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Rosetta 3 - Applications

Topic / Topic startersort descending Replies Views Last post
Normal topic Symmetry definition for apolar helix
by vanrooyenjason » Tue, 2016-01-05 05:20
1
3,170 by rmoretti
Fri, 2016-04-29 09:21
Normal topic Symmetry definition for coiled-coil dimer and trimer
by kszczepaniak » Fri, 2013-10-11 05:33
2
5,698 by kszczepaniak
Mon, 2014-04-21 06:48
Normal topic Symmetry definition question
by mrconde96 » Sun, 2022-10-02 05:34
0
1,336 by mrconde96
Sun, 2022-10-02 05:34
Normal topic Symmetry Docking and Clustering with Ligands
by skovacs » Wed, 2012-03-07 16:46
9
11,608 by Anonymous
Mon, 2014-04-21 06:47
Normal topic Symmetry mode in Remodel for N-terminal extension
by yvonne.chan2 » Mon, 2019-11-04 13:41
0
1,225 by yvonne.chan2
Mon, 2019-11-04 13:41
Normal topic Symmetry-aware Backrub?
by gamacy » Fri, 2014-11-14 02:18
1
2,184 by rmoretti
Tue, 2014-11-18 09:10
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32
2
5,117 by lanselibai
Thu, 2014-11-20 02:15
Hot topic Syntax for relax.linuxgccrelease
by lanselibai » Wed, 2014-09-24 04:34
18
24,099 by lanselibai
Tue, 2014-12-02 09:46
Normal topic Syntax for the alignment file in "minirosetta comparative modeling"
by lanselibai » Thu, 2014-10-16 15:29
3
4,543 by lanselibai
Thu, 2014-10-23 03:26
Normal topic Syntax to build a silent file
by lanselibai » Fri, 2014-09-26 09:13
8
9,851 by lanselibai
Tue, 2014-09-30 03:45
Normal topic Syntax to extract PDB files from a silent file
by lanselibai » Fri, 2014-09-26 13:48
1
3,907 by lanselibai
Fri, 2014-09-26 14:58
Normal topic Template/Input length mismatch error during RosettaCM
by marinok » Mon, 2020-05-04 13:12
4
2,664 by marinok
Mon, 2020-05-11 12:48
Normal topic terminal amino acids of gap has incomplete valency
by malkeet.singh » Wed, 2017-11-29 05:20
6
4,424 by rmoretti
Fri, 2017-12-01 12:05
Normal topic The confussion about an example in tutorial in Rosetta Virtual Workshop 2020
by ldx022 » Tue, 2022-11-29 04:58
3
4,291 by ldx022
Tue, 2022-11-29 08:38
Normal topic the ddg of mutant is same as the wt
by deepanshuiitb » Wed, 2015-03-04 11:56
6
6,655 by jadolfbr
Tue, 2015-04-07 10:50
Normal topic The difference between the H1 regions of modeled camelid antibody and the crystal structure.
by Sunyp_IM » Sun, 2020-06-07 02:34
1
1,311 by nannemdp
Sun, 2020-06-07 08:01
Normal topic The energy terms in InterfaceAnalyzer
by Sunyp_IM » Tue, 2021-11-02 18:43
2
1,418 by zivben
Sat, 2021-11-13 04:49
Normal topic the extracted pdb file
by benniu2004 » Fri, 2013-01-04 17:55
12
13,731 by benniu2004
Mon, 2014-04-21 06:47
Normal topic the flexpepdock refinement and ab-initio
by tfliu » Mon, 2013-12-23 19:17
6
6,360 by tfliu
Mon, 2014-04-21 06:48
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46
2
4,541 by libai2098
Mon, 2014-04-21 06:47
Normal topic The problems on pdb renumbering
by Sunyp_IM » Sun, 2017-08-20 06:39
0
2,161 by Sunyp_IM
Sun, 2017-08-20 06:39
Normal topic The question about ligand score function
by asbelx » Sun, 2018-06-17 02:07
2
3,195 by asbelx
Mon, 2018-06-18 22:34
Normal topic The question of ligand docking with constraints
by asbelx » Mon, 2018-06-11 09:39
3
3,173 by rmoretti
Thu, 2018-06-28 12:58
Normal topic The relax qustion of Rosetta VIP
by asbelx » Mon, 2019-06-10 07:52
1
1,422 by rmoretti
Mon, 2019-06-24 14:42
