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Rosetta 3 - General

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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
2,600 by johnnytam100
Wed, 2019-05-15 18:45
Normal topic How to specify constraints during fold-and-dock?
by sarah_b » Tue, 2020-05-12 01:55
3
2,381 by matteoferla
Thu, 2020-05-14 07:01
Normal topic How to specify a specific rotamer
by Lior_UCSF » Wed, 2018-02-21 20:35
1
1,529 by rmoretti
Thu, 2018-02-22 09:29
Normal topic How to site the scoring application in rosetta3.1?
by doranhen » Thu, 2012-07-05 10:07
1
2,431 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
4,970 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to set the output name for fixbb design
by Lindsay » Mon, 2012-04-30 09:32
1
2,124 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to set the enviroment variable $ROSETTA3, $ $ROSETTA3_DB, $ROSETTA_TOOLS?
by Sunyp_IM » Thu, 2017-07-27 01:07
1
4,358 by SenyorDrew
Sat, 2017-07-29 09:59
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09
3
1,732 by matteoferla
Fri, 2021-08-20 08:37
Normal topic How to set jump between ligands
by Zehui Zhou » Wed, 2023-02-15 04:48
0
390 by Zehui Zhou
Wed, 2023-02-15 07:12
Normal topic How to score the crystal structure?
by vsjasion » Fri, 2011-11-18 15:49
1
2,387 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to run Rosetta3 in parallel
by lennylv » Mon, 2009-03-30 04:21
6
9,634 by rmoretti
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
3,913 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
3,054 by Anatol
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
2,609 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
14,164 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to relax a protein model calling Rosetta functions from my C++ code
by sncrivelli » Tue, 2011-10-25 00:16
1
3,028 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to recover out files when run crashs
by samuelrpita » Tue, 2015-07-28 12:54
2
2,974 by samuelrpita
Thu, 2015-08-06 14:23
Normal topic How to read the output score file from rosetta?
by Sunyp_IM » Sun, 2017-08-27 05:29
1
2,926 by rmoretti
Mon, 2017-08-28 09:32
Normal topic How to put rdc data in refinement protocol?
by zhisheng » Tue, 2012-11-20 03:55
13
11,628 by rmoretti
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
970 by lanselibai
Wed, 2021-06-23 14:53
Normal topic How to prevent rotamers from being pruned from the interaction graph?
by msun » Wed, 2013-04-17 14:19
2
2,807 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to prepare the pdblist file for docking_ensmble in Rosetta3.4
by sunlufinal » Mon, 2015-06-01 19:27
1
2,721 by rmoretti
Fri, 2015-07-03 12:58
Normal topic how to perform model quality assessment of rosetta generated models?
by Danielsebas » Tue, 2019-09-24 05:03
0
929 by Danielsebas
Tue, 2019-09-24 05:03
Normal topic how to output a structure when scoring it?
by tianbu » Tue, 2012-07-31 09:38
3
4,118 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40
7
6,191 by rmoretti
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
17,180 by sabine
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
2,828 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to model a protein that dimerizes to a small molecule?
by pholland » Wed, 2011-05-25 07:29
3
5,289 by pholland
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
2,416 by Ronghai Cheng
Tue, 2018-11-13 21:56
Normal topic How to make Rosetta's sampling more aggresive ?
by jiongzhang » Mon, 2012-03-12 11:04
1
2,212 by rmoretti
Mon, 2014-04-21 06:47
Hot topic how to make benchmark?
by albumns » Wed, 2012-04-04 05:23
23
29,182 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
4,487 by smlewis
Wed, 2017-11-08 12:08
Normal topic how to make a combined PDB file?
by fenghc » Mon, 2013-04-01 06:27
3
14,948 by smlewis
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
4,163 by zlni
Mon, 2014-04-21 06:47
Normal topic how to keep modeling ignored ERROR?
by eunwook » Sat, 2013-04-27 05:44
3
3,833 by eunwook
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
2,658 by rmoretti
Tue, 2015-07-14 15:27
Normal topic How to integrate Rosetta code to my program?
by Lsg » Tue, 2011-06-28 07:18
3
4,228 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
5,458 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
3,188 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
3,897 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
9,098 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to import SymmDock models into Rosetta for local docking and energy minimization
by devroop » Fri, 2012-07-20 13:20
1
3,188 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to identify selected interface residues
by vijayaraj81 » Mon, 2014-03-31 01:40
3
4,333 by rmoretti
Tue, 2014-04-01 08:12
Normal topic How to handle/retain Metals (Zn, Ca) inside the Protein?
