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Rosetta 3 - Applications

Topic / Topic starter Repliessort ascending Views Last post
Normal topic Regarding the efficiency of the new low resolution ligand-docking movement “Transform”.
by Martin Floor » Mon, 2017-05-15 09:19
2
2,199 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
2,623 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
1,278 by amorin
Fri, 2021-02-12 08:53
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32
2
4,720 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
950 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
2,685 by banshee
Mon, 2016-09-12 23:41
Normal topic select_best_unique_ligand_poses output
by ast » Thu, 2013-07-11 02:33
2
2,936 by ast
Mon, 2014-04-21 06:48
Normal topic Remodel: neighbor cutoff
by felipet » Wed, 2014-07-16 08:11
2
2,309 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
3,082 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
2,549 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
2,753 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
1,402 by Sunyp_IM
Thu, 2020-06-04 08:20
Normal topic getting a3m files
by alonwenger » Wed, 2021-12-15 02:38
2
1,318 by alonwenger
Sat, 2021-12-18 12:32
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
2,588 by lanselibai
Fri, 2014-10-17 03:36
Normal topic How to scan double mutations in RosettaScripts?
by msardejani » Mon, 2016-12-12 16:52
2
2,073 by msardejani
Mon, 2016-12-12 17:48
Normal topic FlexPepDock Concatenation
by cam11 » Mon, 2014-08-11 07:39
2
2,433 by cam11
Wed, 2014-08-13 10:06
Normal topic score_jd2.mpi.linuxgccrelease failed
by fred » Wed, 2014-03-26 13:54
2
4,799 by fred
Tue, 2014-04-01 08:24
Normal topic Homology Modeling-no PDB output
by jlawrie » Wed, 2020-08-12 06:30
2
1,294 by jlawrie
Wed, 2020-08-12 08:56
Normal topic GeneralizedKIC loop closure error
by chenna » Sat, 2021-04-10 00:21
2
966 by chenna
Mon, 2021-04-12 22:08
Normal topic Score - Strange message
by Ashafix » Wed, 2013-11-20 15:23
2
3,151 by Ashafix
Mon, 2014-04-21 06:48
Normal topic Idealize in Rosetta 3.3
by jadolfbr » Tue, 2011-12-06 11:59
2
2,832 by jadolfbr
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
1,822 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
934 by chenna
Wed, 2021-04-28 07:18
Normal topic ProteinLigandInterfaceUpweighter for protein-protein interactions?
by ahonegger » Mon, 2014-06-02 06:53
2
2,807 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
2,546 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
1,469 by orionshih
Wed, 2019-06-26 03:54
Normal topic make_fragments.pl error
by almeida85 » Mon, 2020-08-31 04:39
2
1,422 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
2,538 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
3,158 by rmoretti
Thu, 2015-09-17 12:47
Normal topic membrane ab initio modeling application with constraints
by ytao » Thu, 2012-11-08 11:56
2
3,869 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
2,112 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
2,442 by staciekim
Thu, 2017-08-17 17:06
Normal topic RosettaAntibody core.pose.util error
by rishibedi » Fri, 2018-10-05 01:31
2
2,098 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
1,047 by Nicole Deng
Thu, 2020-11-05 03:04
Normal topic minimize_with_cst problems (ddg_monomer)
by alexn » Tue, 2011-09-20 13:46
2
3,141 by alexn
Mon, 2014-04-21 06:47
Normal topic Structure determination combining X-ray diffraction data and NMR chemical shift
by MajorID » Mon, 2011-10-17 19:55
2
3,383 by rmoretti
Mon, 2014-04-21 06:47
Normal topic cross correlation calculation
by jingwei xu » Sat, 2016-04-16 19:11
2
2,302 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
2,706 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
1,601 by BuddySphinx
Tue, 2019-07-02 12:03
Normal topic Fold and Dock - chains not in contact
by arthuc01 » Wed, 2012-06-13 01:45
2
2,699 by smlewis
Mon, 2014-04-21 06:47
Normal topic ERROR: Specified chain does not exist.
by ajaniharesh » Fri, 2019-04-05 11:14
2
2,080 by ajaniharesh
Tue, 2019-04-09 06:53
Normal topic Fragment files for membrane_abinitio application
by sumukh21 » Tue, 2011-02-15 17:23
2
3,042 by sumukh21
Mon, 2014-04-21 06:47
Normal topic How to use Rosetta to DISCARD a protein-protein docking interface?
