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Rosetta 3 - General

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Normal topic How to use the <CavityVolume> filter in the released version of Rosetta
by BioPython » Sun, 2019-05-12 20:07 		0
 1,132 by BioPython
Sun, 2019-05-12 20:07
Normal topic How to use RotamerDump to access one and two-body energy tables?
by msun » Wed, 2013-01-16 12:26 		3
 3,364 by msun
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
 4,276 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
 2,362 by libai2098
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
 3,564 by vanita
Mon, 2014-04-21 06:47
Normal topic how to use backrub in rosetta3.1
by lqzhang » Mon, 2010-01-11 14:43 		3
 3,491 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to use AbinitioRelax.mpi.linuxgccrelease?
by albumns » Mon, 2012-03-26 22:50 		5
 6,866 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to turn off output of POSE_ENERGIES_TABLE
by lah435 » Tue, 2015-02-03 21:21 		4
 4,640 by jwillis
Sat, 2015-02-07 20:40
Normal topic How to transform a pose from symmetric into non-symmetric?
by msardejani » Tue, 2016-10-04 16:55 		2
 2,699 by msardejani
Wed, 2016-10-05 10:53
Normal topic how to transfer the rosetta score to physical unit?
by Lindsay » Thu, 2012-06-28 09:33 		7
 8,280 by Lindsay
Mon, 2014-04-21 06:47
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
 2,992 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
 2,588 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
 1,633 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
 2,534 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
 5,216 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
 2,227 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
 4,624 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
 2,024 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
 521 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
 2,506 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
 10,096 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
 4,012 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
 3,197 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
 2,776 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
 14,890 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
 3,142 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
 3,131 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
 3,103 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
 12,248 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
 1,091 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
 2,981 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
 2,913 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
 991 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
 4,292 by rmoretti
Mon, 2014-04-21 06:47
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40 		7
 6,550 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
 17,860 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
 2,936 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
 5,607 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
 2,601 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
 2,312 by rmoretti
Mon, 2014-04-21 06:47
Hot topic how to make benchmark?
by albumns » Wed, 2012-04-04 05:23 		23
 30,826 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26 		3
 4,868 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
 15,277 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
 4,409 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
 4,039 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
 2,800 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
 4,423 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
 5,608 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
 3,307 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
 3,996 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13 		7
 9,595 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
 3,312 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
 4,620 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
 1,971 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
 3,581 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
 5,779 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
 5,012 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
 9,535 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
 1,588 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
 446 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
 3,231 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
 3,336 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
 3,872 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
 2,555 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
 16,010 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
 1,700 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
 873 by whiteqiu
Mon, 2021-03-01 18:32
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03 		1
 2,727 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
 4,862 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
 2,258 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
 4,600 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
 12,818 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
 1,501 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
 1,750 by rmoretti
Tue, 2019-07-09 15:48
Normal topic how to design binding interface?
by Lindsay » Mon, 2013-12-02 19:06 		8
 10,932 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
 2,266 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
 13,029 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
 1,095 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
 7,349 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
 1,965 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
 10,684 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
 2,536 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
 893 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
 2,290 by rmoretti
Wed, 2015-09-02 12:48
Normal topic how to cluster loop?
by albumns » Wed, 2011-01-05 19:48 		6
 6,673 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
 11,599 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
 1,540 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
 4,764 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
 4,255 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
 1,323 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
 578 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
 2,439 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
 3,171 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
 6,557 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
 2,866 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
 956 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
 2,200 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
 448 by JasonIsaac
Tue, 2023-05-02 03:39
Normal topic how does rosetta handle hydrogens?
by patcD » Tue, 2021-08-31 00:48 		2
 1,593 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
 7,153 by Anonymous
Mon, 2014-04-21 06:47