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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
4,701 by admin
Fri, 2015-09-04 16:17
Normal topic Denovo density corrupted silent file
by ahmadkhalifa » Mon, 2018-04-23 07:30
4
35 by ahmadkhalifa
Thu, 2018-04-26 09:11
Normal topic The concept of unsatisfied hydrogen bond
by asbelx » Wed, 2018-04-25 01:32
2
29 by asbelx
Thu, 2018-04-26 00:23
Normal topic Encouraging better packing in enzyme_design
by linucks » Thu, 2018-03-01 07:05
5
189 by linucks
Wed, 2018-04-25 08:50
Normal topic Molfile to Params File Issue
by jferrie » Mon, 2018-04-23 15:25
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12 by jferrie
Mon, 2018-04-23 15:25
Normal topic Error running GenericMonteCarlo mover within MultipleOutputWrapper mover
by abhi_pe_acharya » Mon, 2018-04-16 04:58
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34 by abhi_pe_acharya
Thu, 2018-04-19 03:49
Normal topic Refinement of a PDB structure containing multiple models
by ahmadkhalifa » Wed, 2018-04-18 07:44
3
43 by smlewis
Wed, 2018-04-18 19:03
Normal topic FARFAR and RNA_Tools: problem executing the command helix_preassemble_setup.py
by obdulia » Wed, 2018-04-18 00:45
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22 by obdulia
Wed, 2018-04-18 00:45
Normal topic Segmentation fault (core dumped) denovo_density.linuxgccrelease
by ahmadkhalifa » Sun, 2018-04-15 17:52
1
33 by smlewis
Mon, 2018-04-16 16:32
Normal topic Modeling transmembrane and intracellular domain
by Sunyp_IM » Sun, 2018-04-08 06:44
1
48 by jkleman
Sat, 2018-04-14 10:55
Normal topic Structure refinement guided by Cryo-EM density maps
by ahmadkhalifa » Thu, 2018-03-08 08:22
6
172 by ahmadkhalifa
Fri, 2018-04-13 09:15
Normal topic segmentation fault when using design_hpatch scoring function
by rbjacob » Mon, 2018-04-09 11:05
5
79 by smlewis
Wed, 2018-04-11 11:45
Normal topic Multiprocessing and running jobs on server using slurm
by ahmadkhalifa » Mon, 2018-04-09 10:59
1
43 by rmoretti
Tue, 2018-04-10 16:00
Normal topic Abinitio isolated
by ac.research » Wed, 2018-04-04 07:36
3
71 by smlewis
Wed, 2018-04-04 10:42
Normal topic build local user guide
by coomteng@gmail.com » Wed, 2018-03-28 13:55
3
84 by coomteng@gmail.com
Wed, 2018-03-28 14:58
Normal topic Secondary Structure Relax
by ac.research » Sat, 2018-03-17 10:50
5
131 by smlewis
Wed, 2018-03-21 08:42
Normal topic Running a ReportFSC mover between two .mrc maps
by ahmadkhalifa » Mon, 2018-03-12 07:52
9
206 by brandon.frenz
Tue, 2018-03-20 10:28
Normal topic Calling a Rosetta xml script in a Python script gives fail to validate error
by ahmadkhalifa » Tue, 2018-03-06 08:00
3
105 by rmoretti
Mon, 2018-03-19 12:35
Normal topic hbnet
by mintseris » Mon, 2018-03-19 09:02
1
53 by rmoretti
Mon, 2018-03-19 09:08
Normal topic The algorithm of adding missing Hydrogen to a backbone
by ac.research » Tue, 2018-03-06 03:48
1
61 by rmoretti
Sat, 2018-03-17 10:43
Normal topic Rosetta matching error
by purvi24 » Mon, 2018-03-12 02:38
1
60 by smlewis
Mon, 2018-03-12 09:57
Normal topic ERROR: Assertion Fdensity.u2 and Fdensity.u3 failed
by ahmadkhalifa » Wed, 2017-12-06 07:38
13
510 by brandon.frenz
Thu, 2018-03-08 09:28
Normal topic demos/public/ideal_proteins Segmentation fault
by coomteng@gmail.com » Wed, 2018-03-07 00:15
5
121 by rmoretti
Thu, 2018-03-08 07:46
Normal topic Problems with "pdb_renumber.py" in tutorial Advanced Protein-Protein Docking
by Sunyp_IM » Sun, 2017-06-25 02:40
7
776 by jadolfbr
Wed, 2018-03-07 10:04
Normal topic Rosetta relax application for generating ensemble of structures.
