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PyRosetta - General

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Normal topic pymover = PyMOL_Mover() hangs IPython?
by cossio » Fri, 2015-04-10 07:38 		4
 5,154 by cossio
Wed, 2015-04-15 12:31
Normal topic Large Memory usage in Windows r10 Build
by ajasja » Fri, 2014-08-22 09:09 		4
 7,567 by ajasja
Mon, 2014-09-22 09:51
Normal topic Strange fold tree problem with classic and fast relax
by jadolfbr » Mon, 2011-03-21 11:58 		4
 5,452 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Alternatives to DockMCMProtocol
by swirt » Thu, 2021-01-28 17:37 		4
 3,112 by swirt
Thu, 2021-02-25 21:54
Normal topic DockingHighResLegacy repacks all sidechains on first apply(), interface sidechains on subsequent apply()
by msellers » Wed, 2012-02-22 22:46 		4
 5,772 by rmoretti
Thu, 2019-05-09 15:03
Normal topic Fragments file
by Run » Tue, 2013-11-26 02:40 		4
 5,287 by rmoretti
Mon, 2014-04-21 06:48
Normal topic hbond_sr_bb, hbond_lr_bb, fa_intra_rep energies from ScoreFunction()
by gerdos » Tue, 2017-04-18 04:46 		4
 4,539 by gerdos
Fri, 2017-04-21 01:53
Normal topic Pose is full atom and mover expects centroid, how do I handle it the best?
by hlinn » Thu, 2022-01-27 05:55 		4
 2,495 by hlinn
Tue, 2022-02-08 07:23
Normal topic Problem importing AlphaFold PDB
by Rick Neubig » Mon, 2023-01-09 09:48 		4
 2,628 by Rick Neubig
Tue, 2023-01-10 04:11
Normal topic set constraints
by zgcarvalho » Wed, 2010-02-24 09:42 		3
 3,733 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic input_pdb
by evo_umich » Sat, 2011-10-01 14:20 		3
 4,905 by evo_umich
Mon, 2014-04-21 06:47
Normal topic pose.replace_residue() & incorrect scoring
by msun » Tue, 2015-10-06 10:51 		3
 4,208 by rmoretti
Wed, 2015-10-07 16:35
Normal topic Allowing cysteines to repack
by eyliaw » Thu, 2012-07-05 14:46 		3
 4,374 by rmoretti
Mon, 2014-04-21 06:47
Normal topic Rosetta score vs Experiment
by thorx020 » Tue, 2012-09-04 12:38 		3
 6,933 by smlewis
Mon, 2014-04-21 06:47
Normal topic Designating Fold Tree Edges as Flexible or Rigid
by nleroy » Tue, 2019-07-23 11:34 		3
 3,164 by smlewis
Tue, 2019-07-23 13:27
Normal topic Iterating over graph edges in PyRosetta.
by ajasja » Mon, 2014-09-22 07:21 		3
 4,754 by rmoretti
Mon, 2014-09-29 00:06
Normal topic Dunbrack Library
by jadolfbr » Tue, 2011-05-10 13:59 		3
 4,352 by weitzner
Mon, 2014-04-21 06:47
Normal topic Using OStream objects in PyRosetta
by ggyimesi » Mon, 2014-02-10 03:10 		3
 4,718 by ggyimesi
Mon, 2014-02-17 09:52
Normal topic preparation the fragment files for mutants
by Victor » Wed, 2012-02-22 11:04 		3
 3,765 by smlewis
Mon, 2014-04-21 06:47
Normal topic Atom-wise energy terms from nearest N-neighbors
by jasiozaucha » Thu, 2021-03-25 14:49 		3
 2,579 by matteoferla
Fri, 2021-05-28 02:41
Normal topic fragment building
by StevPChem » Tue, 2015-08-04 09:01 		3
 4,768 by StevPChem
Thu, 2015-08-06 11:07
Normal topic Username and Password for download link?
by juden99 » Thu, 2011-02-17 03:30 		3
 4,130 by juden99
Mon, 2014-04-21 06:47
Normal topic Disuplhide bonds
by batch2k » Tue, 2009-12-15 09:57 		3
 5,121 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic Getting chi rotamers
by ajasja » Tue, 2014-08-26 12:11 		3
 4,988 by rmoretti
Tue, 2014-09-23 08:36
Normal topic ERROR: unrecognized element Rp when using pose_from_pdb
by johnnytam100 » Thu, 2020-07-09 02:53 		3
 3,185 by rmoretti
Thu, 2020-07-09 08:35
Normal topic "No Python class registered..." when trying to access SymDofs
by pitmand » Tue, 2015-03-17 14:29 		3
 5,270 by Sergey
Fri, 2015-03-27 14:34
Normal topic Peptide design
by AOK » Thu, 2011-02-03 11:35 		3
 4,980 by smlewis
Mon, 2014-04-21 06:47
Normal topic How to create an ObjexxFCL FArray?
