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Rosetta 3 - Applications

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Normal topic Should I trust the score output from relax used with a protein complex?
by cossio » Thu, 2015-05-07 06:08
1
2,203 by rmoretti
Mon, 2015-05-25 12:37
Normal topic Loopmodel with DNA has no energy score
by Nicky_Learning_... » Sun, 2015-05-10 19:31
1
2,308 by rmoretti
Mon, 2015-05-25 12:30
Normal topic SymDock with constraints
by felipet » Thu, 2015-05-14 09:01
1
3,157 by rmoretti
Mon, 2015-05-25 11:49
Normal topic loop modeling scoring
by Nicky_Learning_... » Wed, 2015-05-13 20:00
1
2,739 by rmoretti
Mon, 2015-05-25 11:30
Normal topic Error while reading in silent file
by rweisse » Mon, 2015-04-20 00:31
4
5,528 by rmoretti
Thu, 2015-04-30 16:46
Normal topic Failing Fragment libraries us Chemical shifts with Robettaa
by kalabharath » Tue, 2015-04-28 19:33
2
2,762 by kalabharath
Wed, 2015-04-29 16:21
Normal topic Pepspec options
by shaunmk » Mon, 2015-04-27 02:33
0
1,669 by shaunmk
Mon, 2015-04-27 02:33
Normal topic JobDistributor problem in antibody modeling
by Wizard » Wed, 2015-04-22 00:35
2
3,421 by Wizard
Sun, 2015-04-26 22:36
Normal topic Enzdes: increase weight of energy term for steric clashes with ligand
by eyong123 » Wed, 2015-03-25 09:12
5
6,116 by rmoretti
Fri, 2015-04-24 12:02
Normal topic Enzdes scorefile lost, can I recreate it
by eyong123 » Wed, 2015-04-15 05:55
2
2,742 by eyong123
Wed, 2015-04-22 11:33
Normal topic Can't append or prepend with pepspec
by danzinho » Tue, 2015-03-31 01:19
3
3,924 by dswhit
Tue, 2015-04-21 10:14
Normal topic ddg_monomer: what is the meaning of "total score" and "score"?
by lanselibai » Tue, 2015-01-13 14:49
4
6,847 by rmoretti
Thu, 2015-04-16 11:23
Normal topic Enzdes constraint file not defined correctly
by eyong123 » Fri, 2015-03-27 07:16
3
3,859 by rmoretti
Thu, 2015-04-16 10:38
Normal topic Repeatability of DDG calculation
by jennifer » Wed, 2015-04-08 05:29
0
1,623 by jennifer
Wed, 2015-04-08 05:29
Normal topic the ddg of mutant is same as the wt
by deepanshuiitb » Wed, 2015-03-04 11:56
6
6,737 by jadolfbr
Tue, 2015-04-07 10:50
Normal topic Conformers in EnzDes
by JorickF » Fri, 2015-03-06 04:41
5
7,202 by rmoretti
Tue, 2015-03-31 08:56
Normal topic Warning messages in Interface analyzer output
by Pernille » Wed, 2015-03-25 00:53
4
4,589 by rmoretti
Tue, 2015-03-31 08:20
Normal topic Total score problems with high-res ddg_monomer
by jklesmith » Tue, 2015-03-10 15:54
2
3,612 by jennifer
Fri, 2015-03-27 05:56
Normal topic Design a peptide linked to small molecule ligand
by shaunmk » Mon, 2015-03-02 09:05
1
2,571 by rmoretti
Wed, 2015-03-25 12:39
Normal topic References where Rosetta is used to compute ddG of binding after mutation?
by cossio » Tue, 2015-03-17 05:13
1
2,935 by rmoretti
Wed, 2015-03-25 11:33
Normal topic Calculate_protein_protein_ddg
by kamau » Fri, 2015-01-30 11:27
2
3,032 by deepanshuiitb
Thu, 2015-03-19 19:14
Normal topic Floppy tail: sidechain mutation during calculation
by syoifczeri » Mon, 2015-03-09 19:01
2
3,145 by syoifczeri
Tue, 2015-03-10 23:08
Normal topic ddg_monomer: How the ddG is actually calculated based on the 50 trajectories? What scorefunction is used?
by lanselibai » Tue, 2015-02-24 02:38
4
6,348 by lanselibai
Sun, 2015-03-01 15:00
Normal topic Filter ddg_filter reports failure!
by deepanshuiitb » Fri, 2015-02-27 18:19
2
3,042 by deepanshuiitb
Sat, 2015-02-28 19:24
Normal topic Executing the clean_pdb.py script
by Rkfoury » Fri, 2015-02-20 10:16
1
3,883 by lanselibai
Tue, 2015-02-24 02:36
Normal topic Pmut_scan with symmetry
by felipet » Thu, 2015-02-05 08:53
5
5,871 by felipet
Wed, 2015-02-11 05:13
Normal topic Output structures from docking_prepack_protocol: initial__*.pdb vs prepack__*.pdb, which one should I send to docking_protocol?
