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Rosetta 3 - General

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Sticky topic Sticky: FAQ
by admin » Mon, 2010-08-30 04:16
0
4,658 by admin
Fri, 2015-09-04 16:17
Normal topic How to specify a specific rotamer
by Lior_UCSF » Wed, 2018-02-21 20:35
1
22 by rmoretti
Thu, 2018-02-22 09:29
Normal topic Unrecognised resiudues when rescoring PDB files generated by enzyme_design under MPI
by linucks » Tue, 2018-02-13 03:41
1
44 by rmoretti
Wed, 2018-02-21 12:37
Normal topic Denovo density didn't output a structure
by ahmadkhalifa » Mon, 2018-02-12 08:10
2
69 by ahmadkhalifa
Fri, 2018-02-16 09:17
Normal topic log files
by shadrinams » Fri, 2018-01-26 07:29
7
120 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
27 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
59 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
65 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
75 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
42 by rmoretti
Wed, 2018-01-31 14:57
Normal topic ERROR: Assertion Fdensity.u2 and Fdensity.u3 failed
by ahmadkhalifa » Wed, 2017-12-06 07:38
10
287 by brandon.frenz
Tue, 2018-01-30 11:04
Normal topic Structure refinement with RDC constraint
by shushunur » Thu, 2018-01-18 00:44
1
139 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
73 by rmoretti
Tue, 2018-01-30 08:29
Normal topic changing the chain id
by aneamtu » Tue, 2018-01-09 00:08
2
84 by aneamtu
Thu, 2018-01-18 00:56
Normal topic Histidine protonation
by DmitriiN » Mon, 2016-09-26 13:15
11
3,506 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
170 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
124 by rmoretti
Mon, 2018-01-15 15:24
Normal topic Expanding the silent file
by jharamesh » Fri, 2018-01-12 09:15
2
62 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
70 by rmoretti
Mon, 2018-01-15 14:23
Normal topic H3 modelling scoring function
by aneamtu » Wed, 2017-12-27 23:10
2
94 by aneamtu
Mon, 2018-01-08 23:49
Normal topic Converting charmm parameter files (.par)
by ajasja » Mon, 2014-09-29 07:19
3
1,087 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
124 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
205 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
64 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
93 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
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66 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
104 by ahmadkhalifa
Wed, 2017-12-06 12:30
Normal topic fastdesign with constraints in RosettaScripts
by staciekim » Wed, 2017-11-29 13:33
1
100 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
151 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
84 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
116 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
120 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
106 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
304 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
103 by ziqi1234
Fri, 2017-11-10 04:04
Normal topic How to make a resfile
by dflaher » Fri, 2017-11-03 10:26
3
166 by smlewis
Wed, 2017-11-08 12:08
Normal topic Rosetta/PyRosetta on GPU
by ac.research » Mon, 2017-11-06 05:18
1
138 by rmoretti
Mon, 2017-11-06 07:36
Normal topic Error running RosettaAntibodyDesign application
by SenyorDrew » Mon, 2017-10-30 08:13
1
110 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
96 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
174 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
267 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
205 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
117 by fmerino
Mon, 2017-10-16 04:02
Normal topic Abinitio Video
by ac.research » Tue, 2017-09-12 04:00
3
258 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
441 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
162 by rmoretti
Fri, 2017-09-08 15:15
Normal topic Ineffective Constraints
by Sandy » Tue, 2017-09-05 19:36
1
162 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
149 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
366 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
753 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
245 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
180 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
189 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
444 by ac.research
Fri, 2017-08-18 00:57
Normal topic Protein Docking Error
by ac.research » Thu, 2017-08-17 02:57
2
241 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
361 by smlewis
Wed, 2017-08-16 08:30
Normal topic De novo Protein Design
by ac.research » Sat, 2017-07-15 10:39
5
688 by rmoretti
Mon, 2017-08-14 09:06
Normal topic Modeling protonated histidine
by SenyorDrew » Mon, 2016-07-18 07:34
