1
3,303 by rmoretti
Tue, 2015-11-10 11:52
Normal topic what is "-relax:sequence" ?
by Anonymous » Fri, 2012-06-08 06:31
10
5,117 by smlewis
Mon, 2014-04-21 06:47
Normal topic what factors determine the lowest (best) LigInterfaceEnergy score?
by jmaly » Wed, 2020-08-26 13:07
0
131 by jmaly
Wed, 2020-09-02 16:16
Normal topic Weird results from flexpepdock MPI
by gerdos » Fri, 2016-06-24 01:18
3
1,499 by smlewis
Thu, 2016-06-30 08:44
Normal topic weird prolines with hydroxyls from fixbb.linuxgccrelease
by louisclark » Wed, 2010-08-25 15:01
2
1,608 by louisclark
Mon, 2014-04-21 06:47
Normal topic Webinar?
by IgaK » Thu, 2009-11-19 03:26
0
911 by IgaK
Mon, 2014-04-21 06:47
Normal topic Warning when running cluster program
by Anonymous » Fri, 2012-06-15 02:39
14
6,234 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation
by jurkm » Mon, 2011-05-02 03:00
1
2,426 by smlewis
Mon, 2014-04-21 06:47
Normal topic Using rosetta 3 to make a fragment library and then use it to model loop of a protein structure
by bharat_46010 » Sun, 2011-01-23 05:22
4
5,034 by dgront
Mon, 2014-04-21 06:47
Normal topic Using Relax to asses conformational space
by glapidoth11 » Sat, 2011-07-30 05:09
2
1,735 by smlewis
Mon, 2014-04-21 06:47
Normal topic Using Patches in Rosetta
by JS » Wed, 2010-03-10 13:32
6
4,945 by JS
Mon, 2014-04-21 06:47
Normal topic Using NCAAs in protocols with native heme proteins
by htorres » Wed, 2018-01-24 08:32
2
1,025 by htorres
Mon, 2018-02-05 06:53
Normal topic Using mode=profile
by Biokhar » Fri, 2012-07-06 00:29
2
2,041 by scombs
Mon, 2014-04-21 06:47
Normal topic Using logic in resfile, Rosetta Scripts
by tsztain » Wed, 2017-03-22 13:50
1
798 by smlewis
Wed, 2017-03-22 14:02
Normal topic Using FastSAXS Scoring Protocol
by jurkm » Tue, 2011-09-20 07:40
0
1,255 by jurkm
Mon, 2014-04-21 06:47
Normal topic Using Degenerate Protons in Rosetta3.x
by jurkm » Wed, 2011-06-08 03:25
10
7,013 by jurkm
Mon, 2014-04-21 06:47
Normal topic using defined WATERS in PACKING
by ast » Wed, 2012-01-11 09:11
4
2,441 by smlewis
Mon, 2014-04-21 06:47
Normal topic Using D-amino acids in Rosetta docking
by moehle » Wed, 2011-06-01 00:49
7
5,598 by moehle
Mon, 2014-04-21 06:47
Normal topic using constraints with AbinitioRelax (Rosetta 3.1)
by ndousis » Fri, 2009-12-18 08:56
8
5,115 by ndousis
Mon, 2014-04-21 06:47
Normal topic Using a broker file with relax
by Al52 » Mon, 2015-11-30 20:24
2
1,336 by Al52
Tue, 2015-12-01 18:22
Normal topic Using 2 non-standard residues in one run
by einew » Tue, 2011-03-08 21:24
5
3,935 by einew
Mon, 2014-04-21 06:47
Normal topic use_truncated_termini not working in combination with params files
by georg » Thu, 2020-03-26 13:14
1
271 by matteoferla
Tue, 2020-04-14 03:36
Normal topic Updated publications/details on Rosetta score function?
by nitroamos » Tue, 2009-10-20 19:48
4
2,864 by rmoretti
Mon, 2015-03-30 14:43
Normal topic Unrecognized residue Glc
by cgautier » Tue, 2015-03-31 02:20
5
3,526 by rmoretti
Thu, 2015-04-16 10:09
Normal topic Unrecognized atom parameter with denovo_density
by kalabharath » Mon, 2020-06-29 06:59
0
113 by kalabharath
Mon, 2020-06-29 06:59
Normal topic Unrecognized aa NO3
by JadAbbass » Sun, 2013-07-14 10:48
3
2,596 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41
4
1,503 by linucks
Fri, 2018-02-23 08:08
Normal topic unknown constraint function type: AtomPair ?