by cossio » Thu, 2015-02-05 07:10
1
2,343 by rmoretti
Mon, 2015-02-09 12:33
Normal topic Is there a way to restrict memory usage of ddg_monomer?
by cossio » Fri, 2015-01-30 14:35
5
5,237 by rmoretti
Mon, 2015-02-09 12:04
Normal topic minirosetta: how to reserve (inter-chain) disulfides after relax ?
by lanselibai » Sat, 2015-01-24 10:56
0
2,257 by lanselibai
Thu, 2015-01-29 00:50
Hot topic Ab initio with multiple metal ions
by cheyuk » Sun, 2013-12-29 17:58
19
20,360 by masterofpuppets
Tue, 2015-01-27 04:26
Normal topic extract_pdbs fails to open silent file when -auto_setup_metals enabled
by attesor » Thu, 2015-01-15 03:22
4
5,040 by attesor
Tue, 2015-01-27 02:20
Normal topic Relax with a ligand is messing up the coordinates of the ligand
by brspurri » Sat, 2015-01-24 12:39
1
2,918 by rmoretti
Mon, 2015-01-26 12:15
Normal topic How to build disulfide bond between two cysteine, i.e. change two "-SH" (sulfydryl) into "-S-S-"?
by lanselibai » Sat, 2015-01-17 11:19
1
3,167 by lanselibai
Wed, 2015-01-21 02:40
Normal topic Reproduce Robetta's ddg values of interface alanine scan using Rosetta?
by cossio » Mon, 2015-01-19 07:14
0
2,754 by cossio
Mon, 2015-01-19 07:14
Normal topic How to output all iteration structures from ddg_monomer?
by cossio » Fri, 2014-12-26 13:40
4
4,906 by cossio
Mon, 2015-01-19 07:10
Normal topic FloppyTail as a rosettascripts file
by tiagogomes89 » Mon, 2015-01-19 02:45
0
1,421 by tiagogomes89
Mon, 2015-01-19 02:45
Normal topic remodel: what are the exact meanings of notations for secondary structure?
by lanselibai » Sat, 2015-01-17 04:53
0
1,520 by lanselibai
Sat, 2015-01-17 07:57
Normal topic Does relax.linuxgccrelease fully relax the structure compared to ddg_monomer.linuxgccrelease?
by lanselibai » Thu, 2015-01-08 03:23
3
3,655 by lanselibai
Tue, 2015-01-13 14:25
Normal topic ddg_monomer with -ddg::local_opt_only true, will it affect other chains that are close?
by cossio » Fri, 2014-12-26 13:11
1
2,123 by rmoretti
Tue, 2015-01-13 07:44
Normal topic ddg_monomer: if MPI executable is reproducible and efficient?
by lanselibai » Sun, 2015-01-11 09:48
0
1,660 by lanselibai
Sun, 2015-01-11 10:50
Normal topic "ddg_monomer.linuxgccrelease" by following "High Resolution Protocol"
by lanselibai » Wed, 2014-10-01 09:54
7
10,826 by lanselibai
Sat, 2015-01-03 08:18
Normal topic Segmentation fault when running Abinito Relax
by Hongtham » Mon, 2014-12-15 07:16
1
3,174 by rmoretti
Fri, 2015-01-02 11:45
Normal topic score application
by Hongtham » Tue, 2014-12-23 06:38
1
2,042 by rmoretti
Fri, 2015-01-02 11:06
Normal topic Docking with constraint
by Hongtham » Sat, 2014-12-27 09:56
2
2,853 by rmoretti
Fri, 2015-01-02 09:43
Normal topic algebric library for rosetta
by yigallah » Mon, 2014-12-15 08:46
0
1,415 by yigallah
Mon, 2014-12-15 08:46
Normal topic csrosetta.org login
by jfeuva » Tue, 2014-12-09 14:49
0
24,417 by jfeuva
Tue, 2014-12-09 14:49
Normal topic Checkpoint with rosetta3.4
by AmelieH » Mon, 2014-12-01 15:51
1
2,658 by rmoretti
Wed, 2014-12-03 19:07
Normal topic crazy loopmodel: linear output pdbs
by fred » Wed, 2014-12-03 12:27
0
1,404 by fred
Wed, 2014-12-03 12:28
Hot topic Syntax for relax.linuxgccrelease
by lanselibai » Wed, 2014-09-24 04:34
18
24,447 by lanselibai
Tue, 2014-12-02 09:46
Normal topic If "clustering.py" can be used for PDBs contain two chains?