3
861 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
672 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
298 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
231 by SenyorDrew
Sat, 2017-07-29 09:59
Normal topic Error using InterfaceHoles filter
by SenyorDrew » Fri, 2017-04-14 08:55
4
420 by SenyorDrew
Mon, 2017-07-24 11:06
Normal topic SNUGDOCK
by adva » Sun, 2017-07-16 00:49
1
195 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
1,086 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
315 by jcminerlanl
Thu, 2017-07-06 09:22
Normal topic Minimizing across jumps
by SenyorDrew » Thu, 2017-07-06 06:26
2
273 by SenyorDrew
Thu, 2017-07-06 07:48
Normal topic Problems with "pdb_renumber.py" in tutorial Advanced Protein-Protein Docking
by Sunyp_IM » Sun, 2017-06-25 02:40
5
595 by smlewis
Tue, 2017-07-04 11:34
Normal topic Error when running enzyme_design tutorial
by linucks » Fri, 2017-06-30 12:26
4
407 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
211 by smlewis
Wed, 2017-06-28 06:59
Normal topic Problems with output control
by Sunyp_IM » Thu, 2017-06-22 15:30
3
343 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
344 by rmoretti
Mon, 2017-05-15 09:03
Normal topic rosetta compile
by MA » Wed, 2017-04-26 00:46
2
338 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
345 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
324 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
391 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
330 by smlewis
Tue, 2017-04-18 08:33
Normal topic can not find a residue type that matches the residue HIS_P:NtermProteinFull
by tarsis » Wed, 2017-04-05 08:51
1
314 by rmoretti
Fri, 2017-04-14 08:37
Normal topic constraints
by lah435 » Sun, 2017-03-12 03:25
2
364 by lah435
Mon, 2017-04-03 19:50
Normal topic Data Check for a newb
by ac.research » Sun, 2017-03-12 23:42
2
390 by ac.research
Fri, 2017-03-31 07:36
Normal topic Extremely low interface scores with "local refinement"
by eminegenetics » Wed, 2017-03-29 12:24
1
281 by rmoretti
Wed, 2017-03-29 12:37
Normal topic Computing energy gradients for side chain minimization
by pachecoj » Wed, 2017-03-29 08:03
5
607 by pachecoj
Wed, 2017-03-29 12:32
Normal topic Error running snugdock
by SenyorDrew » Tue, 2017-03-14 10:00
5
721 by SenyorDrew
Wed, 2017-03-29 06:40
Normal topic Error while trying to run r_noe_assign
by sn » Mon, 2017-03-13 11:40
1
264 by rmoretti
Tue, 2017-03-28 09:02
Normal topic Using logic in resfile, Rosetta Scripts
by tsztain » Wed, 2017-03-22 13:50
1
286 by smlewis
Wed, 2017-03-22 14:02
Normal topic [dev] not seeing energy in pose row for new energy term in design
by ipetrik_ambry » Fri, 2017-03-03 13:16
1
313 by ipetrik_ambry
Tue, 2017-03-14 14:09
Normal topic scoring with omega energy term
by SergeyP » Thu, 2017-03-09 12:03
2
411 by SergeyP
Fri, 2017-03-10 11:16
Normal topic Rosetta Antibody Prepack - Problem HL_A vs. LH_A
by cannond » Fri, 2017-03-03 02:41
5
828 by cannond
Wed, 2017-03-08 03:00
Normal topic combine_silent ERROR: unknown atom_name: CYS SG
by freedman » Mon, 2017-03-06 10:56
5
598 by freedman
Mon, 2017-03-06 13:24
Normal topic Looking for collaboration.
by ac.research » Mon, 2017-03-06 04:54
1
283 by rmoretti
Mon, 2017-03-06 08:37
Normal topic [dev] Using h-bonding values in new energy term
by ipetrik_ambry » Wed, 2017-03-01 11:33
4
627 by ipetrik_ambry
Thu, 2017-03-02 15:35
Normal topic Antibody Homology Modeling - Antibody vs. Antibody_legacy
by cannond » Tue, 2017-02-14 05:53
4
777 by cannond
Wed, 2017-03-01 08:05
Normal topic Antibody homology modeling fails after blastp
by sunhwan » Sat, 2017-02-18 11:25
7
896 by sunhwan
Mon, 2017-02-27 11:02
Hot topic protein design question
by bo » Fri, 2012-08-24 10:41
32
11,335 by ac.research
Sat, 2017-02-11 07:33
Normal topic Robetta nstruct number
by ac.research » Tue, 2017-01-31 14:27
1
343 by rmoretti
Thu, 2017-02-02 08:52
Normal topic Does the fold count reset if abinitio is restarted?
by burkheadlab » Mon, 2011-06-13 11:39
10
3,283 by rmoretti
Thu, 2017-02-02 08:32
Normal topic ETABLE constraint function type
by allan.ferrari » Tue, 2017-01-10 08:01
8
1,299 by smlewis
Sun, 2017-01-15 18:14
Normal topic Different weights in the constraints for each stage of AbinitioRelax
by allan.ferrari » Sun, 2017-01-15 04:35
2
501 by smlewis
Sun, 2017-01-15 18:10
Normal topic Error with non-canonical amino acid in SnugDock.
by sk0319 » Thu, 2016-12-29 16:12
8
1,215 by sk0319
Wed, 2017-01-11 10:52
Normal topic Rotamer Library Generation in Rosetta3
by jcminerlanl » Wed, 2016-11-30 07:34
3
788 by sk0319
Thu, 2017-01-05 17:07
Normal topic distances definition in course-grained (centroid mode) steps
by allan.ferrari » Tue, 2017-01-03 05:15
6
1,114 by allan.ferrari
Tue, 2017-01-03 11:15

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