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Rosetta 3 - General

Topic / Topic startersort descending Replies Views Last post
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
363 by rmoretti
Mon, 2023-02-20 16:07
Normal topic how to identify selected interface residues
by vijayaraj81 » Mon, 2014-03-31 01:40
3
3,716 by rmoretti
Tue, 2014-04-01 08:12
Normal topic How to import SymmDock models into Rosetta for local docking and energy minimization
by devroop » Fri, 2012-07-20 13:20
1
2,902 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
8,188 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input pdb to rosetta format add "missing" residues to pdb file
by zhisheng » Tue, 2011-06-07 09:51
1
3,659 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to insert a TER line between docking partners
by devroop » Sun, 2012-07-29 13:48
1
2,922 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to install Rosetta in Redhat Linux ?
by ajaniharesh » Fri, 2012-02-24 02:32
1
5,077 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to integrate Rosetta code to my program?
by Lsg » Tue, 2011-06-28 07:18
3
3,801 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to judge docking success for two proteins without knowledge of native structure
by jasnyderjr » Fri, 2015-07-10 14:27
1
2,353 by rmoretti
Tue, 2015-07-14 15:27
Normal topic how to keep modeling ignored ERROR?
by eunwook » Sat, 2013-04-27 05:44
3
3,327 by eunwook
Mon, 2014-04-21 06:47
Normal topic how to keep native structure when do loop modeling
by zlni » Sun, 2009-05-03 10:12
4
3,606 by zlni
Mon, 2014-04-21 06:47
Normal topic how to make a combined PDB file?
by fenghc » Mon, 2013-04-01 06:27
3
14,191 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
3,597 by smlewis
Wed, 2017-11-08 12:08
Hot topic how to make benchmark?
by albumns » Wed, 2012-04-04 05:23
23
25,781 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to make Rosetta's sampling more aggresive ?
by jiongzhang » Mon, 2012-03-12 11:04
1
1,968 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to minimize only a few key residues' orientation
by Ronghai Cheng » Mon, 2018-11-05 18:37
2
2,010 by Ronghai Cheng
Tue, 2018-11-13 21:56
Normal topic How to model a protein that dimerizes to a small molecule?
by pholland » Wed, 2011-05-25 07:29
3
4,648 by pholland
Mon, 2014-04-21 06:47
Normal topic How to modify disulfide bonds constrain in homology modeling
by eunwook » Mon, 2013-05-13 04:56
1
2,535 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to obtain alignment file for comparative modeling under Rosetta 3.1?
by lennylv » Tue, 2010-05-25 01:29
11
15,677 by sabine
Mon, 2014-04-21 06:47
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40
7
5,422 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to output a structure when scoring it?
by tianbu » Tue, 2012-07-31 09:38
3
3,722 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to perform model quality assessment of rosetta generated models?
by Danielsebas » Tue, 2019-09-24 05:03
0
751 by Danielsebas
Tue, 2019-09-24 05:03
Normal topic How to prepare the pdblist file for docking_ensmble in Rosetta3.4
by sunlufinal » Mon, 2015-06-01 19:27
1
2,353 by rmoretti
Fri, 2015-07-03 12:58
Normal topic How to prevent rotamers from being pruned from the interaction graph?
by msun » Wed, 2013-04-17 14:19
2
2,441 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to provide multiple templates for Robetta with RosettaCM option?
by lanselibai » Wed, 2021-06-23 14:06
1
685 by lanselibai
Wed, 2021-06-23 14:53
Normal topic How to put rdc data in refinement protocol?
by zhisheng » Tue, 2012-11-20 03:55
13
10,129 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to read the output score file from rosetta?
by Sunyp_IM » Sun, 2017-08-27 05:29
1
2,470 by rmoretti
Mon, 2017-08-28 09:32
Normal topic How to recover out files when run crashs
by samuelrpita » Tue, 2015-07-28 12:54
2
2,610 by samuelrpita
Thu, 2015-08-06 14:23
Normal topic How to relax a protein model calling Rosetta functions from my C++ code
by sncrivelli » Tue, 2011-10-25 00:16
1
2,754 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to relax only one domain of a protein and keep the rest of them fixed
by tevang » Sun, 2011-04-10 03:16
14
12,600 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to relax structure constraining CA in Rosetta3.2?
by albumns » Tue, 2011-02-15 06:15
2
2,268 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to remove clashes in peptide bonds and proline residue?
by Anatol » Fri, 2012-08-31 09:26
2
2,732 by Anatol
Mon, 2014-04-21 06:47
Normal topic How to run docking in rosetta with small molecule
by ajaniharesh » Tue, 2012-02-28 03:58
1
3,666 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to run Rosetta3 in parallel
by lennylv » Mon, 2009-03-30 04:21
6
8,632 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to score the crystal structure?
by vsjasion » Fri, 2011-11-18 15:49
1
2,134 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to set jump between ligands
by Zehui Zhou » Wed, 2023-02-15 04:48
0
95 by Zehui Zhou
Wed, 2023-02-15 07:12
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09
3
1,144 by matteoferla
Fri, 2021-08-20 08:37
Normal topic How to set the enviroment variable $ROSETTA3, $ $ROSETTA3_DB, $ROSETTA_TOOLS?