by lanselibai » Wed, 2014-11-05 06:05
7
7,182 by lanselibai
Tue, 2014-12-02 09:43
Normal topic Error encountered during Rosetta loop modeling
by max » Tue, 2014-11-25 02:17
3
3,835 by max
Thu, 2014-11-27 02:56
Normal topic Instructing design scripts to use noncanonical AA instead of canonical
by zcrook » Tue, 2014-11-25 10:43
1
2,132 by rmoretti
Wed, 2014-11-26 07:51
Normal topic Disulfide prediction from primary sequence
by zcrook » Wed, 2014-11-12 14:44
2
5,027 by zcrook
Tue, 2014-11-25 10:27
Normal topic Antibody protocol: unusual antibodies, and chainbreaks
by Cyril Cros » Mon, 2014-07-21 17:03
5
6,320 by Cyril Cros
Tue, 2014-11-25 08:21
Normal topic Steric clashes in RNA minimization
by brianmlee » Tue, 2014-11-18 18:29
5
6,141 by brianmlee
Mon, 2014-11-24 19:40
Normal topic scoring of beta sandwich protein
by attesor » Mon, 2014-11-17 08:24
6
6,097 by rmoretti
Thu, 2014-11-20 10:46
Normal topic Syntax for python-based (.py) command line on cluster
by lanselibai » Fri, 2014-11-14 09:32
2
5,157 by lanselibai
Thu, 2014-11-20 02:15
Normal topic Docking flags
by AmelieH » Thu, 2014-11-13 08:46
5
5,369 by AmelieH
Wed, 2014-11-19 11:26
Normal topic Symmetry-aware Backrub?
by gamacy » Fri, 2014-11-14 02:18
1
2,217 by rmoretti
Tue, 2014-11-18 09:10
Normal topic How can I prevent coordinates shift when using "loopmodel.linuxgccrelease"?
by lanselibai » Tue, 2014-11-04 14:56
7
7,782 by lanselibai
Wed, 2014-11-12 11:17
Normal topic Rotamers used in fixbb
by lanselibai » Thu, 2014-11-06 02:47
6
6,141 by lanselibai
Tue, 2014-11-11 15:28
Normal topic Got error when running minirosetta.linuxgccrelease on cluster but fine on Ubuntu
by lanselibai » Mon, 2014-11-10 08:12
2
2,924 by lanselibai
Tue, 2014-11-11 04:42
Normal topic loop_length_changing
by lanselibai » Tue, 2014-10-14 04:10
14
13,862 by lanselibai
Fri, 2014-11-07 02:06
Normal topic latest version of rosetta unable to build models
by pramod » Mon, 2014-11-03 11:31
1
2,864 by rmoretti
Tue, 2014-11-04 10:33
Normal topic Abinitio Relax Error from -kill_hairpins
by attesor » Tue, 2014-10-28 05:33
7
7,611 by rmoretti
Tue, 2014-11-04 10:28
Normal topic "Segmentation fault" for "minirosetta.linuxgccrelease"
by lanselibai » Tue, 2014-11-04 03:17
1
2,850 by rmoretti
Tue, 2014-11-04 08:53
Normal topic suppress pdb output from backrub
by attesor » Mon, 2014-10-27 11:16
7
7,207 by rmoretti
Mon, 2014-11-03 15:47
Normal topic Can I assume the outputs from different runs are from a same batch?
by lanselibai » Mon, 2014-11-03 06:34
4
4,745 by lanselibai
Mon, 2014-11-03 13:15
Normal topic Ligand docking: ERROR: set_atom_base: atoms must be bonded!
by mengzhang » Mon, 2014-05-12 12:36
1
3,016 by jharamesh
Mon, 2014-11-03 12:50
Normal topic Adding 'virtual' residues for N- and C-terminal optimisation
by Derek Smith » Thu, 2014-08-14 23:18
1
2,346 by jadolfbr
Fri, 2014-10-31 09:00
Normal topic Script for loop modeling: how to define loop sequence
by batch2k » Thu, 2014-10-30 12:58
1
2,272 by jadolfbr
Fri, 2014-10-31 08:45
Normal topic problem with modelling of protein (140 and 150 residues respectively)
by krlitros87 » Wed, 2014-10-22 09:39
1
2,151 by rmoretti
Thu, 2014-10-23 13:55
Normal topic Syntax for the alignment file in "minirosetta comparative modeling"
by lanselibai » Thu, 2014-10-16 15:29
3
4,580 by lanselibai
Thu, 2014-10-23 03:26
Normal topic ab initio modelling - what to do next?
by krlitros87 » Thu, 2014-10-16 13:05
2
3,392 by krlitros87
Wed, 2014-10-22 09:31
Normal topic Snugdock+ensembledock usage
by Anouk » Mon, 2014-09-22 08:09
1
3,100 by jadolfbr
Mon, 2014-10-20 13:42
Normal topic What are "-nstruct" and "cluster_histogram.txt" for "clustering.py"?