by aniyaz » Wed, 2023-01-11 03:21
6
1,456 by rmoretti
Mon, 2023-02-20 16:07
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
3,456 by rmoretti
Wed, 2014-12-03 18:52
Normal topic How to get the GDT_TS?
by JadAbbass » Thu, 2013-09-05 11:59
3
5,500 by rmoretti
Mon, 2014-04-21 06:48
Normal topic how to get reliable results for carbohydrate docking?
by albumns » Sun, 2010-09-05 23:12
3
4,827 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to get multiple chains in PDB from Fold and Dock
by arthuc01 » Tue, 2012-05-29 02:05
9
9,044 by arthuc01
Mon, 2014-04-21 06:47
Normal topic How to get fragment library from robetta server for mre than 1000 residue sequence?
by Danielsebas » Wed, 2019-09-18 07:53
1
1,478 by rmoretti
Wed, 2019-09-18 10:49
Normal topic how to generate _prepro.rama file for a customized beta-amino acid residues?
by wwwmrzkwww » Sun, 2023-04-23 14:25
0
303 by wwwmrzkwww
Sun, 2023-04-23 14:25
Normal topic How to generate symmdef file for translational symmetry only?
by pitmand » Thu, 2015-05-14 11:34
2
3,056 by pitmand
Tue, 2015-05-26 12:20
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
3,203 by zhisheng
Mon, 2014-04-21 06:47
Normal topic How to generate constraints of active sites from a pdb file of an enzyme
by Albert » Sun, 2013-05-26 20:07
3
3,683 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to generate a symmetry definition file for octahedral symmetry?
by Anonymous » Wed, 2012-08-15 05:20
0
2,458 by Anonymous
Mon, 2014-04-21 06:47
Normal topic How to extract specific pdb from silent files
by eunwook » Tue, 2013-05-14 05:29
5
15,393 by nawsad
Mon, 2014-04-21 06:47
Normal topic How to extract antibody from a set of pdb file may may contain antigen?
by Sunyp_IM » Mon, 2017-11-13 17:11
1
1,554 by ac.research
Sat, 2017-11-18 06:54
Normal topic How to export high energy state pdb out of backrub?
by whiteqiu » Mon, 2021-03-01 18:32
0
793 by whiteqiu
Mon, 2021-03-01 18:32
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03
1
2,576 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to dock 3 missing domains onto a multi-domain protein
by tevang » Sun, 2011-04-10 15:22
3
4,685 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to do ensemble docking using rosetta3.1
by lqzhang » Mon, 2010-01-11 10:31
1
2,138 by sid
Mon, 2014-04-21 06:47
Normal topic how to do cluster after low resolution protein-protein docking?
by albumns » Sat, 2010-11-27 01:17
4
4,398 by albumns
Mon, 2014-04-21 06:47
Normal topic How to do ab initio with fixed part of protein
by eunwook » Tue, 2013-04-16 03:00
11
12,164 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
1,392 by rmoretti
Tue, 2019-07-09 15:59
Normal topic How to determine the value size in block of *.cst files?
by weifulei » Sun, 2019-05-05 19:56
1
1,626 by rmoretti
Tue, 2019-07-09 15:48
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06
8
10,414 by rmoretti
Tue, 2019-07-09 12:50
Normal topic How to design a stand-alone loop from a binding interface?
by guangdianzi3 » Fri, 2011-02-11 21:11
1
2,163 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to design a protein complex
by Lindsay » Tue, 2013-11-05 20:24
11
12,394 by Lindsay
Mon, 2014-04-21 06:48
Normal topic How to define the surface (???.surf) for surface_docking?
by Anpu » Thu, 2018-09-27 07:34
0
1,021 by Anpu
Thu, 2018-09-27 23:36
Normal topic How to define specific residues in alascan ?
by Park » Mon, 2011-06-13 19:56
6
6,992 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to define a theozyme from the .pdb crystal structure without ligand?
by weifulei » Mon, 2019-05-20 21:18
1
1,825 by rmoretti
Tue, 2019-07-09 12:31
Normal topic How to deal with Cu-as a ligand or as part of the receptor?
by hanypao » Fri, 2011-09-30 18:50
7
10,240 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to create a rotamer set that includes all possible rotamers of all possible amino acids
by AyushGoyal » Thu, 2014-11-06 10:37
1
2,414 by smlewis
Fri, 2014-11-07 12:03
Normal topic How to create a native file for Protein-Protein docking
by Kotimedidhi » Mon, 2020-06-22 08:10
0
821 by Kotimedidhi
Mon, 2020-06-22 08:10
Normal topic How to convert fragments to PDB format?
by JadAbbass » Wed, 2015-08-19 04:05
1
2,168 by rmoretti
Wed, 2015-09-02 12:48
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48
6
6,343 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to calculate the binding energy of peptide and a protein?