by Sunyp_IM » Thu, 2017-07-27 01:07
1
3,696 by SenyorDrew
Sat, 2017-07-29 09:59
Normal topic how to set the output name for fixbb design
by Lindsay » Mon, 2012-04-30 09:32
1
1,881 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to set up options in rosetta
by alejandro » Wed, 2011-04-06 02:08
3
4,500 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to site the scoring application in rosetta3.1?
by doranhen » Thu, 2012-07-05 10:07
1
2,187 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to specify a specific rotamer
by Lior_UCSF » Wed, 2018-02-21 20:35
1
1,217 by rmoretti
Thu, 2018-02-22 09:29
Normal topic How to specify constraints during fold-and-dock?
by sarah_b » Tue, 2020-05-12 01:55
3
1,849 by matteoferla
Thu, 2020-05-14 07:01
Normal topic How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers?
by johnnytam100 » Wed, 2019-05-08 02:30
2
1,610 by johnnytam100
Wed, 2019-05-15 18:45
Normal topic how to transfer the rosetta score to physical unit?
by Lindsay » Thu, 2012-06-28 09:33
7
7,060 by Lindsay
Mon, 2014-04-21 06:47
Normal topic How to transform a pose from symmetric into non-symmetric?
by msardejani » Tue, 2016-10-04 16:55
2
2,172 by msardejani
Wed, 2016-10-05 10:53
Normal topic How to turn off output of POSE_ENERGIES_TABLE
by lah435 » Tue, 2015-02-03 21:21
4
3,826 by jwillis
Sat, 2015-02-07 20:40
Normal topic how to use AbinitioRelax.mpi.linuxgccrelease?
by albumns » Mon, 2012-03-26 22:50
5
5,925 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to use backrub in rosetta3.1
by lqzhang » Mon, 2010-01-11 14:43
3
2,911 by smlewis
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
3,017 by vanita
Mon, 2014-04-21 06:47
Normal topic How to use Rosetta Position constraint docking?
by libai2098 » Mon, 2011-05-09 01:08
1
2,018 by libai2098
Mon, 2014-04-21 06:47
Normal topic how to use rosettadesign to do mutations on protein structure
by lqzhang » Thu, 2010-03-04 07:43
3
3,670 by vanita
Mon, 2014-04-21 06:47
Normal topic How to use RotamerDump to access one and two-body energy tables?
by msun » Wed, 2013-01-16 12:26
3
2,803 by msun
Mon, 2014-04-21 06:47
Normal topic How to use the <CavityVolume> filter in the released version of Rosetta
by BioPython » Sun, 2019-05-12 20:07
0
861 by BioPython
Sun, 2019-05-12 20:07
Normal topic Hydrogen bond detection and shape complementarity
by sujigeorge1979 » Fri, 2019-06-14 02:39
3
1,919 by sujigeorge1979
Thu, 2019-06-27 01:30
Normal topic hydrophobicity patch
by Lindsay » Fri, 2012-05-04 08:24
7
7,993 by Lindsay
Mon, 2014-04-21 06:47
Normal topic hydroxyproline patching problem
by aaj » Mon, 2016-02-22 07:33
2
2,511 by aaj
Mon, 2016-02-29 04:45
Normal topic I am a beginner in rosetta software and need help to build params file
by nais » Fri, 2011-03-18 13:37
3
6,238 by rmoretti
Mon, 2014-04-21 06:47
Normal topic I can't find the workflow about modeling disordered regsion using rosetta?
by lihowe » Thu, 2011-12-29 03:45
2
2,760 by wangyr
Mon, 2014-04-21 06:47
Normal topic I generated a table of images & info of the premade NCAA params in the database
by matteoferla » Sun, 2020-02-16 06:27
4
2,282 by matteoferla
Sat, 2020-03-21 09:14
Normal topic I got so many atoms in one residue
by ylwang » Tue, 2020-03-24 04:40
3
1,567 by ylwang
Tue, 2020-03-24 19:35
Normal topic I got the message "bad format in first line of silent file". How do I resolve this?
by monos_morpheus » Thu, 2011-02-03 21:09
1
2,104 by smlewis
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
3,314 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic I have a .tab file. How do I extract information from it?
by monos_morpheus » Tue, 2011-02-08 09:30
4
4,664 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic I made a params file generation webpage
by matteoferla » Wed, 2020-07-22 03:08
0
687 by matteoferla
Wed, 2020-07-22 03:08
Normal topic I made a RDKit Chem.Mol to params converter — feedback welcome!
by matteoferla » Sun, 2020-05-03 10:14
1
1,355 by jadolfbr
Sun, 2020-05-03 19:38
Normal topic I Need Help on Validation for a Ligand Docking Experiment.