by matteoferla » Tue, 2020-08-18 03:22 		3
 2,450 by matteoferla
Thu, 2021-07-08 06:02
Normal topic add missing residues into rna
by galvaner » Tue, 2015-09-15 16:41 		3
 4,774 by galvaner
Mon, 2015-09-21 13:37
Normal topic ClassicRelax: how to block the backbone
by oppopomoz » Fri, 2015-11-27 08:17 		3
 4,410 by rmoretti
Tue, 2015-12-01 15:18
Normal topic Problems with SmoothFragmentMover
by epalovcak » Wed, 2013-10-02 09:20 		3
 4,635 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic adding nucleotides to a dna model
by jadolfbr » Wed, 2012-12-05 11:40 		3
 4,863 by smlewis
Mon, 2014-04-21 06:47
Normal topic Generating random number using numeric.random
by resiros » Thu, 2014-10-23 09:25 		3
 4,221 by rmoretti
Wed, 2014-10-29 10:00
Normal topic Deprotonated LYS
by Arik » Wed, 2011-06-22 16:34 		3
 5,001 by smlewis
Mon, 2014-04-21 06:47
Normal topic change dihedral angles of any residue
by bharat_46010 » Fri, 2013-11-15 00:30 		3
 5,507 by bharat_46010
Mon, 2014-04-21 06:48
Normal topic Getting which rigid body a residue belongs to?
by JuliusSu » Thu, 2014-04-17 21:12 		3
 4,256 by jadolfbr
Mon, 2014-04-21 17:28
Normal topic Energy of individual loop/region
by jadolfbr » Mon, 2012-04-02 13:15 		3
 3,774 by smlewis
Mon, 2014-04-21 06:47
Normal topic RosettaModel blueprint for PyRosetta
by bbrown11 » Tue, 2015-03-03 13:53 		3
 4,868 by matteoferla
Thu, 2021-04-29 06:30
Normal topic Noob question about optimizing a pose
by AleksanderK » Fri, 2019-04-26 10:49 		3
 3,362 by AleksanderK
Fri, 2019-05-03 10:57
Normal topic Questions on rotamer-rotamer energies
by pachecoj » Fri, 2013-07-26 05:01 		3
 4,679 by rmoretti
Mon, 2014-04-21 06:48
Normal topic PyRosetta memory footprint
by LiorZ » Thu, 2016-06-16 04:36 		3
 4,222 by LiorZ
Fri, 2016-06-17 08:20
Normal topic Rosetta get_fa_scorefxn()
by israeldesta » Thu, 2019-10-31 10:18 		3
 4,928 by jadolfbr
Thu, 2019-11-14 15:33
Normal topic Rotamer bin vector from chi angles of a residue in pose not found in Dunbrack rotamer library
by AyushGoyal » Mon, 2014-02-24 22:18 		3
 5,219 by rmoretti
Wed, 2014-02-26 09:40
Normal topic Mistake about rosetta.init()
by sprinkle166 » Tue, 2017-09-26 09:46 		3
 3,841 by sprinkle166
Wed, 2017-09-27 09:17
Normal topic About missing disulfide partners for residue...
by Mon » Wed, 2014-12-17 05:37 		3
 6,075 by jadolfbr
Thu, 2014-12-18 09:37
Normal topic Symmetric pose initialization fails
by gudmal » Tue, 2013-11-26 06:42 		3
 4,063 by Sergey
Mon, 2014-04-21 06:48
Normal topic Generating Atom Pair Constraints
by Peik » Wed, 2020-08-05 15:39 		3
 2,892 by Peik
Thu, 2020-08-06 11:50
Normal topic Namespace PyRosetta Build for Windows?
by protos_heis » Sat, 2015-08-15 10:49 		3
 4,548 by Sergey
Wed, 2015-08-19 15:47
Normal topic How to fold membrane protein in PyRosetta?