by abhi_pe_acharya » Mon, 2018-02-26 09:08
3
129 by ssrb
Tue, 2018-03-06 14:15
Normal topic RestrictToRepackingRLT and PreventRepackingRLT
by coomteng@gmail.com » Mon, 2018-03-05 11:19
2
67 by coomteng@gmail.com
Tue, 2018-03-06 02:31
Normal topic Molecular oxygen
by matteoferla » Sat, 2018-02-24 06:05
3
120 by matteoferla
Mon, 2018-02-26 02:05
Normal topic Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41
4
175 by linucks
Fri, 2018-02-23 08:08
Normal topic How to specify a specific rotamer
by Lior_UCSF » Wed, 2018-02-21 20:35
1
80 by rmoretti
Thu, 2018-02-22 09:29
Normal topic Denovo density didn't output a structure
by ahmadkhalifa » Mon, 2018-02-12 08:10
2
145 by ahmadkhalifa
Fri, 2018-02-16 09:17
Normal topic log files
by shadrinams » Fri, 2018-01-26 07:29
7
259 by shadrinams
Mon, 2018-02-12 11:47
Normal topic Icouldnot find DDMI protocol for design protein
by ladimafakher » Mon, 2018-02-12 09:22
1
73 by rmoretti
Mon, 2018-02-12 09:39
Normal topic Repeating sequence in Rosetta de novo protein folding
by orionshih » Wed, 2018-02-07 20:52
2
126 by sheehajh
Thu, 2018-02-08 21:18
Normal topic Calculate ddG in mutation scan of a homodimer
by zachdebruine » Thu, 2018-02-01 10:02
1
123 by rmoretti
Mon, 2018-02-05 15:44
Normal topic Using NCAAs in protocols with native heme proteins
by htorres » Wed, 2018-01-24 08:32
2
140 by htorres
Mon, 2018-02-05 06:53
Normal topic ERROR: FragmentIO: could not open file
by ahmadkhalifa » Wed, 2018-01-31 13:30
1
97 by rmoretti
Wed, 2018-01-31 14:57
Normal topic Structure refinement with RDC constraint
by shushunur » Thu, 2018-01-18 00:44
1
229 by rmoretti
Tue, 2018-01-30 09:08
Normal topic [dev] quickest way to determine bond distance between polymeric-bonded residues in Pose/Conformation
by ipetrik_ambry » Thu, 2018-01-18 12:26
1
136 by rmoretti
Tue, 2018-01-30 08:29
Normal topic changing the chain id
by aneamtu » Tue, 2018-01-09 00:08
2
144 by aneamtu
Thu, 2018-01-18 00:56
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
4,055 by rmoretti
Mon, 2018-01-15 15:37
Normal topic The question about  protonation of Rosetta
by asbelx » Tue, 2017-12-19 05:44
3
246 by rmoretti
Mon, 2018-01-15 15:34
Normal topic RosettaCM rename or swap the order of sequences in your alignment file
by ahmadkhalifa » Fri, 2017-12-22 08:42
4
225 by rmoretti
Mon, 2018-01-15 15:24
Normal topic Expanding the silent file
by jharamesh » Fri, 2018-01-12 09:15
2
105 by rmoretti
Mon, 2018-01-15 14:35
Normal topic Can I thread a two chained structure in RosettaCM?
by ahmadkhalifa » Mon, 2018-01-08 09:41
2
126 by rmoretti
Mon, 2018-01-15 14:23
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
152 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Converting charmm parameter files (.par)
by ajasja » Mon, 2014-09-29 07:19
3
1,158 by jcminerlanl
Tue, 2017-12-19 14:03
Normal topic error for the pose reading:TRP:NtermProteinFull:triazolamerC missing: C1
by wyb » Fri, 2017-12-01 17:50
3
188 by rmoretti
Sat, 2017-12-16 12:19
Normal topic Problems with disulphide bonds during KIC
by Loki01 » Tue, 2017-11-28 03:11
5
281 by Loki01
Thu, 2017-12-14 06:20
Normal topic What is the expected behaviour when minimizing a jump edge?
by bio_james » Wed, 2017-12-13 09:13
0
102 by bio_james
Wed, 2017-12-13 09:13
Normal topic Can I use next generation KIC with fragments?
by Loki01 » Thu, 2017-12-07 06:19
1
141 by Loki01
Wed, 2017-12-13 05:27
Normal topic lDDT: local Distance Difference Test implemented?
