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Rosetta 3 - General

Topic / Topic startersort descending Replies Views Last post
Normal topic How to put rdc data in refinement protocol?
by zhisheng » Tue, 2012-11-20 03:55
13
9,212 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
2,094 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
2,305 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
2,580 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
11,551 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
2,064 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
2,478 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
3,518 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
7,957 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
1,982 by rmoretti
Mon, 2014-04-21 06:47
Normal topic How to set start coordinates for ligand when doing protein_ligand docking
by Huanhuan » Wed, 2021-08-18 21:09
3
725 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
3,254 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
1,730 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
4,156 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
2,002 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
1,019 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
1,480 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
1,279 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
6,478 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
1,944 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
3,471 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
5,552 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
2,631 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
2,729 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
1,868 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
3,419 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
2,489 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
717 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
1,630 by sujigeorge1979
Thu, 2019-06-27 01:30
Normal topic hydrophobicity patch
by Lindsay » Fri, 2012-05-04 08:24
7
7,282 by Lindsay
Mon, 2014-04-21 06:47
Normal topic hydroxyproline patching problem
by aaj » Mon, 2016-02-22 07:33
2
2,254 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
5,888 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
2,567 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
1,924 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
1,265 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
1,938 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
3,130 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
4,264 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
544 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
1,100 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
714 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
2,139 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
8,948 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
1,479 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
1,123 by rmoretti
Mon, 2018-02-12 09:39
Normal topic idealization error
by albumns » Mon, 2011-02-07 01:28
1
1,698 by smlewis
Mon, 2014-04-21 06:47
Normal topic Identical decoys
by aroop » Tue, 2012-09-25 12:50
4
3,728 by smlewis
Mon, 2014-04-21 06:47
Normal topic ignore loops on threading
by fred » Tue, 2014-11-11 11:33
5
4,144 by rmoretti
Tue, 2014-11-18 10:01
Normal topic incomparable ddG values
by ela » Fri, 2018-08-31 02:53
0
801 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
257 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
3,989 by banshee
Tue, 2016-04-26 00:47
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36
2
1,561 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
3,106 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
2,052 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
7,256 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
1,592 by smlewis
Mon, 2014-04-21 06:47
Normal topic Installing rosetta 3.0
by dalemu » Thu, 2009-09-24 13:28
1
2,208 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
2,686 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
2,022 by smlewis
Mon, 2014-04-21 06:47
Normal topic Interface energy vs binding energy
by Apiwat » Wed, 2014-02-05 00:47
2
4,572 by Apiwat
Sat, 2014-02-08 01:41
Normal topic Interface rmsd calculation Irms
by mahajanr » Wed, 2010-07-07 18:24
5
6,439 by mahajanr
Mon, 2014-04-21 06:47
Normal topic InterfaceAnalyzer atom subset
by Parker.deWaal » Sun, 2016-03-13 13:41
2
2,077 by rmoretti
Mon, 2016-03-14 07:58
Normal topic InterfaceAnalyzer packstat score = 0.000
by vmc99 » Fri, 2018-11-16 11:30
11
5,791 by SenyorDrew
Wed, 2019-06-12 14:10
Normal topic InterfaceAnalyzer total score = 0.000
by vmc99 » Wed, 2019-06-12 14:06
3
1,908 by jadolfbr
Wed, 2019-06-12 20:17
Normal topic Intermediate file insertion
by exchhattu » Wed, 2009-09-02 18:44
2
2,058 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
540 by rmoretti
Wed, 2021-06-23 02:17
Normal topic Interpreting decoy ensemble
by lah435 » Wed, 2015-06-10 10:25
1
1,511 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
2,804 by smlewis
Mon, 2014-04-21 06:47
Normal topic intrensic disrodered proteins
by ac.research » Thu, 2019-04-04 07:20
1
1,009 by vmulligan
Mon, 2019-04-08 14:49
Normal topic Introduction or tutorial about RosettaMatch
by kwak » Thu, 2010-10-21 06:37
4
5,219 by kwak
Mon, 2014-04-21 06:47
Normal topic Is cis-Glycine okay?
by matteoferla » Tue, 2019-11-19 07:26
5
2,058 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
1,587 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
1,699 by smlewis
Mon, 2018-11-19 13:20
Normal topic Is it CS-HM Rosetta restraint derivation i.e cm_scripts in Rosetta 3.3 bundles?
by nh_prt » Tue, 2013-03-26 12:22
3
2,805 by smlewis
Mon, 2014-04-21 06:47
Normal topic is it possbile to cluster pdb files?
by albumns » Wed, 2010-10-06 02:38
3
4,395 by smlewis
Mon, 2014-04-21 06:47
Normal topic is it possible to ab initio only a part of a protein?
