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Rosetta 3 - Applications

Topic / Topic starter Repliessort ascending Views Last post
Normal topic rotamer library in coupled_moves
by mtyras » Fri, 2015-05-29 07:46
2
3,832 by mtyras
Mon, 2015-06-08 03:18
Normal topic Structure determination combining X-ray diffraction data and NMR chemical shift
by MajorID » Mon, 2011-10-17 19:55
2
3,858 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Pre-packing a model for SWA loop building
by franfdez » Sun, 2014-07-27 02:16
2
3,096 by franfdez
Mon, 2014-07-28 01:04
Normal topic PIKAA in resfile does not mutate Cys in disulfide bond to specified residue
by attesor » Fri, 2014-03-14 07:53
2
3,518 by attesor
Mon, 2014-06-16 07:34
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
2,360 by Corvin
Wed, 2019-06-12 00:04
Normal topic Segmentation Fault in Rosetta CM Hybridize
by yliang20 » Mon, 2022-06-06 17:25
2
1,500 by yliang20
Tue, 2022-06-07 08:36
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Tue, 2011-02-15 17:23
2
3,555 by sumukh21
Mon, 2014-04-21 06:47
Normal topic Symmetry definition for coiled-coil dimer and trimer
by kszczepaniak » Fri, 2013-10-11 05:33
2
5,778 by kszczepaniak
Mon, 2014-04-21 06:48
Normal topic Use "loopmodel.linuxgccrelease" CCD to build missing residue positions
by lanselibai » Sun, 2014-10-12 09:00
2
3,535 by lanselibai
Mon, 2014-10-13 10:10
Normal topic antibody modeling error
by mxp » Mon, 2019-09-16 18:29
2
1,983 by mxp
Mon, 2019-09-23 01:40
Normal topic Building loop extensions in a membrane protein with Remodel
by benhardy » Tue, 2020-06-02 08:21
2
2,199 by benhardy
Sun, 2020-09-20 11:15
Normal topic Missing atoms and cannot find atom pose when refining ligand position with EM density
by BuddySphinx » Mon, 2018-12-31 16:22
2
3,744 by e3lm
Tue, 2021-09-14 10:02
Normal topic A problem with "make_fragments.pl" script dependencies
by Corvin » Fri, 2019-08-16 04:30
2
2,534 by Corvin
Tue, 2019-08-27 00:46
Normal topic how to reconstruct the whole complex after symmetric docking
by Anonymous » Tue, 2012-07-03 02:44
2
3,307 by felipet
Wed, 2014-07-02 07:26
Normal topic regarding extracting silent file - renamed tag
by shrutikhare » Thu, 2014-04-17 01:19
2
2,796 by shrutikhare
Fri, 2014-04-18 23:11
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46
2
4,617 by libai2098
Mon, 2014-04-21 06:47
Normal topic GrowLigand
by allan.ferrari » Sat, 2019-10-19 05:32
2
2,095 by allan.ferrari
Tue, 2019-11-05 16:52
Normal topic limit_cluster_size default value
by sacch » Thu, 2011-11-24 17:57
2
2,963 by sacch
Mon, 2014-04-21 06:47
Normal topic Multistate design issues with -run:msd_job_dist option and MSDMover
by elaine.thai » Wed, 2020-05-13 18:07
2
3,121 by Jane_002
Thu, 2023-08-03 19:47
Normal topic RoseTTaFold
by ozsolomon » Thu, 2021-10-07 05:27
2
2,369 by ozsolomon
Thu, 2021-10-07 14:25
Normal topic creating compound task mover
by aaj » Wed, 2016-02-24 04:48
2
2,687 by aaj
Wed, 2016-02-24 07:37
Normal topic Strong bias in sampling observed in RosettaDock
by chenna » Thu, 2020-08-27 22:23
2
1,892 by chenna
Tue, 2021-10-12 20:51
Normal topic Number of Monte Carlo Cycles for FARFAR2
by mandar » Tue, 2024-03-12 19:11
2
191 by mandar
Tue, 2024-03-12 23:07
Normal topic Regarding the efficiency of the new low resolution ligand-docking movement “Transform”.