by cossio » Tue, 2015-05-26 06:24
2
2,773 by rmoretti
Sat, 2015-07-11 13:38
Normal topic RMSD calculation
by hamedkhakzad » Tue, 2016-09-13 04:56
2
3,475 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
1,748 by Corvin
Thu, 2019-10-10 01:12
Normal topic setup_RosettaCM.py
by browns02 » Mon, 2021-06-28 07:13
2
814 by browns02
Tue, 2021-06-29 11:41
Normal topic where to look for positive sign for solution in mr-rosetta3.4?
by lchen » Tue, 2012-07-10 09:38
2
2,729 by lchen
Mon, 2014-04-21 06:47
Normal topic Remodel with residue constraints
by sn » Fri, 2017-03-10 01:40
2
1,997 by rmoretti
Mon, 2017-03-13 08:01
Normal topic the meaning of total_score in docking
by libai2098 » Mon, 2011-03-21 05:46
2
4,137 by libai2098
Mon, 2014-04-21 06:47
Normal topic problems with generating the params file
by dyu » Thu, 2017-09-28 13:34
2
1,871 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
1,322 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
2,541 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
1,566 by everyday847
Fri, 2019-03-29 13:13
Normal topic Membrane protein protocol on PyRosetta
by jlapin » Sat, 2018-07-28 14:41
2
1,723 by jlapin
Wed, 2018-08-01 07:15
Normal topic limit_cluster_size default value
by sacch » Thu, 2011-11-24 17:57
2
2,527 by sacch
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
3,424 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
1,451 by chenna
Wed, 2020-03-04 03:24
Normal topic flexpep docking, select the decoy to do the further docking, questions
by michael_luntan » Fri, 2011-04-22 04:43
2
3,129 by michael_luntan
Mon, 2014-04-21 06:47
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
1,365 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
1,305 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
782 by guowuchen
Mon, 2022-03-07 23:34
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
2,911 by Wizard
Sun, 2015-04-26 22:36
Normal topic Pepspec - random runtime segfaults (rosetta 3.3 database replaced) [solved]
by loreseeker » Wed, 2011-09-14 08:13
2
3,245 by loreseeker
Mon, 2014-04-21 06:47
Normal topic Multiple Chain Comparative Modeling - End result is not even close to template structure
by eskici » Wed, 2012-08-29 08:09
2
3,404 by eskici
Mon, 2014-04-21 06:47
Normal topic Space Swap!!!
by jrcf » Sun, 2016-02-14 11:43
2
2,232 by jrcf
Mon, 2016-02-15 17:59
Normal topic nstruct vs. trials?
by chrisHKL » Mon, 2020-03-02 13:22
2
1,273 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
501 by SeongRyeong Go
Mon, 2022-08-15 18:31
Normal topic RosettaScripts - SetupNCS mover
by felipet » Fri, 2016-03-25 12:42
2
2,305 by rmoretti
Fri, 2016-04-29 08:26
Normal topic Ligand Docking with RosettaScripts gives a ParsedProtocol exception
by brspurri » Sun, 2017-05-14 17:51
2
2,511 by brspurri
Mon, 2017-05-15 11:48
Normal topic Any progress on getting intermediate structures during a design?
by broomsday » Mon, 2020-03-16 06:46
2
1,383 by vmulligan
Tue, 2020-03-17 11:35
Normal topic do mpi apps share memory?
by fred » Thu, 2014-01-23 11:49
2
2,965 by fred
Mon, 2014-04-21 06:48
Normal topic Generate fragment file on my computer
by jrcf » Mon, 2015-09-21 15:41
2
3,638 by jrcf
Mon, 2015-10-05 21:32
Normal topic antibody H3 modelling protocol for nanobody gives "[ ERROR ] Inaccurate G!" messages
by AlfredoKCL » Sun, 2021-02-28 16:42
2
929 by AlfredoKCL
Mon, 2021-03-01 04:07
Normal topic Ways to improve AbRelax performance?