by tianbu » Thu, 2014-02-13 20:44
9
10,961 by tianbu
Mon, 2014-02-17 03:36
Normal topic how to build homology based models?
by albumns » Thu, 2010-06-24 10:27
0
1,480 by albumns
Mon, 2014-04-21 06:47
Normal topic How to automatically position new peptides into the binding site of a enzime, in order to run peptide-protein docking approaches
by zaldini » Fri, 2015-01-02 05:53
4
4,504 by zaldini
Wed, 2015-01-07 20:35
Normal topic How to allow rosetta to recognize the ASP and protonated ASP?
by Jeffrey_Chen » Mon, 2014-03-24 20:34
2
3,954 by Jeffrey_Chen
Tue, 2014-03-25 23:06
Normal topic How to add uncommon metal elements into Rosetta and make it recognizable?
by JasonIsaac » Thu, 2023-02-09 00:08
4
947 by JasonIsaac
Sat, 2023-02-11 00:44
Normal topic How to add new Movers to Rosetta
by mb0261 » Thu, 2022-06-30 10:48
0
461 by mb0261
Thu, 2022-06-30 10:48
Normal topic how to add constrains in flexible peptide docking
by kingbo2008 » Fri, 2011-04-29 07:55
1
2,335 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to set the cyana format of distance restraint in rosetta?
by zhisheng » Mon, 2011-04-25 02:21
1
3,069 by smlewis
Mon, 2014-04-21 06:47
Normal topic How the Rosetta score (dG) is actually related to dH (enthalpy) and dS (entropy)?
by lanselibai » Thu, 2014-12-04 13:16
4
6,247 by lanselibai
Fri, 2014-12-12 10:27
Normal topic how same random seeds can be used in rosetta for mpi run.
by exchhattu » Wed, 2009-10-28 22:09
1
2,753 by smlewis
Mon, 2014-04-21 06:47
Normal topic How RosettaCM can perform part of C terminal domain (CTD) structure prediction without proper template structures (coordinates)
by haom » Tue, 2020-09-01 13:21
0
875 by haom
Tue, 2020-09-01 18:50
Normal topic How NMR structures can be inputted to Rosetta?
by exchhattu » Mon, 2015-02-09 17:44
1
2,082 by rmoretti
Wed, 2015-02-18 09:19
Normal topic How many rifdock can I run at a time on a 64 CPUs and 512GB memory server?
by JasonIsaac » Tue, 2023-05-02 03:39
0
305 by JasonIsaac
Tue, 2023-05-02 03:39
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48
2
1,356 by patcD
Wed, 2021-09-01 06:54
Normal topic How does one prevent Rosetta from connecting two separate chains?
by jhbrown » Thu, 2011-12-15 14:08
7
6,812 by Anonymous
Mon, 2014-04-21 06:47
Normal topic How do you implement phosphoserine in ab -initio folding?
by smiruthi » Fri, 2011-12-16 14:45
10
9,781 by brspurri
Mon, 2014-04-21 06:47
Normal topic How do the homology sequences exclude from fragment files?
by exchhattu » Mon, 2010-04-05 03:04
1
2,043 by smlewis
Mon, 2014-04-21 06:47
Normal topic How do I add virtual atom to my cofactor (metal ion) in rosettadock?
by monos_morpheus » Sat, 2011-02-05 21:24
2
3,309 by monos_morpheus
Mon, 2014-04-21 06:47
Normal topic How do I add hydrogen atoms to my PDB file?
by monos_morpheus » Wed, 2011-03-30 03:30
6
13,609 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How did you begin to learn Rosetta?
by mdeklotz » Mon, 2018-07-30 10:08
1
2,153 by jkleman
Tue, 2018-07-31 13:19
Normal topic How can move peptide on cleft of enzyme on Flexpepdock?
by phanvy » Thu, 2014-06-05 02:22
4
4,476 by zaldini
Fri, 2015-01-02 05:38
Normal topic How can I use InterfaceScore terms in docking as GenericMonteCarlo criterion
by wwwmrzkwww » Sun, 2021-08-15 00:19
0
781 by wwwmrzkwww
Sun, 2021-08-15 00:19
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56
3
3,326 by smlewis
Fri, 2016-07-29 07:43
Normal topic Homology modeling starter script
by gobli033 » Thu, 2010-04-01 07:27
0
1,505 by gobli033
Mon, 2014-04-21 06:47
Normal topic Homology modeling
by mchldln » Mon, 2009-08-17 13:04
2
3,647 by smlewis
Mon, 2014-04-21 06:47
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