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Rosetta 3 - General

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Normal topic Error when clustering the output from a docking study
by jos » Thu, 2011-09-08 03:26
2
2,870 by jos
Mon, 2014-04-21 06:47
Normal topic backrub score different from calculated score
by attesor » Wed, 2014-04-09 07:34
3
2,868 by rmoretti
Thu, 2014-04-10 07:38
Normal topic protocols.jd2.JobDistributor: [ ERROR ]
by johnnytam100 » Thu, 2019-04-11 09:30
5
2,859 by jadolfbr
Tue, 2019-04-16 09:15
Normal topic How to get the RMSD between two .pdb structures?
by cossio » Wed, 2014-12-03 05:33
1
2,856 by rmoretti
Wed, 2014-12-03 18:52
Normal topic the meaning of "maxsub" in score.fsc
by exchhattu » Tue, 2009-11-10 04:37
2
2,853 by smlewis
Mon, 2014-04-21 06:47
Normal topic Unknow atom_name: LYS 1HZ in enzdes after match
by petrikigor » Fri, 2012-10-19 09:35
1
2,846 by rmoretti
Mon, 2014-04-21 06:47
Normal topic fixbb and HETATM
by doranhen » Mon, 2013-01-14 07:50
2
2,841 by doranhen
Mon, 2014-04-21 06:47
Normal topic Re: Basic python scripts for File Manipulation
by bharat_46010 » Mon, 2011-03-14 19:44
1
2,837 by smlewis
Mon, 2014-04-21 06:47
Normal topic combine silent.out file
by venkatazb » Fri, 2016-07-22 05:22
1
2,831 by smlewis
Fri, 2016-07-22 07:31
Normal topic Version of VALL Database and Corresponding Constraint Coordinate File for Fragment Generation
by jurkm » Mon, 2011-05-02 03:00
1
2,821 by smlewis
Mon, 2014-04-21 06:47
Normal topic demos/public/ideal_proteins Segmentation fault
by coomteng@gmail.com » Wed, 2018-03-07 00:15
5
2,821 by rmoretti
Thu, 2018-03-08 07:46
Normal topic Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41
4
2,811 by linucks
Fri, 2018-02-23 08:08
Normal topic ERROR: PDB reader is ignoring atom
by phanvy » Wed, 2014-04-16 17:59
2
2,808 by phanvy
Mon, 2014-04-21 03:58
Normal topic Question about homology modelling
by DmitriiN » Sun, 2016-08-21 13:44
3
2,804 by smlewis
Mon, 2016-08-22 10:28
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
2,802 by smlewis
Mon, 2014-04-21 06:47
Normal topic interpreting score values in silent output file after running abinitiorelax
by burkheadlab » Wed, 2011-03-09 15:42
3
2,802 by smlewis
Mon, 2014-04-21 06:47
Normal topic NOE constraints with Rosetta 3.1
by mpiuzzi » Wed, 2010-02-24 02:40
3
2,799 by mpiuzzi
Mon, 2014-04-21 06:47
Normal topic a question about protein-ligand docking in generating 1SW2 conformers
by Ryhon Wang » Wed, 2014-05-28 22:27
2
2,796 by rmoretti
Tue, 2014-06-03 11:45
Normal topic Models which are not recorded (Abinitio protocol)
by allan.ferrari » Fri, 2015-08-28 13:39
3
2,795 by rmoretti
Thu, 2015-09-17 12:42
Normal topic Structure prediction based on template -> Documentation comparative modeling of protein structures
by maxebert » Sun, 2011-03-20 01:15
1
2,785 by rmoretti
Mon, 2014-04-21 06:47
Normal topic fixbb program
by Lindsay » Tue, 2012-05-08 13:56
3
2,784 by AndrewLeaver-Fay
Mon, 2014-04-21 06:47
Normal topic Problems with output control
by Sunyp_IM » Thu, 2017-06-22 15:30
3
2,783 by rmoretti
Wed, 2017-06-28 01:33
Normal topic Creating new residue type for pyridoxal phosphate bound to lysine (LLP) [Solved]
by franfdez » Sat, 2012-01-28 11:39
1
2,782 by franfdez
Mon, 2014-04-21 06:47
Normal topic Memory leak when PDB preparation
by Jacky010 » Mon, 2019-05-06 01:28
6
2,781 by Jacky010
Tue, 2019-05-14 01:24
Normal topic Rosetta3.5 src/core/pack/dunbrack/RotamerLibrary.cc permission problem
by ytao » Fri, 2013-06-28 12:13
2
2,779 by ytao
Mon, 2014-04-21 06:48
Normal topic why docking results are different?