by lanselibai » Fri, 2014-10-17 06:06
3
21,063 by rmoretti
Fri, 2014-10-17 10:17
Normal topic "OSError: [Errno 2]” in “clustering.py”
by lanselibai » Sat, 2014-10-11 14:30
4
7,451 by lanselibai
Fri, 2014-10-17 05:10
Normal topic How to eliminate "NUL"s when scoring PDBs?
by lanselibai » Tue, 2014-10-14 10:04
2
3,021 by lanselibai
Fri, 2014-10-17 03:36
Normal topic How to only constructure the tail conformation when using "FloppyTail.linuxgccrelease"?
by lanselibai » Mon, 2014-10-13 10:26
5
5,595 by lanselibai
Wed, 2014-10-15 03:52
Normal topic "score vs RMSD plots" & "cluster models"
by lanselibai » Thu, 2014-09-25 06:51
12
24,609 by lanselibai
Wed, 2014-10-15 01:54
Normal topic Use "loopmodel.linuxgccrelease" CCD to build missing residue positions
by lanselibai » Sun, 2014-10-12 09:00
2
3,501 by lanselibai
Mon, 2014-10-13 10:10
Normal topic Membrane homology modeling loop building gives very strange outputs
by chelsell » Tue, 2014-09-30 14:46
2
3,209 by chelsell
Wed, 2014-10-08 12:25
Normal topic residues_patch_selectors CENTROID_HA
by Pernille » Fri, 2014-10-03 03:53
2
3,047 by Pernille
Wed, 2014-10-08 10:41
Normal topic Abinitio.relax problem on centos
by krlitros87 » Wed, 2014-09-24 11:27
4
5,842 by jadolfbr
Tue, 2014-10-07 16:05
Normal topic Questions for "modeling_instructions.pdf" in "Homology or Loop Modelling"
by lanselibai » Sun, 2014-09-21 09:02
10
10,840 by lanselibai
Tue, 2014-10-07 02:58
Normal topic clustering
by ays » Tue, 2014-09-30 08:26
2
3,337 by rmoretti
Mon, 2014-10-06 16:00
Normal topic How to sort a Silent File based on RMSD
by JadAbbass » Sun, 2013-08-04 14:40
2
3,591 by lanselibai
Mon, 2014-10-06 15:30
Normal topic Missing "Bio.PDB" module when running "remove_loop_coords.py"
by lanselibai » Mon, 2014-09-29 04:34
6
10,261 by lanselibai
Wed, 2014-10-01 02:13
Normal topic flexpepdock_score_only
by ays » Sun, 2014-09-21 06:17
2
2,696 by ays
Tue, 2014-09-30 08:31
Normal topic Syntax to build a silent file
by lanselibai » Fri, 2014-09-26 09:13
8
9,971 by lanselibai
Tue, 2014-09-30 03:45
Normal topic Some wrong with the flag "-l" for score_jd2.linuxgccrelease
by lanselibai » Mon, 2014-09-29 02:29
2
4,324 by lanselibai
Tue, 2014-09-30 02:28
Normal topic Failed glycine check when running RosettaRemodel to build disulfide
by cheyuk » Fri, 2014-06-27 02:31
1
2,186 by everyday847
Sun, 2014-09-28 21:16
Normal topic Syntax to extract PDB files from a silent file
by lanselibai » Fri, 2014-09-26 13:48
1
3,938 by lanselibai
Fri, 2014-09-26 14:58
Normal topic clean_pdb.py of Rosetta VS cleanATOM of PyRosetta
by lanselibai » Wed, 2014-09-24 03:02
2
5,043 by lanselibai
Wed, 2014-09-24 13:21
Normal topic Fixing and Building disulfide bonds in homology modeling
by kamau » Wed, 2014-09-24 11:33
0
2,468 by kamau
Wed, 2014-09-24 11:35
Normal topic fixing disulfides in homolgy modeling
by pdbb » Wed, 2013-02-13 11:43
10
12,017 by kamau
Mon, 2014-09-22 09:39
Normal topic Problem in using "loopmodel" application to add missing residues
by sushreet » Wed, 2014-08-27 12:43
1
2,121 by rmoretti
Thu, 2014-08-28 09:42
Normal topic Error in using “loopmodel” for selective rebuilding
by sushreet » Mon, 2014-07-14 11:57
2
2,921 by sushreet
Tue, 2014-08-26 13:02
Normal topic Incorporating iron-sulfur cluster into ROSETTA applications
by Derek Smith » Thu, 2014-08-14 23:12
1
2,715 by rmoretti
Fri, 2014-08-15 08:06
Normal topic FlexPepDock Concatenation
by cam11 » Mon, 2014-08-11 07:39
2
2,851 by cam11
Wed, 2014-08-13 10:06
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