by ipetrik_ambry » Wed, 2017-12-06 13:11
0
101 by ipetrik_ambry
Wed, 2017-12-06 13:11
Normal topic Fitting a structure with an unrecognized residue to an EM density
by ahmadkhalifa » Tue, 2017-12-05 14:44
2
160 by ahmadkhalifa
Wed, 2017-12-06 12:30
Normal topic fastdesign with constraints in RosettaScripts
by staciekim » Wed, 2017-11-29 13:33
1
149 by rmoretti
Sat, 2017-12-02 10:22
Normal topic score_jd2.macosclangrelease No such file or directory
by ahmadkhalifa » Mon, 2017-11-27 09:26
3
236 by everyday847
Tue, 2017-11-28 13:07
Normal topic Method to keep ATP in the certain position in the prepack step
by ziqi1234 » Tue, 2017-11-21 05:55
0
120 by ziqi1234
Tue, 2017-11-21 05:55
Normal topic Docking Local Refine Not Moving Input
by SenyorDrew » Sat, 2017-10-21 08:26
1
156 by SenyorDrew
Mon, 2017-11-20 13:27
Normal topic MET, MSE, and fMET Amino Acids
by ac.research » Sat, 2017-11-18 06:33
1
190 by smlewis
Sun, 2017-11-19 20:08
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
145 by ac.research
Sat, 2017-11-18 06:54
Normal topic Design constraints on pairs of residues
by SenyorDrew » Mon, 2017-10-02 07:25
3
390 by SenyorDrew
Mon, 2017-11-13 11:44
Normal topic keep ATP in the kinase-peptide structure while docking
by ziqi1234 » Fri, 2017-11-10 04:04
0
136 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
232 by smlewis
Wed, 2017-11-08 12:08
Normal topic Rosetta/PyRosetta on GPU
by ac.research » Mon, 2017-11-06 05:18
1
203 by rmoretti
Mon, 2017-11-06 07:36
Normal topic Error running RosettaAntibodyDesign application
by SenyorDrew » Mon, 2017-10-30 08:13
1
151 by jadolfbr
Wed, 2017-11-01 10:11
Normal topic [dev] examples for implementing setup_for_packing, prepare_rotamers_for_packing?
by ipetrik_ambry » Mon, 2017-10-30 17:03
0
127 by ipetrik_ambry
Mon, 2017-10-30 17:03
Normal topic [dev] determine which score_type's enabled in create_energy_method?
by ipetrik_ambry » Fri, 2017-10-27 15:37
3
247 by rmoretti
Mon, 2017-10-30 12:02
Normal topic Comparative Modeling Tutorial Script not working
by Srinivas23 » Thu, 2017-09-21 12:00
4
360 by Srinivas23
Tue, 2017-10-24 10:58
Normal topic This element is not expected.
by ac.research » Fri, 2017-10-13 03:47
2
321 by rmoretti
Mon, 2017-10-16 12:17
Normal topic Helical symmetry for cryo-EM refinement
by fmerino » Mon, 2017-10-16 04:02
0
162 by fmerino
Mon, 2017-10-16 04:02
Normal topic Abinitio Video
by ac.research » Tue, 2017-09-12 04:00
3
335 by ac.research
Sun, 2017-09-24 11:25
Normal topic Produces a set of rotamers from a given residue
by a-eatemadi@razi... » Tue, 2017-08-15 08:05
5
551 by a-eatemadi@razi...
Fri, 2017-09-15 07:45
Normal topic extract pdbs segmentation fault
by Swillard » Fri, 2017-09-08 07:20
1
209 by rmoretti
Fri, 2017-09-08 15:15
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36
1
213 by smlewis
Fri, 2017-09-08 11:05
Normal topic Docking individual residue ussing RosettaDock
by a-eatemadi@razi... » Wed, 2017-09-06 05:50
1
191 by rmoretti
Wed, 2017-09-06 08:47
Normal topic The vall.jul19.2011.gz Database
by ac.research » Fri, 2017-09-01 02:29
4
473 by ac.research
Mon, 2017-09-04 16:43
Normal topic What is the general protocol for antibody-antigen docking without the native antibody-antigen structures?
by Sunyp_IM » Sun, 2017-08-13 05:42
11
1,006 by smlewis
Tue, 2017-08-29 08:56
Normal topic How to read the output score file from rosetta?