by albumns » Sat, 2010-12-18 23:53
3
2,778 by smlewis
Mon, 2014-04-21 06:47
Normal topic Only 430 models are generated for membrane prediction
by justin » Wed, 2010-01-06 00:04
3
2,759 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error when using RabD with a nanobody.
by zhangying1990 » Mon, 2018-12-17 04:40
5
2,752 by jadolfbr
Mon, 2019-01-28 08:46
Normal topic Clustering and Protein Preparation for docking
by MRH » Sun, 2013-08-25 22:01
1
2,751 by rmoretti
Mon, 2014-04-21 06:48
Normal topic When does Rosetta switch from centroid to FA mode?
by MarkW » Fri, 2015-07-03 04:48
3
2,748 by rmoretti
Sun, 2015-07-05 14:28
Normal topic about the option -constraints:cst_fa_file & -constraints:cst_fa_weight
by jiongzhang » Sat, 2010-12-25 12:55
1
2,745 by smlewis
Mon, 2014-04-21 06:47
Normal topic Library of unnatural amino acid parameters
by saxen » Mon, 2017-04-17 11:08
1
2,742 by smlewis
Tue, 2017-04-18 08:33
Normal topic Problems with Cterm_amidation.txt
by helenah » Thu, 2020-10-08 04:52
8
2,736 by helenah
Tue, 2020-11-03 04:33
Normal topic What is "residue packing", "repacking", and so on?
by cossio » Wed, 2014-12-03 08:49
2
2,732 by cossio
Wed, 2014-12-03 14:51
Normal topic How to use Rosetta 3.1 to model the structure of an antibody?
by sylvia » Mon, 2009-10-26 14:06
2
2,728 by vanita
Mon, 2014-04-21 06:47
Normal topic Question about run FLEXPEPDOCK with 3 chain
by phanvy » Wed, 2014-07-02 08:46
3
2,727 by phanvy
Wed, 2014-07-02 23:32
Normal topic obtaing pdb files
by knutjbj » Fri, 2011-02-25 11:05
3
2,726 by scombs
Mon, 2014-04-21 06:47
Normal topic Error when running enzyme_design tutorial
by linucks » Fri, 2017-06-30 12:26
4
2,722 by linucks
Mon, 2017-07-03 09:50
Normal topic How to insert a TER line between docking partners
by devroop » Sun, 2012-07-29 13:48
1
2,721 by smlewis
Mon, 2014-04-21 06:47
Normal topic get_distances command in rosetta 3.5
by pramod » Mon, 2014-01-20 11:31
3
2,715 by rmoretti
Mon, 2014-04-21 06:48
Normal topic question about scoring silent output files and their contents
by burkheadlab » Wed, 2011-07-27 16:28
2
2,709 by rmoretti
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
2,708 by smlewis
Mon, 2014-04-21 06:47
Normal topic Error score_scatter_plot.py
by jrcf » Wed, 2015-12-30 05:46
2
2,698 by jrcf
Fri, 2016-02-12 16:41
Normal topic How to generate score file for loop refinement or modelling?
by zhisheng » Fri, 2011-12-09 05:15
2
2,695 by zhisheng
Mon, 2014-04-21 06:47
Normal topic Installing Rosetta Abinitio make_fragments.pl
by ctaylor » Thu, 2009-09-17 09:20
2
2,683 by ctaylor
Mon, 2014-04-21 06:47
Normal topic what is 05.2009 ideal coordinates
by Lindsay » Tue, 2014-09-23 20:36
3
2,683 by rmoretti
Mon, 2014-09-29 13:45
Normal topic "caught exception" for PDB with membrane "DUM" residues
by nitroamos » Wed, 2018-05-30 08:35
2
2,681 by Awagner7
Tue, 2020-04-28 10:51
Normal topic -fake_native Error - not found in command line of rosetta 3.2.1
by vsjasion » Wed, 2011-10-05 12:01
2
2,680 by vsjasion
Mon, 2014-04-21 06:47
Normal topic AnchoredPDBcreator
by spraha » Wed, 2012-03-14 23:34
3
2,676 by smlewis
Mon, 2014-04-21 06:47
Normal topic Cannot use SimpleMetrics
by Vedasheersh » Sun, 2018-06-10 23:38
5
2,675 by smlewis
Tue, 2018-06-12 10:54
Normal topic Multiple jobs for homology modeling
by justin » Fri, 2011-06-24 08:03
1
2,672 by smlewis
Mon, 2014-04-21 06:47
Normal topic Loop modeling FLAGS
by jklett » Fri, 2009-12-04 02:45
3
2,672 by jklett
Mon, 2014-04-21 06:47
Normal topic What is the difference between F and S labeled decoys?