by tbelec » Sat, 2021-03-20 13:27
1
1,008 by matteoferla
Mon, 2021-03-22 08:29
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
6
2,946 by jadolfbr
Thu, 2020-09-24 10:04
Normal topic I'm a total beginner to Rosetta 3.2 and there are no tutorials for me to follow. Can someone help.? =)
by monos_morpheus » Wed, 2011-02-02 08:11
12
9,719 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic I've got two doubts
by jrcf » Sun, 2016-01-10 07:45
1
1,683 by smlewis
Sun, 2016-01-10 10:02
Normal topic Icouldnot find DDMI protocol for design protein
by ladimafakher » Mon, 2018-02-12 09:22
1
1,335 by rmoretti
Mon, 2018-02-12 09:39
Normal topic idealization error
by albumns » Mon, 2011-02-07 01:28
1
1,867 by smlewis
Mon, 2014-04-21 06:47
Normal topic Identical decoys
by aroop » Tue, 2012-09-25 12:50
4
4,099 by smlewis
Mon, 2014-04-21 06:47
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33
5
4,526 by rmoretti
Tue, 2014-11-18 10:01
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53
0
940 by ela
Fri, 2018-08-31 02:53
Normal topic Inconsistent scoring by "aa_composition" term
by chenna » Thu, 2022-02-24 03:00
1
532 by vmulligan
Thu, 2022-03-03 18:48
Normal topic industrial example of ROSETTA modeled protein
by banshee » Sat, 2016-04-23 23:40
5
4,438 by banshee
Tue, 2016-04-26 00:47
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36
2
1,940 by CameronJA
Wed, 2022-01-19 20:50
Normal topic Information about “membrane_highres_Menv_smooth.wts”
by Groros » Sun, 2011-10-02 03:59
3
3,343 by smlewis
Mon, 2014-04-21 06:47
Normal topic input secondary structure prediction to AbinitioRelax
by biofisikx » Mon, 2010-08-09 12:36
2
2,263 by biofisikx
Mon, 2014-04-21 06:47
Normal topic input_score_filter not taken by program cluster ?
by Anonymous » Mon, 2012-06-11 09:14
9
7,863 by attesor
Fri, 2014-10-31 04:49
Normal topic Installing on windows using MinGW
by abdullah_ahmed » Wed, 2010-09-15 08:45
1
1,758 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing rosetta 3.0
by dalemu » Thu, 2009-09-24 13:28
1
2,437 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing Rosetta Abinitio make_fragments.pl
by ctaylor » Thu, 2009-09-17 09:20
2
2,988 by ctaylor
Mon, 2014-04-21 06:47
Normal topic Intel Compiler and OS X Intel
by bene » Tue, 2009-10-20 10:20
1
2,220 by smlewis
Mon, 2014-04-21 06:47
Normal topic Interface energy vs binding energy
by Apiwat » Wed, 2014-02-05 00:47
2
5,097 by Apiwat
Sat, 2014-02-08 01:41
Normal topic Interface rmsd calculation Irms
by mahajanr » Wed, 2010-07-07 18:24
5
6,952 by mahajanr
Mon, 2014-04-21 06:47
Normal topic Interface scores comparison
by NingNing » Tue, 2022-08-09 17:36
0
194 by NingNing
Tue, 2022-08-09 17:36
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41
2
2,333 by rmoretti
Mon, 2016-03-14 07:58
Normal topic InterfaceAnalyzer packstat score = 0.000
by vmc99 » Fri, 2018-11-16 11:30
11
6,739 by SenyorDrew
Wed, 2019-06-12 14:10
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06
3
2,339 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic Intermediate file insertion
by exchhattu » Wed, 2009-09-02 18:44
2
2,330 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Internal error while running AbinitioRelax
by Subhrodeep Saha » Sun, 2021-06-13 03:44
1
809 by rmoretti
Wed, 2021-06-23 02:17
Normal topic Interpreting decoy ensemble
by lah435 » Wed, 2015-06-10 10:25
1
1,690 by rmoretti
Fri, 2015-07-03 13:51
Normal topic interpreting score values in silent output file after running abinitiorelax
by burkheadlab » Wed, 2011-03-09 15:42
3
3,061 by smlewis
Mon, 2014-04-21 06:47
Normal topic intrensic disrodered proteins
by ac.research » Thu, 2019-04-04 07:20
1
1,210 by vmulligan
Mon, 2019-04-08 14:49
Normal topic Introduction or tutorial about RosettaMatch
by kwak » Thu, 2010-10-21 06:37
4
5,652 by kwak
Mon, 2014-04-21 06:47
Normal topic Is cis-Glycine okay?
by matteoferla » Tue, 2019-11-19 07:26
5
2,638 by matteoferla
Wed, 2019-11-20 02:32
Normal topic Is CST_Design required for enzdes protocol?
by dasdevashishdas » Mon, 2018-09-03 00:51
2
1,912 by dasdevashishdas
Thu, 2018-09-27 03:35
Normal topic Is it better to have smaller nstruct but many runs?
by Loki01 » Mon, 2018-11-19 11:50
3
2,017 by smlewis
Mon, 2018-11-19 13:20
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