by Martin Floor » Mon, 2017-05-15 09:19
2
2,684 by Martin Floor
Mon, 2017-05-15 11:13
Normal topic The question about ligand score function
by asbelx » Sun, 2018-06-17 02:07
2
3,312 by asbelx
Mon, 2018-06-18 22:34
Normal topic Number of max allowed mutations from WT sequence
by mouung » Fri, 2020-09-04 02:33
2
1,876 by amorin
Fri, 2021-02-12 08:53
Normal topic flexpep docking, select the decoy to do the further docking, questions
by michael_luntan » Fri, 2011-04-22 04:43
2
3,564 by michael_luntan
Mon, 2014-04-21 06:47
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32
2
5,191 by lanselibai
Thu, 2014-11-20 02:15
Normal topic Error from clean_pdb.py
by code_Monkey » Mon, 2021-03-01 17:00
2
1,447 by code_Monkey
Thu, 2021-03-04 12:14
Normal topic refining crystal structure using phenix without CIF file
by banshee » Fri, 2016-09-09 01:14
2
3,271 by banshee
Mon, 2016-09-12 23:41
Normal topic Pepspec - random runtime segfaults (rosetta 3.3 database replaced) [solved]
by loreseeker » Wed, 2011-09-14 08:13
2
3,690 by loreseeker
Mon, 2014-04-21 06:47
Normal topic select_best_unique_ligand_poses output
by ast » Thu, 2013-07-11 02:33
2
3,361 by ast
Mon, 2014-04-21 06:48
Normal topic Remodel: neighbor cutoff
by felipet » Wed, 2014-07-16 08:11
2
2,779 by felipet
Thu, 2014-07-17 10:13
Normal topic Total score problems with high-res ddg_monomer
by jklesmith » Tue, 2015-03-10 15:54
2
3,650 by jennifer
Fri, 2015-03-27 05:56
Normal topic KeyError: 'subject-id' in antibody modelling
by bogac » Mon, 2017-03-06 02:00
2
3,161 by bogac
Tue, 2017-03-07 02:11
Normal topic Membrane homology modeling loop building gives very strange outputs
by chelsell » Tue, 2014-09-30 14:46
2
3,249 by chelsell
Wed, 2014-10-08 12:25
Normal topic The usage of antibody_H3.linuxgccrelease
by Sunyp_IM » Thu, 2020-05-28 22:50
2
2,024 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
2,771 by alonwenger
Sat, 2021-12-18 12:32
Normal topic How to scan double mutations in RosettaScripts?
by msardejani » Mon, 2016-12-12 16:52
2
2,540 by msardejani
Mon, 2016-12-12 17:48
Normal topic CC (or similar) calculation for cryoEM fitting
by almeida85 » Tue, 2023-05-16 01:32
2
721 by almeida85
Tue, 2023-05-23 08:23
Normal topic FlexPepDock Concatenation
by cam11 » Mon, 2014-08-11 07:39
2
2,886 by cam11
Wed, 2014-08-13 10:06
Normal topic score_jd2.mpi.linuxgccrelease failed
by fred » Wed, 2014-03-26 13:54
2
5,488 by fred
Tue, 2014-04-01 08:24
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
1,889 by jlawrie
Wed, 2020-08-12 08:56
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
1,575 by chenna
Mon, 2021-04-12 22:08
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
3,060 by lanselibai
Fri, 2014-10-17 03:36
Normal topic ddG Monomer Low Res Protocol Convergence
by harshkhare » Thu, 2012-03-01 00:45
2
3,857 by harshkhare
Mon, 2014-04-21 06:47
Normal topic Score - Strange message
by Ashafix » Wed, 2013-11-20 15:23
2
3,581 by Ashafix
Mon, 2014-04-21 06:48
Normal topic cluster.mpi running in MPI mode?
by sacch » Fri, 2011-11-18 23:30
2
4,484 by sacch
Mon, 2014-04-21 06:47
Normal topic Floppytail modelling
by felipet » Fri, 2011-06-24 09:23
2
3,804 by felipet
Mon, 2014-04-21 06:47
Normal topic RosettaSurface in 3.4?
by skovacs » Tue, 2012-07-10 16:02
2
3,064 by mpacella
Mon, 2014-04-21 06:47
Normal topic Trouble running MPI docking protocol, please help!
by Rob_Barringer » Tue, 2020-08-18 06:40
2
2,892 by Rob_Barringer
Fri, 2020-09-25 05:45
Normal topic Generalized KIC loop closure affects downstream residues without perturbations
by chenna » Mon, 2021-04-26 02:16
2
1,470 by chenna
Wed, 2021-04-28 07:18
Normal topic ProteinLigandInterfaceUpweighter for protein-protein interactions?