by assignfit » Fri, 2011-02-25 21:39 		3
 4,374 by assignfit
Mon, 2014-04-21 06:47
Normal topic Dock antibody at the epitope of antigen
by styang » Fri, 2012-06-22 05:44 		3
 5,658 by smlewis
Mon, 2014-04-21 06:47
Normal topic Resfile Error
by ac.research » Wed, 2019-07-17 13:25 		3
 5,117 by vmulligan
Fri, 2019-07-26 15:08
Normal topic Documentation of ``mysterious'' protocols
by ñ » Wed, 2013-10-30 08:19 		3
 4,424 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic Using pose.set_xyz() to move chains causes increase in only pro_close energy
by msellers » Mon, 2011-07-25 06:57 		3
 4,595 by msellers
Mon, 2014-04-21 06:47
Normal topic Writing out individual residues to a pdbfile
by SenyorDrew » Thu, 2016-12-08 07:33 		3
 4,064 by SenyorDrew
Thu, 2016-12-08 13:10
Normal topic Best Way to Append/Insert Residue
by jaulicino » Tue, 2020-07-21 10:24 		3
 4,072 by matteoferla
Sat, 2020-07-25 03:52
Normal topic BluePrintBDRMover set_atom_type error
by ac.research » Sat, 2017-12-09 02:16 		3
 3,435 by rmoretti
Sat, 2017-12-16 14:06
Normal topic generate_nonstandard_residue_set Exception
by lah435 » Tue, 2017-06-13 18:28 		3
 3,574 by lah435
Fri, 2017-06-16 12:24
Normal topic PyRosetta + PyMol
by reve_etrange » Mon, 2009-11-23 16:44 		3
 4,768 by reve_etrange
Mon, 2014-04-21 06:47
Normal topic [Solved] Docking in metalloprotease (Zinc problem)
by zgcarvalho » Wed, 2010-01-20 16:04 		3
 5,296 by reve_etrange
Mon, 2014-04-21 06:47
Normal topic rmsd and Lrmsd in loop modeling
by Victor » Tue, 2012-01-24 09:52 		3
 4,829 by Victor
Mon, 2014-04-21 06:47
Normal topic Pyrosetta 2.0 - Dunbrak library binary not loading - strange repacking score
by msellers » Wed, 2011-05-11 06:24 		3
 4,417 by smlewis
Mon, 2014-04-21 06:47
Normal topic Rotamers one- and two-body energies
by ajfmdm » Thu, 2024-04-04 00:48 		3
 564 by ajfmdm
Wed, 2024-05-29 05:39
Normal topic interaction energies between atoms
by Stefan » Thu, 2011-04-14 06:15 		3
 6,150 by smlewis
Mon, 2014-04-21 06:47
Normal topic Gradient Descent
by nasim.soltani58 » Thu, 2020-10-01 16:02 		3
 2,755 by vmulligan
Tue, 2020-10-06 15:13
Normal topic Regarding the Documentation of Rosetta and PyRosetta
by jai_INMAS » Tue, 2013-10-22 23:41 		3
 4,388 by jai_INMAS
Mon, 2014-04-21 06:48
Normal topic Simple mover that holds lowest energy pose
by jadolfbr » Fri, 2013-03-15 13:23 		3
 3,944 by jadolfbr
Mon, 2014-04-21 06:47
Normal topic FastRelax results in bad structure
by Eden » Mon, 2021-04-26 08:39 		2
 2,005 by Eden
Wed, 2021-06-23 01:13
Normal topic individual residue score
by yijietseng » Wed, 2019-05-29 09:59 		2
 2,514 by yijietseng
Fri, 2019-05-31 12:21
Normal topic Weird message whenever I try to calculate energies
by astrofunk » Fri, 2010-08-20 05:55 		2
 3,760 by astrofunk
Mon, 2014-04-21 06:47
Normal topic Problem with sending individual energy terms using PyMOL Mover
by jadolfbr » Fri, 2011-12-23 10:54 		2
 3,209 by Sergey
Mon, 2014-04-21 06:47
Normal topic is_aromatic function
by jadolfbr » Mon, 2013-12-02 19:31 		2
 3,083 by jadolfbr
Mon, 2014-04-21 06:48
Normal topic How To Read PyRosetta Documentation - GenericMonteCarloMover as example
by ac.research » Wed, 2017-07-05 09:08 		2
 3,126 by ac.research
Thu, 2017-07-06 11:09
Normal topic [Solved] PyRosetta segmentation fault in Linux
by AlexI » Wed, 2010-02-03 22:59 		2
 4,650 by AlexI
Mon, 2014-04-21 06:47
Normal topic Coordinates in pose do not match those in PDB
by ajasja » Tue, 2014-10-28 12:29 		2
 3,686 by ajasja
Thu, 2014-10-30 08:32