by Corvin » Tue, 2022-04-19 06:10
2
643 by Corvin
Thu, 2022-04-21 00:50
Normal topic cartesian_ddg output
by cossio » Thu, 2018-10-11 14:58
2
2,626 by cossio
Fri, 2018-10-12 04:43
Normal topic "make" error in "pdb2vall/structure_profile_scripts/DEPTH-CLONE-2.8.7"
by Danielsebas » Mon, 2019-09-02 08:14
2
1,545 by Danielsebas
Sun, 2019-09-08 02:08
Normal topic Error in using “loopmodel” for selective rebuilding
by sushreet » Mon, 2014-07-14 11:57
2
2,482 by sushreet
Tue, 2014-08-26 13:02
Normal topic Floppy tail: sidechain mutation during calculation
by syoifczeri » Mon, 2015-03-09 19:01
2
2,723 by syoifczeri
Tue, 2015-03-10 23:08
Normal topic Modeling more than one protein loop at the same time
by hzhekova » Mon, 2018-01-15 14:03
2
2,589 by hzhekova
Tue, 2018-01-16 10:31
Normal topic RosettaLigand ERROR: Error in core::conformation::check_good_cutpoint_neighbour()
by sam_dc » Thu, 2021-03-25 09:32
2
1,726 by sam_dc
Mon, 2021-04-12 07:24
Normal topic clustering
by ays » Tue, 2014-09-30 08:26
2
2,884 by rmoretti
Mon, 2014-10-06 16:00
Normal topic How to make new VALL database?
by Danielsebas » Sun, 2019-09-08 02:16
2
1,996 by Danielsebas
Wed, 2019-09-11 00:44
Normal topic rosetta_cm segfault
by browns02 » Fri, 2021-07-09 13:35
2
857 by rmoretti
Fri, 2021-07-09 15:05
Normal topic cluster.mpi running in MPI mode?
by sacch » Fri, 2011-11-18 23:30
2
3,989 by sacch
Mon, 2014-04-21 06:47
Normal topic Floppytail modelling
by felipet » Fri, 2011-06-24 09:23
2
3,337 by felipet
Mon, 2014-04-21 06:47
Normal topic RosettaScripts - FastRelax loops
by jtmacd » Wed, 2015-11-18 09:32
2
3,607 by jtmacd
Fri, 2015-12-04 03:11
Normal topic Relax structure with metal cofactors
by h_trasatti » Tue, 2017-03-14 14:04
2
2,514 by rmoretti
Tue, 2017-03-28 08:51
Normal topic Choosing weight file for interface design?
by johnnytam100 » Tue, 2019-05-07 00:47
2
1,697 by johnnytam100
Tue, 2019-05-21 22:33
Normal topic how to know the precedure of solving a actural bio problem? like interface design?
by qq7678500549 » Thu, 2020-08-06 18:45
2
1,117 by qq7678500549
Sun, 2020-08-09 18:59
Normal topic MaxSub and MaxSub2.0
by JadAbbass » Tue, 2013-10-15 13:36
2
3,229 by JadAbbass
Mon, 2014-04-21 06:48
Normal topic Including ab-initio predicted model in fragment library generation
by ashu4487 » Thu, 2016-12-08 17:49
2
1,991 by ashu4487
Sun, 2016-12-11 19:03
Normal topic Abinitio protocol and X-Ray diffraction data
by allan.ferrari » Wed, 2015-08-12 12:49
2
2,508 by allan.ferrari
Fri, 2015-08-28 12:07
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Fri, 2020-06-19 08:58
2
1,259 by Kotimedidhi
Mon, 2020-06-22 16:19
Normal topic ddG filter gives deltaG calculation number?
by jarod » Tue, 2013-05-28 23:43
2
3,502 by jarod
Mon, 2014-04-21 06:47
Normal topic Calculate_protein_protein_ddg
by kamau » Fri, 2015-01-30 11:27
2
2,600 by deepanshuiitb
Thu, 2015-03-19 19:14
Normal topic RosettaScript Segmentation Fault (crash log attached)
by chrisHKL » Thu, 2020-03-05 07:21
2
1,709 by chrisHKL
Thu, 2020-03-05 09:11
Normal topic Disulfide Bonds in Loop Modeling
by code_Monkey » Mon, 2021-05-03 08:27
2
994 by code_Monkey
Thu, 2021-05-06 07:14
Normal topic Reproducing the exact result using information from previos run
by nawsad » Thu, 2013-03-14 12:05
2
2,245 by nawsad
Mon, 2014-04-21 06:47
Normal topic FlexPepDock and total score problem
by tkellici » Fri, 2014-01-17 06:07
2
2,874 by Ora Schueler-Furman
Mon, 2014-04-21 06:48
Normal topic OptimizeMembranePositionMover - This element is not expected
by bjharris » Wed, 2020-07-01 23:21
2
1,396 by bjharris
Thu, 2020-07-02 11:09
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