by jiongzhang » Sun, 2012-07-15 02:13
4
2,626 by jiongzhang
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
2,396 by rmoretti
Mon, 2014-04-21 06:47
Normal topic unit and scientific tests
by tricia » Sat, 2009-05-09 23:29
1
1,155 by smlewis
Mon, 2014-04-21 06:47
Normal topic uninstalling or rebuilding rosetta
by rlwoltz » Thu, 2013-04-11 11:45
5
4,605 by rlwoltz
Mon, 2014-04-21 06:47
Closed topic unidentifiable C++ exception in both linux and window.
by wajidarshad » Tue, 2015-10-27 08:12
1
1,045 by rmoretti
Tue, 2015-10-27 08:46
Normal topic Undocumented changes in BackrubDD
by abhi_pe_acharya » Mon, 2018-07-16 00:24
2
770 by abhi_pe_acharya
Sun, 2018-08-05 22:03
Normal topic Unable to create col_complex.pdb file
by sayan500 » Tue, 2019-07-30 22:08
1
385 by rmoretti
Mon, 2019-08-26 14:52
Normal topic UBQ chemically conjugated docking error
by cheyuk » Fri, 2015-09-18 06:57
4
2,545 by cheyuk
Sun, 2015-09-20 02:08
Normal topic tyrosine structure error
by dave » Mon, 2012-04-30 04:38
1
1,304 by frichter
Mon, 2014-04-21 06:47
Normal topic Typical relax options not applied in relax.mpi.linuxiccrelease??
by David Weis » Mon, 2017-02-27 11:35
5
2,190 by rmoretti
Thu, 2017-08-03 09:01
Normal topic type of docking
by rohi » Mon, 2020-07-06 06:55
11
655 by rohi
Sun, 2020-07-26 17:03
Normal topic two questions about "Prepare structures for use in Rosetta"
by Anonymous » Wed, 2012-06-06 08:13
6
3,475 by Anonymous
Mon, 2014-04-21 06:47
Normal topic trying to create heme.params
by einew » Mon, 2011-02-28 13:33
3
2,745 by einew
Mon, 2014-04-21 06:47
Normal topic Troubles using RigidBodyTransMover and RigidBodyPerturbMover
by alejandro » Thu, 2011-04-21 06:11
3
2,274 by alejandro
Mon, 2014-04-21 06:47
Normal topic total score
by score » Mon, 2010-05-03 02:03
1
1,383 by smlewis
Mon, 2014-04-21 06:47
Normal topic Total Rama Score
by jcminerlanl » Thu, 2018-05-10 07:19
1
855 by rmoretti
Thu, 2018-06-28 14:28
Normal topic total energy score of the pdb structure
by Lindsay » Tue, 2012-05-01 12:14
4
4,280 by Lindsay
Mon, 2014-04-21 06:47
Normal topic To smlewis............parallel job submission
by anusmita_sahoo » Mon, 2010-04-19 22:28
0
949 by anusmita_sahoo
Mon, 2014-04-21 06:47
Normal topic This element is not expected.
by ac.research » Fri, 2017-10-13 03:47
6
2,521 by vmulligan
Thu, 2020-07-16 23:31
Normal topic The vall.jul19.2011.gz Database
by ac.research » Fri, 2017-09-01 02:29
4
2,027 by ac.research
Mon, 2017-09-04 16:43
Normal topic The question about  protonation of Rosetta
by asbelx » Tue, 2017-12-19 05:44
3
1,602 by rmoretti
Mon, 2018-01-15 15:34
Normal topic The question about FavorNativeResidue
by asbelx » Fri, 2019-04-12 20:02
1
506 by rmoretti
Tue, 2019-07-09 15:57
Normal topic the problem in making fragments
by croshong » Thu, 2009-12-03 17:15
1
1,514 by smlewis
Mon, 2014-04-21 06:47
Normal topic the output of ligand docking
by phanvy » Fri, 2015-07-03 01:27
1
1,139 by rmoretti
Fri, 2015-07-03 13:14
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37
2
2,100 by smlewis
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
2,228 by jrcf
Fri, 2015-10-16 10:57
Normal topic The design of a helical peptide
by Jacob-kong » Tue, 2012-06-26 06:26
6
5,293 by Jacob-kong
Mon, 2014-04-21 06:47
Normal topic The concept of unsatisfied hydrogen bond
by asbelx » Wed, 2018-04-25 01:32
2
970 by asbelx
Thu, 2018-04-26 00:23

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