by albumns » Sun, 2011-02-13 08:10
6
3,761 by albumns
Mon, 2014-04-21 06:47
Normal topic Is it possible to do Abinitio folding from a linear structure.?
by monos_morpheus » Sat, 2011-04-16 09:13
11
7,656 by monos_morpheus
Mon, 2014-04-21 06:47
Hot topic Is it possible to do alanine scanning in Rosetta 3.2.1.?
by monos_morpheus » Tue, 2011-04-12 02:36
21
17,575 by smlewis
Mon, 2014-04-21 06:47
Normal topic is it possible to generate models without hydrogen?
by albumns » Fri, 2012-03-02 12:24
9
6,698 by albumns
Mon, 2014-04-21 06:47
Normal topic Is it possible to use two broker files
by kalabharath » Wed, 2011-06-08 01:01
1
2,002 by smlewis
Mon, 2014-04-21 06:47
Normal topic Is the Fold&Dock protocol availabe in Rosetta3.1
by justin » Mon, 2011-01-17 02:41
2
1,984 by smlewis
Mon, 2014-04-21 06:47
Normal topic Is the packer aware of non canonical amino acids?
by krdav » Tue, 2016-08-16 08:16
7
5,020 by krdav
Wed, 2016-08-17 12:57
Normal topic is the RosettaNMR protocol available in Rosetta 3.x?
by murgantia » Wed, 2011-01-26 00:39
1
1,764 by smlewis
Mon, 2014-04-21 06:47
Normal topic is there a preferred way to enforce an hydrogen bond ?
by logandonaldson » Wed, 2013-03-20 13:14
2
2,192 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Is there a way to calculate chi1 and chi1+chi differences between two structures?
by sn » Thu, 2017-04-20 21:46
1
1,519 by rmoretti
Fri, 2017-04-21 07:52
Normal topic Is there any significant improvement of model generation in rosetta3.4 comparing to rosetta3.3?
by jiongzhang » Fri, 2012-04-20 13:35
2
2,333 by rmoretti
Mon, 2014-04-21 06:47
Normal topic IS there any source code about protein structure prediction with only sequences information?
by ylwang » Mon, 2019-07-08 02:36
1
1,061 by rmoretti
Mon, 2019-07-08 08:05
Normal topic Is there other online server for generate fragment?
by ylwang » Wed, 2020-04-01 01:39
1
912 by rmoretti
Wed, 2020-04-01 10:10
Normal topic Issue with Loop Analyzer Mover ouput
by abhi_pe_acharya » Mon, 2018-04-30 09:55
2
1,378 by abhi_pe_acharya
Mon, 2018-04-30 22:54
Normal topic Issues running the Matcher in 3.4 and 3.5
by Jhreed » Tue, 2015-05-26 11:38
1
1,664 by rmoretti
Wed, 2015-06-17 12:43
Normal topic Issues with angle Constraints during Docking
by LeonhardJS » Thu, 2021-01-28 04:40
2
863 by LeonhardJS
Fri, 2021-01-29 01:12
Normal topic Issues with residues and structure changing with FlexPepDock; is this normal?
by rnelson » Tue, 2017-08-08 10:06
1
1,285 by Ora Schueler-Furman
Sun, 2017-08-20 00:54
Normal topic Iterative local rebuilding vs automated structure refinement
by ahmadkhalifa » Fri, 2018-09-14 07:44
4
2,415 by rmoretti
Wed, 2018-11-21 14:11
Normal topic I_sc
by Soler » Sat, 2022-02-12 00:16
1
319 by rmoretti
Fri, 2022-02-18 11:14
Normal topic jd2 time out error
by ytao » Mon, 2013-03-04 20:47
2
2,115 by ytao
Mon, 2014-04-21 06:47
Normal topic Job Distribution Error
by ac.research » Mon, 2020-02-10 08:22
2
1,214 by ac.research
Fri, 2020-02-14 23:33
Normal topic Jump::random_trans strange behavior
by SergeyP » Tue, 2015-11-03 07:56
2
2,000 by SergeyP
Sat, 2015-12-19 05:20
Normal topic keep ATP in the kinase-peptide structure while docking
by ziqi1234 » Fri, 2017-11-10 04:04
0
774 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic keep crystal structure hydrogens
by gw » Wed, 2011-07-20 03:54
2
2,668 by gw
Mon, 2014-04-21 06:47
Normal topic kinematic loop modeling/sequence design keeps crashing with segmentation fault
by banshee » Thu, 2013-03-28 09:52
8
6,724 by smlewis
Mon, 2014-04-21 06:47
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