Normal topic Alternative to MinMover
by MNP1986 » Tue, 2018-07-31 02:18 		2
 3,321 by MNP1986
Tue, 2018-07-31 23:50
Normal topic Nonstandard residue parameters fail
by lah435 » Wed, 2014-08-06 17:53 		2
 3,947 by lah435
Mon, 2014-08-18 17:23
Normal topic Less silly way to get number of iterations of Relax
by matteoferla » Tue, 2021-07-20 07:00 		2
 1,887 by matteoferla
Tue, 2021-07-20 13:44
Normal topic Repeat study
by thomashrabe » Tue, 2017-06-20 11:21 		2
 2,601 by parmef
Sat, 2017-06-24 03:18
Normal topic Questions of Cartesian_ddG calculation in PyRosetta
by CKS2001 » Fri, 2022-01-07 01:36 		2
 2,201 by CKS2001
Sat, 2022-01-08 02:14
Normal topic loop modeling error 'CcdLoopClosureMover' object is not callable
by jai_INMAS » Tue, 2013-10-22 01:49 		2
 3,581 by jai_INMAS
Mon, 2014-04-21 06:48
Normal topic Where can I found the dictory of all function of Pyrosetta？
by sprinkle166 » Mon, 2017-10-16 13:58 		2
 2,713 by sprinkle166
Wed, 2017-10-18 09:06
Normal topic Individual Residue Energy
by Peik » Fri, 2021-02-19 10:13 		2
 2,592 by Peik
Fri, 2021-02-19 10:30
Normal topic read parameters of metal ions
by Stefan » Tue, 2011-07-19 08:38 		2
 4,294 by Stefan
Mon, 2014-04-21 06:47
Normal topic Problems when inserting spin-label R1A
by ajasja » Fri, 2014-06-27 04:14 		2
 3,550 by ajasja
Thu, 2014-07-03 05:36
Normal topic Cutout part of a protein
by ac.research » Wed, 2017-05-31 11:55 		2
 2,934 by jadolfbr
Sat, 2017-06-03 19:20
Normal topic installing PyRosetta on Mac OSX 10.6 and Linux in VMWare
by sid » Tue, 2009-10-06 09:04 		2
 4,358 by reve_etrange
Mon, 2014-04-21 06:47
Normal topic libmini.dylib
by evo_umich » Fri, 2011-09-23 14:08 		2
 3,659 by evo_umich
Mon, 2014-04-21 06:47
Normal topic How to pop off terminus variants
by xfliu » Mon, 2012-09-03 03:12 		2
 3,337 by xfliu
Mon, 2014-04-21 06:47
Normal topic Forum webpage not working
by ajasja » Mon, 2014-09-22 06:14 		2
 2,994 by ajasja
Mon, 2014-09-22 09:53
Normal topic Different types of MinMover
by nasim.soltani58 » Sun, 2020-12-20 11:44 		2
 2,072 by nasim.soltani58
Tue, 2020-12-22 13:37
Normal topic Constraint files, section formatted
by srballard » Fri, 2010-11-05 11:55 		2
 3,049 by drluca77
Mon, 2014-04-21 06:47
Normal topic How does one convert a PDB file of an antibody to AHO scheme?
by kylevaccaro » Mon, 2023-02-13 18:14 		2
 1,694 by kylevaccaro
Wed, 2023-02-15 19:18
Normal topic PyRosetta coding subtleties
by lah435 » Wed, 2013-03-27 02:59 		2
 4,515 by Sergey
Mon, 2014-04-21 06:47
Normal topic why two packing setting return different energy?
by zhangying1990 » Wed, 2019-01-30 00:18 		2
 2,748 by zhangying1990
Fri, 2019-02-01 00:30
Normal topic Complex DNA Protein docking
by kim-nguyen » Wed, 2015-07-22 13:49 		2
 4,222 by kim-nguyen
Fri, 2015-07-24 23:04
Normal topic EnergyMethodCreator error when writing custom energy method
by furybubu » Mon, 2017-12-11 15:46 		2
 2,815 by furybubu
Tue, 2017-12-12 10:04
Normal topic Error in core/scoring/methods/VDW_Energy.cc line: 169
by pepfolder » Thu, 2012-05-31 11:13 		2
 4,633 by pepfolder
Mon, 2014-04-21 06:47
Normal topic Reading constraints from a file
by lah435 » Wed, 2017-06-14 18:56 		2
 3,087 by rmoretti
Fri, 2017-06-16 07:22
Normal topic Classic Relax
by iGemBoulder » Fri, 2019-06-28 09:24 		2
 2,815 by sheehajh
Wed, 2019-07-17 12:43
Normal topic Can I export command line & result from iPython PyRosetta shell to a text file?
by lanselibai » Mon, 2014-08-25 04:05 		2
 3,890 by lanselibai
Tue, 2014-08-26 01:49