by PaulaBanks » Tue, 2013-08-27 06:09
3
2,670 by PaulaBanks
Mon, 2014-04-21 06:48
Normal topic segmentation fault when using design_hpatch scoring function
by rbjacob » Mon, 2018-04-09 11:05
5
2,668 by smlewis
Wed, 2018-04-11 11:45
Normal topic Using mode=profile
by Biokhar » Fri, 2012-07-06 00:29
2
2,668 by scombs
Mon, 2014-04-21 06:47
Normal topic keep crystal structure hydrogens
by gw » Wed, 2011-07-20 03:54
2
2,667 by gw
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
2,666 by monos_morpheus
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
2,664 by smlewis
Mon, 2014-04-21 06:47
Normal topic CDR Cluster Constrained Relax Equivalent
by SenyorDrew » Wed, 2016-04-27 08:04
3
2,656 by SenyorDrew
Tue, 2016-06-14 06:43
Normal topic RosettaCM rename or swap the order of sequences in your alignment file
by ahmadkhalifa » Fri, 2017-12-22 08:42
4
2,650 by rmoretti
Mon, 2018-01-15 15:24
Normal topic rama vs p_aa_pp vs ref score terms
by jharamesh » Thu, 2015-12-03 14:24
1
2,650 by rmoretti
Thu, 2015-12-03 15:14
Normal topic [dev] Using h-bonding values in new energy term
by ipetrik_ambry » Wed, 2017-03-01 11:33
4
2,648 by ipetrik_ambry
Thu, 2017-03-02 15:35
Normal topic Silent Files
by ctaylor » Tue, 2009-12-22 09:22
3
2,637 by smlewis
Mon, 2014-04-21 06:47
Normal topic score_jd2.macosclangrelease No such file or directory
by ahmadkhalifa » Mon, 2017-11-27 09:26
3
2,637 by everyday847
Tue, 2017-11-28 13:07
Normal topic Loop Modeling
by ctaylor » Fri, 2009-12-18 11:42
3
2,635 by ctaylor
Mon, 2014-04-21 06:47
Normal topic how to use backrub in rosetta3.1
by lqzhang » Mon, 2010-01-11 14:43
3
2,630 by smlewis
Mon, 2014-04-21 06:47
Normal topic Residue variant types and fragments
by jadolfbr » Mon, 2013-01-21 09:01
2
2,625 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic # decoys of silent
by fred » Wed, 2014-04-02 06:00
3
2,623 by fred
Fri, 2014-04-04 11:34
Normal topic symmetric docking application rosetta3.2: the docking_local_refine flag
by doranhen » Sun, 2012-05-06 02:20
2
2,622 by doranhen
Mon, 2014-04-21 06:47
Normal topic relax NOT CONVERGED
by albumns » Thu, 2010-06-24 21:25
3
2,616 by smlewis
Mon, 2014-04-21 06:47
Normal topic ddG from backrub
by jte » Tue, 2010-10-05 14:09
3
2,600 by smlewis
Mon, 2014-04-21 06:47
Normal topic Problems in Loop Modeling
by jklett » Mon, 2009-10-19 07:26
2
2,596 by jklett
Mon, 2014-04-21 06:47
Normal topic should rosetta3.1 do prepacking before docking?