Normal topic the results obtained after docking using RosettaDock and ZDOCK
by aha » Thu, 2024-01-04 21:13
1
215 by rmoretti
Thu, 2024-01-11 14:39
Normal topic The usage of antibody_H3.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 22:50
2
1,927 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic The Usage of motifgraft
by Sunyp_IM » Sun, 2017-11-19 20:22
2
3,363 by Sunyp_IM
Mon, 2017-11-20 19:20
Normal topic Thread target sequence
by duz » Thu, 2021-04-01 10:09
4
2,085 by duz
Mon, 2021-05-03 07:50
Normal topic Threading a sequence onto a template with ligands/metal ions included
by ajkal » Wed, 2017-04-19 11:53
3
3,572 by ahmadkhalifa
Sun, 2019-03-31 23:27
Normal topic Threading with Ligand
by ekwan » Thu, 2018-12-06 15:10
1
1,560 by rmoretti
Fri, 2019-03-29 13:21
Normal topic to create the template pdb file
by benniu2004 » Sat, 2012-12-29 23:04
8
8,594 by benniu2004
Mon, 2014-04-21 06:47
Normal topic too many constraints result in no output pose
by Yao Wu » Sun, 2012-11-18 23:45
5
6,079 by smlewis
Mon, 2014-04-21 06:47
Normal topic Topobuilder segmentation fault
by tatsiana.bylund » Mon, 2021-08-09 07:10
0
1,169 by tatsiana.bylund
Mon, 2021-08-09 07:10
Normal topic Total score problems with high-res ddg_monomer
by jklesmith » Tue, 2015-03-10 15:54
2
3,565 by jennifer
Fri, 2015-03-27 05:56
Normal topic Translate mover chain X doesnot exist.
by surya » Thu, 2020-07-09 08:36
6
3,299 by rmoretti
Tue, 2020-07-14 10:54
Normal topic Transmembrane helix fold-and-dock?
by sarah_b » Tue, 2020-05-12 02:09
3
2,262 by jkleman
Tue, 2020-05-19 15:02
Normal topic Trehalose
by jpfuenzalidawx » Thu, 2022-09-08 00:49
0
820 by jpfuenzalidawx
Thu, 2022-09-08 00:49
Normal topic Trouble enforcing a disulfide in loop building
by chelsell » Sun, 2015-05-10 16:31
2
3,662 by chelsell
Wed, 2015-05-27 14:36
Normal topic trouble in floppytail modelling
by ytao » Thu, 2013-06-27 13:15
1
2,436 by ytao
Mon, 2014-04-21 06:48
Normal topic Trouble running Enzyme Design application
by danaitop » Thu, 2016-08-11 13:34
2
2,765 by rmoretti
Mon, 2016-09-05 11:10
Normal topic Trouble running MPI docking protocol, please help!
by Rob_Barringer » Tue, 2020-08-18 06:40
2
2,696 by Rob_Barringer
Fri, 2020-09-25 05:45
Normal topic trRosetta - Nan occuring in Hbond calculation
by y_atsmonraz » Mon, 2021-10-04 09:16
1
1,125 by shivarawat115
Mon, 2022-04-11 16:10
Normal topic trRosetta protocol Segmentation Fault
by nc-ring » Wed, 2021-04-28 11:57
5
2,626 by nc-ring
Tue, 2021-05-04 12:26
Normal topic Two questions on the RosettaScripts flexbb-interfacedesign.xml
by johnnytam100 » Fri, 2019-03-15 04:54
1
1,673 by rmoretti
Fri, 2019-03-29 09:58
Normal topic unable to generate the span file with "mp_span_from_pdb.default.linuxgccrelease" from a PDB file
by Sajjad » Wed, 2022-11-30 11:40
1
4,079 by FJOM
Wed, 2023-05-03 07:21
Normal topic Unable to locate the "compute_ddg.py" file and running the RosettaMP protocol
by Sajjad » Mon, 2022-11-28 14:09
3
4,867 by Sajjad
Wed, 2022-11-30 11:50
Normal topic Unable to run Rosetta LoopModeling application
by BDBorrillo » Tue, 2011-07-19 14:06
2
5,417 by BDBorrillo
Mon, 2014-04-21 06:47
Normal topic Unable to set up interface foldtree because there are no movable jumps - (antibody/antigen docking)
by snorp » Mon, 2014-04-14 13:01
2
3,828 by jadolfbr
Mon, 2014-05-12 10:41
Normal topic Unable to understand fragment picking tutorial points.