by ahonegger » Mon, 2014-06-02 06:53
2
3,362 by ahonegger
Fri, 2014-06-06 09:31
Normal topic cartesian_ddg error: "Assertion `files.size() == 1` failed."
by cossio » Fri, 2018-05-11 09:59
2
3,345 by cossio
Fri, 2018-05-18 09:51
Normal topic Question about fastsaxs and saxs_score
by orionshih » Thu, 2019-06-13 02:30
2
1,995 by orionshih
Wed, 2019-06-26 03:54
Normal topic make_fragments.pl error
by almeida85 » Mon, 2020-08-31 04:39
2
2,025 by almeida85
Tue, 2020-09-01 01:29
Normal topic Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu
by lanselibai » Mon, 2014-11-10 08:12
2
2,968 by lanselibai
Tue, 2014-11-11 04:42
Normal topic Fnat and Irms are nan in score.sc from docking_protocol?
by cossio » Sun, 2015-09-13 07:34
2
3,769 by rmoretti
Thu, 2015-09-17 12:47
Normal topic ValueError("Path %s does not exist!" % path_name) for rna_helix.py
by kameisel » Wed, 2023-08-16 00:39
2
570 by kameisel
Wed, 2023-09-13 02:16
Normal topic membrane ab initio modeling application with constraints
by ytao » Thu, 2012-11-08 11:56
2
4,299 by ytao
Mon, 2014-04-21 06:47
Normal topic Collecting all decoys from batch files
by aep » Sun, 2016-08-07 12:23
2
2,552 by aep
Sat, 2016-08-13 13:03
Normal topic Ligand params file proton_chi parameters
by staciekim » Thu, 2017-08-17 14:50
2
3,093 by staciekim
Thu, 2017-08-17 17:06
Normal topic RosettaAntibody core.pose.util error
by rishibedi » Fri, 2018-10-05 01:31
2
2,717 by esozdemir
Thu, 2019-06-13 12:19
Normal topic How to add additional rounds of design and optimization in Rosetta scripts?
by Nicole Deng » Tue, 2020-11-03 19:05
2
1,579 by Nicole Deng
Thu, 2020-11-05 03:04
Normal topic relax constraints not minimized
by m_grisewood » Fri, 2012-08-10 08:31
2
3,766 by m_grisewood
Mon, 2014-04-21 06:47
Normal topic cross correlation calculation
by jingwei xu » Sat, 2016-04-16 19:11
2
2,792 by jingwei xu
Wed, 2016-05-04 23:26
Normal topic Segmentation Fault in Fragment picking
by ashu4487 » Fri, 2018-07-06 20:47
2
3,296 by ashu4487
Mon, 2018-07-16 19:24
Normal topic De novo structure building with medium resolution map
by BuddySphinx » Tue, 2019-07-02 09:07
2
2,093 by BuddySphinx
Tue, 2019-07-02 12:03
Normal topic ERROR: Specified chain does not exist.
by ajaniharesh » Fri, 2019-04-05 11:14
2
2,740 by ajaniharesh
Tue, 2019-04-09 06:53
Normal topic How to use Rosetta to DISCARD a protein-protein docking interface?
by cossio » Tue, 2015-05-26 06:24
2
3,280 by rmoretti
Sat, 2015-07-11 13:38
Normal topic RMSD calculation
by hamedkhakzad » Tue, 2016-09-13 04:56
2
4,234 by rmoretti
Wed, 2016-09-14 02:05
Normal topic "Make_fragments.pl" can't connect to dependencies links
by Corvin » Wed, 2019-09-04 23:54
2
2,272 by Corvin
Thu, 2019-10-10 01:12
Normal topic setup_RosettaCM.py
by browns02 » Mon, 2021-06-28 07:13
2
1,387 by browns02
Tue, 2021-06-29 11:41
Normal topic Remodel with residue constraints
by sn » Fri, 2017-03-10 01:40
2
2,493 by rmoretti
Mon, 2017-03-13 08:01
Normal topic problems with generating the params file
by dyu » Thu, 2017-09-28 13:34
2
2,350 by dyu
Thu, 2017-09-28 18:54
Normal topic Error with Formatdb of legacy blast when running "install_dependencies.pl"?