by lqzhang » Thu, 2010-01-07 12:15
3
2,596 by smlewis
Mon, 2014-04-21 06:47
Normal topic fragment picking with 100% sequence identity
by nawsad » Thu, 2013-12-05 07:12
1
2,590 by rmoretti
Mon, 2014-04-21 06:48
Normal topic Explanations to membrane_abinitio options
by justin » Wed, 2010-02-10 01:14
3
2,590 by justin
Mon, 2014-04-21 06:47
Normal topic error for the pose reading:TRP:NtermProteinFull:triazolamerC missing: C1
by wyb » Fri, 2017-12-01 17:50
3
2,583 by rmoretti
Sat, 2017-12-16 12:19
Normal topic help with perturbation docking please
by einew » Fri, 2011-03-25 16:16
2
2,583 by einew
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
2,579 by smlewis
Mon, 2014-04-21 06:47
Normal topic sequence_tolerance optimize the binding to chemical compounds
by coomteng@gmail.com » Tue, 2015-05-05 07:32
3
2,573 by rmoretti
Mon, 2015-05-25 11:00
Normal topic Need help with compilation (How to test if compilation is sucessful)
by greenfur » Fri, 2012-06-29 12:29
1
2,573 by smlewis
Mon, 2014-04-21 06:47
Normal topic rosettaremodel
by berk » Fri, 2013-06-07 00:42
3
2,571 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic I can't find the workflow about modeling disordered regsion using rosetta?
by lihowe » Thu, 2011-12-29 03:45
2
2,566 by wangyr
Mon, 2014-04-21 06:47
Normal topic generate full atom coordinates with abinitio rosetta structure prediction
by anusmita_sahoo » Tue, 2010-03-30 00:11
2
2,564 by Trentage
Mon, 2014-04-21 06:47
Normal topic how build (N-terminal 17 residues) structre /fragment file generation
by venkatazb » Wed, 2016-07-27 23:56
3
2,556 by smlewis
Fri, 2016-07-29 07:43
Normal topic Multigraft
by bo » Tue, 2013-12-24 18:06
2
2,545 by Sergey Menis
Mon, 2014-04-21 06:48
Normal topic Rosetta remodel on intel Xeon Phi
by pablogalazdavison » Wed, 2016-09-14 15:35
3
2,541 by pablogalazdavison
Thu, 2016-09-15 16:36
Normal topic disulfide bridges in loop modeling
by pledor » Fri, 2010-08-06 06:49
2
2,535 by pledor
Mon, 2014-04-21 06:47
Normal topic RosettaProtein_Docking
by khadkab@mcmaster.ca » Tue, 2015-06-30 11:28
1
2,534 by rmoretti
Fri, 2015-07-03 13:24
Normal topic RosettaDOM
by ndousis » Sun, 2010-12-12 01:08
2
2,525 by ndousis
Mon, 2014-04-21 06:47
Normal topic Creation of core.* file in current running directory
by alejandro » Tue, 2011-12-06 06:19
2
2,520 by alejandro
Mon, 2014-04-21 06:47
Normal topic No RMS and IRMS values in protein/nucleic acid docking
by rbeier1 » Wed, 2016-01-13 12:41
2
2,518 by smlewis
Thu, 2016-01-14 08:19
Normal topic ERROR: Error reading in FragmentPicker::read_spine_x(): does not match size of query!
by Anonymous » Sat, 2012-09-08 09:33
1
2,517 by Anonymous
Mon, 2014-04-21 06:47
Normal topic No structure mods allowed during scoring! error
by jadolfbr » Wed, 2013-12-04 14:06
2
2,513 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic rosettautil module not imported cleanly by python scripts
by franfdez » Tue, 2013-08-27 01:25
1
2,513 by rmoretti
Mon, 2014-04-21 06:48
Normal topic ERROR: Unable to open file: ./1brs_0001.pdb
by dkeidel » Tue, 2009-09-29 17:46
1
2,512 by smlewis
Mon, 2014-04-21 06:47
Normal topic Symmetric docking - tetramer of trimers
by SenyorDrew » Fri, 2011-04-29 08:26
1
2,508 by IAndre
Mon, 2014-04-21 06:47
Normal topic Combine flags file with command line arguments?
by cossio » Mon, 2014-12-22 13:52
1
2,508 by smlewis
Tue, 2014-12-23 13:58
Normal topic Building Rosetta Problem: Processor architecture unsupported?
by jalfaro » Tue, 2010-03-23 05:48
1
2,507 by reddybg
Mon, 2014-04-21 06:47
Normal topic Potentially incorrect heavyAtoms_end() iterator in core/conformation/Residue.hh
by tsjain » Wed, 2012-08-15 12:20
3
2,503 by smlewis
Mon, 2014-04-21 06:47
Normal topic Does the energy score output by fixbb design have unit?
by Lindsay » Mon, 2012-06-18 15:03
2
2,497 by Lindsay
Mon, 2014-04-21 06:47
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