by Danielsebas » Thu, 2019-09-05 03:44
4
2,966 by danpf
Fri, 2019-09-06 11:29
Normal topic Undesirable behaviour of PoseFromSFRBuilder regarding Hydrogen atoms
by Corvin » Wed, 2020-12-02 04:00
1
1,200 by rmoretti
Wed, 2020-12-02 07:27
Normal topic Unexpected Error with RosettaCM -
by terry » Fri, 2019-02-22 14:26
1
3,268 by rmoretti
Fri, 2019-03-29 12:25
Normal topic UnfoldedStateEnergyCalculator MPI Error
by colin.walsh.brown » Mon, 2017-11-13 09:43
1
1,912 by smlewis
Mon, 2017-11-13 10:43
Normal topic Unknown Element "SE" when generating NCAA params file containing selenium
by liuwenxi » Thu, 2022-08-04 16:24
2
1,255 by liuwenxi
Fri, 2022-08-05 09:50
Normal topic Up to date Vall database
by JadAbbass » Sat, 2013-06-29 10:35
3
5,823 by rmoretti
Tue, 2017-06-20 09:02
Normal topic Urgent issue: Error with submitting a new Rosetta-Vienna RNP-ddG job
by eyaaaan » Sun, 2022-08-07 22:03
0
861 by eyaaaan
Tue, 2022-08-09 21:59
Hot topic usage of score3
by Run » Sat, 2013-09-28 02:06
16
16,931 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic Usage of the TaskOperations "RestrictToCDRsAndNeighbors"
by johnnytam100 » Wed, 2019-04-10 02:58
1
1,595 by rmoretti
Wed, 2019-07-10 10:10
Normal topic Use "loopmodel.linuxgccrelease" CCD to build missing residue positions
by lanselibai » Sun, 2014-10-12 09:00
2
3,460 by lanselibai
Mon, 2014-10-13 10:10
Normal topic Use membrane or non-membrane weights in RosettaCM for a hexon in virus capsid?
by lanselibai » Sat, 2020-04-11 02:10
0
952 by lanselibai
Sat, 2020-04-11 02:10
Normal topic Use NMR ensemble in protein-protein docking?
by cossio » Sun, 2015-09-13 07:57
2
3,132 by cossio
Tue, 2015-09-15 12:48
Normal topic Using abinition to predict a new (previously unsolved) structure.
by ac.research » Mon, 2017-01-09 00:59
0
1,324 by ac.research
Mon, 2017-01-09 00:59
Normal topic using DARC in rosetta
by syntekabio2019 » Thu, 2019-12-12 01:27
0
953 by syntekabio2019
Thu, 2019-12-12 01:27
Normal topic Using different number of 9-mers (UPDATED)
by JadAbbass » Mon, 2017-08-28 07:20
1
1,915 by rmoretti
Mon, 2017-09-04 10:33
Normal topic Using GlycanDock and the Antibody Affinity Maturation protocol.
by tbelec » Mon, 2022-02-28 12:37
0
1,171 by tbelec
Mon, 2022-02-28 12:37
Normal topic Using MoveMap within Relax Application?
by m_grisewood » Mon, 2012-08-13 12:21
5
7,101 by m_grisewood
Mon, 2014-04-21 06:47
Normal topic using piper-flexpepdock
by syntekabio2019 » Thu, 2019-12-12 01:22
0
1,265 by syntekabio2019
Thu, 2019-12-12 01:22
Normal topic Using residue patches in AbinitioRelax
by kent » Fri, 2018-11-02 11:19
1
1,900 by rmoretti
Wed, 2018-11-21 15:40
Normal topic Using Rmsd RosettaScripts filter with alignment files
by bjharris » Sun, 2020-11-08 15:51
1
1,139 by rmoretti
Sun, 2020-11-08 18:56
Normal topic Using Rosetta Docking for nucleic acids
by Adrien Guilhot » Thu, 2011-04-28 06:16
3
5,078 by Adrien Guilhot
Mon, 2014-04-21 06:47
Normal topic using Rosetta to compute pH dependent binding?
by JuliusSu » Sun, 2014-06-15 20:28
3
5,419 by rmoretti
Tue, 2014-06-17 08:51
Normal topic ValueError("Path %s does not exist!" % path_name) for rna_helix.py
by kameisel » Wed, 2023-08-16 00:39
2
448 by kameisel
Wed, 2023-09-13 02:16
Normal topic variable length fragments for Ab initio
by attesor » Wed, 2015-07-01 06:13
7
6,971 by rmoretti
Tue, 2015-08-18 16:47
Normal topic very good I_sc values (if not too good)
by attesor » Tue, 2015-11-03 03:30
2
3,205 by attesor
Tue, 2015-11-17 07:36
Normal topic VH-VL Orientation in antibody
by sujigeorge1979 » Mon, 2019-06-17 01:23
1
1,733 by jeliazkov
Mon, 2019-06-17 06:03
Normal topic wallpaper symmetry definition file
by aaj » Fri, 2016-02-26 08:40
0
1,416 by aaj
Fri, 2016-02-26 08:40
Normal topic Warning messages in Interface analyzer output
by Pernille » Wed, 2015-03-25 00:53
4
4,502 by rmoretti
Tue, 2015-03-31 08:20
Normal topic Warning: Fold tree is not set properly for density scoring
by ahansel » Mon, 2020-07-13 10:50
1
1,316 by danpf
Tue, 2020-07-14 10:27
Normal topic Warnings during relax
by cossio » Thu, 2018-10-11 14:42
2
3,339 by rmoretti
Mon, 2019-11-04 13:56
Normal topic Ways to improve AbRelax performance?
