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Rosetta 3 - General

Topic / Topic startersort descending Replies Views Last post
Normal topic How to dock 3 missing domains onto a multi-domain protein
by tevang » Sun, 2011-04-10 15:22
3
3,213 by smlewis
Mon, 2014-04-21 06:47
Normal topic how to docking including HETATM
by tricia » Tue, 2009-05-05 22:03
1
1,506 by smlewis
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
599 by ac.research
Sat, 2017-11-18 06:54
Normal topic How to extract specific pdb from silent files
by eunwook » Tue, 2013-05-14 05:29
5
9,883 by nawsad
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
1,703 by Anonymous
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
2,137 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
2,056 by zhisheng
Mon, 2014-04-21 06:47
Normal topic How to generate symmdef file for translational symmetry only?
by pitmand » Thu, 2015-05-14 11:34
2
1,684 by pitmand
Tue, 2015-05-26 12:20
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
386 by rmoretti
Wed, 2019-09-18 10:49
Normal topic How to get multiple chains in PDB from Fold and Dock
by arthuc01 » Tue, 2012-05-29 02:05
9
5,429 by arthuc01
Mon, 2014-04-21 06:47
Normal topic how to get reliable results for carbohydrate docking?
by albumns » Sun, 2010-09-05 23:12
3
3,322 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to get the GDT_TS?
by JadAbbass » Thu, 2013-09-05 11:59
3
3,342 by rmoretti
Mon, 2014-04-21 06:48
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
2,089 by rmoretti
Wed, 2014-12-03 18:52
Normal topic how to identify selected interface residues
by vijayaraj81 » Mon, 2014-03-31 01:40
3
2,355 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
2,237 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to input constraints?
by violetsha7 » Wed, 2009-05-13 00:13
7
5,768 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
2,969 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
2,259 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
4,164 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
2,726 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
1,495 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
2,090 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
2,143 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
11,914 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
1,646 by smlewis
Wed, 2017-11-08 12:08
Hot topic how to make benchmark?
by albumns » Wed, 2012-04-04 05:23
23
16,644 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
1,395 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
811 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
3,136 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
1,855 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
11,806 by sabine
Mon, 2014-04-21 06:47
Normal topic how to optimize the weights?
by Lindsay » Tue, 2012-04-10 07:40
7
3,487 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
2,664 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
291 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
1,457 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
1,641 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to put rdc data in refinement protocol?
by zhisheng » Tue, 2012-11-20 03:55
13
6,667 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
1,314 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
1,670 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
2,108 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
8,258 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
1,545 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
1,831 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
2,965 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
5,782 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
1,477 by rmoretti
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
1,986 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
1,289 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
3,314 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
1,546 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
599 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
300 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
580 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
4,592 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
1,351 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
2,457 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
4,224 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
1,905 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
2,064 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
1,478 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
2,599 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
1,702 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
353 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
733 by sujigeorge1979
Thu, 2019-06-27 01:30
Normal topic hydrophobicity patch
by Lindsay » Fri, 2012-05-04 08:24
7
5,258 by Lindsay
Mon, 2014-04-21 06:47
Normal topic hydroxyproline patching problem
by aaj » Mon, 2016-02-22 07:33
2
1,569 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
5,022 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
1,987 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
534 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
298 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
1,514 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
2,563 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
3,246 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
82 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
243 by jadolfbr
Sun, 2020-05-03 19:38
Normal topic I used mpirun/mpiexec and it runs same job 32times
by leygkn » Mon, 2020-09-21 00:53
0
17 by leygkn
Mon, 2020-09-21 01:07
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
6,636 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
1,013 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
585 by rmoretti
Mon, 2018-02-12 09:39
Normal topic idealization error
by albumns » Mon, 2011-02-07 01:28
1
1,250 by smlewis
Mon, 2014-04-21 06:47
Normal topic Identical decoys
by aroop » Tue, 2012-09-25 12:50
4
2,809 by smlewis
Mon, 2014-04-21 06:47
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33
5
2,915 by rmoretti
Tue, 2014-11-18 10:01
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53
0
401 by ela
Fri, 2018-08-31 02:53
Normal topic Incorporating Rosetta Binary and Database to a Web Server Pipeline
by smkim » Fri, 2018-09-28 20:35
1
763 by rmoretti
Fri, 2018-11-09 12:22
Normal topic industrial example of ROSETTA modeled protein
by banshee » Sat, 2016-04-23 23:40
5
2,667 by banshee
Tue, 2016-04-26 00:47
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36
1
800 by smlewis
Fri, 2017-09-08 11:05
Normal topic Information about “membrane_highres_Menv_smooth.wts”
by Groros » Sun, 2011-10-02 03:59
3
2,213 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
1,506 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
5,425 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
1,173 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing rosetta 3.0
by dalemu » Thu, 2009-09-24 13:28
1
1,683 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
1,952 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
1,444 by smlewis
Mon, 2014-04-21 06:47
Normal topic Interface energy vs binding energy
by Apiwat » Wed, 2014-02-05 00:47
2
3,258 by Apiwat
Sat, 2014-02-08 01:41
Normal topic Interface rmsd calculation Irms
by mahajanr » Wed, 2010-07-07 18:24
5
4,914 by mahajanr
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41
2
1,418 by rmoretti
Mon, 2016-03-14 07:58
Normal topic InterfaceAnalyzer packstat score = 0.000
by vmc99 » Fri, 2018-11-16 11:30
11
2,615 by SenyorDrew
Wed, 2019-06-12 14:10
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06
3
813 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic Intermediate file insertion
by exchhattu » Wed, 2009-09-02 18:44
2
1,393 by exchhattu
Mon, 2014-04-21 06:47
Normal topic Interpreting decoy ensemble
by lah435 » Wed, 2015-06-10 10:25
1
1,080 by rmoretti
Fri, 2015-07-03 13:51
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