by Danielsebas » Mon, 2019-09-16 09:30
2
1,876 by Danielsebas
Tue, 2019-09-17 01:03
Normal topic symmetric fixbb design with design_hpatch
by sdh_h » Sat, 2013-02-02 01:48
2
2,954 by ronj
Mon, 2014-04-21 06:47
Normal topic reporting bugs? (erraser in rosetta 3.10)
by meyer » Fri, 2018-12-14 09:40
2
2,062 by everyday847
Fri, 2019-03-29 13:13
Normal topic Membrane protein protocol on PyRosetta
by jlapin » Sat, 2018-07-28 14:41
2
2,260 by jlapin
Wed, 2018-08-01 07:15
Normal topic Ligand docking and protein design of an internal pocket in a protein with a cofactor
by oerbilgin » Mon, 2011-06-20 13:55
2
4,864 by frichter
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
3,895 by jadolfbr
Mon, 2014-05-12 10:41
Normal topic Imitating induced fit protocol in SymDock2 without any symmetry constraints
by chenna » Fri, 2020-02-14 01:35
2
1,989 by chenna
Wed, 2020-03-04 03:24
Normal topic change number of output pose files written out (default=50) in ligand docking XML script
by hdelrisco » Fri, 2019-10-18 13:50
2
1,862 by hdelrisco
Fri, 2019-10-18 17:16
Normal topic "core.kinematics.FoldTree" error upon running RAbD
by Sunyp_IM » Fri, 2020-06-26 17:27
2
1,822 by Sunyp_IM
Fri, 2020-06-26 20:57
Normal topic small ligand docking in Ubuntu 20.04, please help
by guowuchen » Sun, 2022-03-06 18:12
2
1,673 by guowuchen
Mon, 2022-03-07 23:34
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
3,460 by Wizard
Sun, 2015-04-26 22:36
Normal topic ReplicaDock 2.0 Native vs Input Structure Flags Confusion
by katherinemccoy » Tue, 2022-12-27 06:42
2
4,774 by katherinemccoy
Tue, 2023-02-28 18:19
Normal topic Unable to run Rosetta LoopModeling application
by BDBorrillo » Tue, 2011-07-19 14:06
2
5,505 by BDBorrillo
Mon, 2014-04-21 06:47
Normal topic Space Swap!!!
by jrcf » Sun, 2016-02-14 11:43
2
2,716 by jrcf
Mon, 2016-02-15 17:59
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
1,765 by chrisHKL
Wed, 2020-03-04 10:49
Normal topic RIFdocking:Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/
by sia » Tue, 2022-08-02 20:06
2
1,881 by SeongRyeong Go
Mon, 2022-08-15 18:31
Normal topic BuildPeptide - Using Phosphorylated and Sulfated Tyrosine
by jlawrie » Thu, 2020-09-03 14:29
1
1,434 by cryosky
Mon, 2021-03-01 21:37
Normal topic Destination of score.fsc file
by anirbanzz » Wed, 2011-04-20 23:30
1
2,881 by smlewis
Mon, 2014-04-21 06:47
Normal topic Symmetry-aware Backrub?
by gamacy » Fri, 2014-11-14 02:18
1
2,240 by rmoretti
Tue, 2014-11-18 09:10
Normal topic Protein Design
by ac.research » Wed, 2017-02-15 19:25
1
2,840 by cdbahl
Sat, 2017-02-18 13:02
Normal topic Abinitio the Broker protocol
by ac.research » Sun, 2019-03-24 03:56
1
1,633 by rmoretti
Fri, 2019-04-05 00:18
Normal topic Issue with Rosetta LinkResidues Script
by adityapadhi » Wed, 2019-11-20 22:00
1
1,417 by JackMaguire
Fri, 2019-11-22 13:45
Normal topic Cannot install DAlphaBall
by gerdos » Fri, 2023-10-13 07:55
1
618 by Seongsung
Fri, 2023-11-24 04:52
Normal topic loop modeling scoring
by Nicky_Learning_... » Wed, 2015-05-13 20:00
1
2,768 by rmoretti
Mon, 2015-05-25 11:30
Normal topic Using Rmsd RosettaScripts filter with alignment files
by bjharris » Sun, 2020-11-08 15:51
1
1,199 by rmoretti
Sun, 2020-11-08 18:56
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