by Sunyp_IM » Sun, 2017-08-27 05:29
1
328 by rmoretti
Mon, 2017-08-28 09:32
Normal topic Problem with the top 25 fragments used in the library of 200 nine-residue fragments in AbinitioRelax
by MA » Wed, 2017-07-26 01:12
1
231 by rmoretti
Mon, 2017-08-21 09:55
Normal topic Issues with residues and structure changing with FlexPepDock; is this normal?
by rnelson » Tue, 2017-08-08 10:06
1
237 by Ora Schueler-Furman
Sun, 2017-08-20 00:54
Normal topic Cannot run binaries after successful compilation
by ac.research » Mon, 2017-08-14 02:56
6
586 by ac.research
Fri, 2017-08-18 00:57
Normal topic Protein Docking Error
by ac.research » Thu, 2017-08-17 02:57
2
299 by ac.research
Fri, 2017-08-18 00:53
Normal topic Error when running "plot_LHOC.py"
by Sunyp_IM » Sun, 2017-08-13 05:54
5
475 by smlewis
Wed, 2017-08-16 08:30
Normal topic De novo Protein Design
by ac.research » Sat, 2017-07-15 10:39
5
919 by rmoretti
Mon, 2017-08-14 09:06
Normal topic Modeling protonated histidine
by SenyorDrew » Mon, 2016-07-18 07:34
3
959 by matteoferla
Sat, 2017-08-05 07:18
Normal topic Typical relax options not applied in relax.mpi.linuxiccrelease??
by David Weis » Mon, 2017-02-27 11:35
5
794 by rmoretti
Thu, 2017-08-03 09:01
Normal topic Problem with outputing decoys in the process of AbinitioRelax
by MA » Thu, 2017-07-13 23:27
3
374 by rmoretti
Thu, 2017-08-03 08:50
Normal topic How to set the enviroment variable $ROSETTA3, $ $ROSETTA3_DB, $ROSETTA_TOOLS?
by Sunyp_IM » Thu, 2017-07-27 01:07
1
325 by SenyorDrew
Sat, 2017-07-29 09:59
Normal topic Error using InterfaceHoles filter
by SenyorDrew » Fri, 2017-04-14 08:55
4
521 by SenyorDrew
Mon, 2017-07-24 11:06
Normal topic SNUGDOCK
by adva » Sun, 2017-07-16 00:49
1
241 by jeliazkov
Tue, 2017-07-18 09:51
Normal topic B1_SampleSegment1.sh from RosettaES tutorial crashes
by ab » Tue, 2017-07-04 08:42
12
1,324 by brandon.frenz
Sat, 2017-07-08 13:49
Normal topic Cyclizing .pdb of a linear chain.
by jcminerlanl » Wed, 2017-07-05 23:56
3
399 by jcminerlanl
Thu, 2017-07-06 09:22
Normal topic Minimizing across jumps
by SenyorDrew » Thu, 2017-07-06 06:26
2
328 by SenyorDrew
Thu, 2017-07-06 07:48
Normal topic Error when running enzyme_design tutorial
by linucks » Fri, 2017-06-30 12:26
4
493 by linucks
Mon, 2017-07-03 09:50
Normal topic Some problems with the "advanced protein-protein docking" tutorial
by Sunyp_IM » Tue, 2017-06-27 09:33
1
257 by smlewis
Wed, 2017-06-28 06:59
Normal topic Problems with output control
by Sunyp_IM » Thu, 2017-06-22 15:30
3
423 by rmoretti
Wed, 2017-06-28 01:33
Normal topic optimisation of a protein-protein interface
by sdh_h » Thu, 2017-05-04 05:06
1
401 by rmoretti
Mon, 2017-05-15 09:03
Normal topic rosetta compile
by MA » Wed, 2017-04-26 00:46
2
394 by MA
Thu, 2017-04-27 18:53
Normal topic Adding centroid .params files for non-canonical residues based on all-atom .params files
by jcminerlanl » Thu, 2017-04-27 09:28
2
405 by vmulligan
Thu, 2017-04-27 16:41
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
382 by rmoretti
Fri, 2017-04-21 07:52
Normal topic Problem with running turtorial of rna denovo
by myle » Fri, 2017-04-14 09:23
3
453 by rmoretti
Tue, 2017-04-18 13:49
Normal topic Library of unnatural amino acid parameters
by saxen » Mon, 2017-04-17 11:08
1
389 by smlewis
Tue, 2017-04-18 08:33

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