by Corvin » Tue, 2022-04-19 06:10
2
2,673 by Corvin
Thu, 2022-04-21 00:50
Normal topic Weighted scores??
by sizhang » Wed, 2018-12-05 15:22
0
975 by sizhang
Wed, 2018-12-05 15:22
Normal topic weights for pH_protocol
by fmerino » Wed, 2017-04-26 07:14
1
2,098 by rmoretti
Thu, 2017-04-27 07:10
Normal topic What are "-nstruct" and "cluster_histogram.txt" for "clustering.py"?
by lanselibai » Fri, 2014-10-17 06:06
3
21,015 by rmoretti
Fri, 2014-10-17 10:17
Normal topic what does initialize_rigid_body_dofs do?
by attesor » Mon, 2015-10-26 05:12
3
3,924 by rmoretti
Tue, 2015-11-10 11:35
Normal topic What is a rational minimal value for the "-nstruct" option
by Sunyp_IM » Fri, 2020-05-22 01:28
3
2,118 by nannemdp
Sun, 2020-05-24 14:46
Normal topic What is an SS0 predictor?
by ojmel » Fri, 2021-04-02 14:25
0
701 by ojmel
Mon, 2021-04-12 07:50
Normal topic What is interface_cutoff_distance? And why did my residues outside this value get designed?
by chrisHKL » Fri, 2020-02-28 14:52
0
990 by chrisHKL
Fri, 2020-02-28 14:52
Normal topic What means "[ ERROR ] TIME_STAMP: AbrelaxMover: finished ...NO_BATCH S_0001."
by Corvin » Thu, 2020-04-02 00:16
0
965 by Corvin
Thu, 2020-04-02 00:16
Normal topic When using "screening job files" in small molecule-docking I get: Residue type already exists in the cache Error
by Martin Floor » Thu, 2020-09-17 06:01
4
2,688 by Martin Floor
Tue, 2020-09-22 00:48
Normal topic where is generate_ligens.linuxgccrelease?
by Nicole Deng » Thu, 2020-12-03 00:00
2
1,742 by Nicole Deng
Fri, 2020-12-18 00:28
Normal topic where is pdb2vall.py
by tevang » Thu, 2013-01-24 13:35
7
6,998 by dktest
Mon, 2014-04-21 06:47
Normal topic Where is the RosettaHoles2 executable?
by lah435 » Mon, 2012-06-04 15:15
11
8,672 by smlewis
Mon, 2014-04-21 06:47
Normal topic where to look for positive sign for solution in mr-rosetta3.4?
by lchen » Tue, 2012-07-10 09:38
2
3,067 by lchen
Mon, 2014-04-21 06:47
Normal topic Why do non proten ligands get a very high score in kinematic loop modeling/ in general?
by a_s_a » Wed, 2011-06-15 00:03
8
7,841 by a_s_a
Mon, 2014-04-21 06:47
Normal topic Why is proline hydroxylated?
by kwonglynn » Tue, 2013-06-25 02:38
3
5,192 by rmoretti
Mon, 2014-04-21 06:48
Normal topic why is talaris2014 scoring fuction not used with ligand docking?
by banshee » Fri, 2016-09-09 01:19
1
2,127 by rmoretti
Fri, 2016-09-09 07:47
Normal topic Why there are two outputs using pmut_scan_parallel.linuxgccrelease with a mutant list file?
by lanselibai » Sun, 2014-11-16 10:26
3
3,785 by G Mustafa
Thu, 2018-10-18 05:31
Normal topic Write error during saving of PDB-file after working with it in the Rosetta through Unix terminal
by Corvin » Thu, 2019-04-25 01:20
2
2,258 by Corvin
Wed, 2019-06-12 00:04
Normal topic Write one's own constraint type
by djpittdj » Thu, 2012-11-08 12:29
7
6,610 by smlewis
Mon, 2014-04-21 06:47
Normal topic Writing down properties for new atom types
by Corvin » Tue, 2021-01-12 04:30
0
706 by Corvin
Wed, 2021-01-13 04:00
Normal topic XML validation failing
by mb0261 » Fri, 2023-04-14 14:53
11
1,891 by mb0261
Mon, 2023-04-17 17:38
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