You are here
Rosetta 3 - General
Log in to post new content in the forum.
Topic / Topic starter |
Replies | Views | Last post | |
|---|---|---|---|---|
|
how to do cluster after low resolution protein-protein docking? by albumns » Sat, 2010-11-27 01:17 |
4 |
4,301 |
by albumns Mon, 2014-04-21 06:47 |
|
|
how to do ensemble docking using rosetta3.1 by lqzhang » Mon, 2010-01-11 10:31 |
1 |
2,074 |
by sid Mon, 2014-04-21 06:47 |
|
|
How to dock 3 missing domains onto a multi-domain protein by tevang » Sun, 2011-04-10 15:22 |
3 |
4,600 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
how to docking including HETATM by tricia » Tue, 2009-05-05 22:03 |
1 |
2,503 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to export high energy state pdb out of backrub? by whiteqiu » Mon, 2021-03-01 18:32 |
0 |
749 |
by whiteqiu Mon, 2021-03-01 18:32 |
|
|
How to extract antibody from a set of pdb file may may contain antigen? by Sunyp_IM » Mon, 2017-11-13 17:11 |
1 |
1,488 |
by ac.research Sat, 2017-11-18 06:54 |
|
|
How to extract specific pdb from silent files by eunwook » Tue, 2013-05-14 05:29 |
5 |
15,067 |
by nawsad Mon, 2014-04-21 06:47 |
|
|
How to generate a symmetry definition file for octahedral symmetry? by Anonymous » Wed, 2012-08-15 05:20 |
0 |
2,424 |
by Anonymous Mon, 2014-04-21 06:47 |
|
|
How to generate constraints of active sites from a pdb file of an enzyme by Albert » Sun, 2013-05-26 20:07 |
3 |
3,578 |
by jadolfbr Mon, 2014-04-21 06:47 |
|
|
How to generate score file for loop refinement or modelling? by zhisheng » Fri, 2011-12-09 05:15 |
2 |
3,136 |
by zhisheng Mon, 2014-04-21 06:47 |
|
|
How to generate symmdef file for translational symmetry only? by pitmand » Thu, 2015-05-14 11:34 |
2 |
2,950 |
by pitmand Tue, 2015-05-26 12:20 |
|
|
how to generate _prepro.rama file for a customized beta-amino acid residues? by wwwmrzkwww » Sun, 2023-04-23 14:25 |
0 |
234 |
by wwwmrzkwww Sun, 2023-04-23 14:25 |
|
|
How to get fragment library from robetta server for mre than 1000 residue sequence? by Danielsebas » Wed, 2019-09-18 07:53 |
1 |
1,410 |
by rmoretti Wed, 2019-09-18 10:49 |
|
|
How to get multiple chains in PDB from Fold and Dock by arthuc01 » Tue, 2012-05-29 02:05 |
9 |
8,853 |
by arthuc01 Mon, 2014-04-21 06:47 |
|
|
how to get reliable results for carbohydrate docking? by albumns » Sun, 2010-09-05 23:12 |
3 |
4,744 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to get the GDT_TS? by JadAbbass » Thu, 2013-09-05 11:59 |
3 |
5,379 |
by rmoretti Mon, 2014-04-21 06:48 |
|
|
How to get the RMSD between two .pdb structures? by cossio » Wed, 2014-12-03 05:33 |
1 |
3,387 |
by rmoretti Wed, 2014-12-03 18:52 |
|
|
How to handle/retain Metals (Zn, Ca) inside the Protein? by aniyaz » Wed, 2023-01-11 03:21 |
6 |
1,181 |
by rmoretti Mon, 2023-02-20 16:07 |
|
|
how to identify selected interface residues by vijayaraj81 » Mon, 2014-03-31 01:40 |
3 |
4,186 |
by rmoretti Tue, 2014-04-01 08:12 |
|
|
How to import SymmDock models into Rosetta for local docking and energy minimization by devroop » Fri, 2012-07-20 13:20 |
1 |
3,145 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to input constraints? by violetsha7 » Wed, 2009-05-13 00:13 |
7 |
8,870 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to input pdb to rosetta format add "missing" residues to pdb file by zhisheng » Tue, 2011-06-07 09:51 |
1 |
3,842 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to insert a TER line between docking partners by devroop » Sun, 2012-07-29 13:48 |
1 |
3,136 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to install Rosetta in Redhat Linux ? by ajaniharesh » Fri, 2012-02-24 02:32 |
1 |
5,375 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to integrate Rosetta code to my program? by Lsg » Tue, 2011-06-28 07:18 |
3 |
4,138 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to judge docking success for two proteins without knowledge of native structure by jasnyderjr » Fri, 2015-07-10 14:27 |
1 |
2,598 |
by rmoretti Tue, 2015-07-14 15:27 |
|
|
how to keep modeling ignored ERROR? by eunwook » Sat, 2013-04-27 05:44 |
3 |
3,720 |
by eunwook Mon, 2014-04-21 06:47 |
|
|
how to keep native structure when do loop modeling by zlni » Sun, 2009-05-03 10:12 |
4 |
4,033 |
by zlni Mon, 2014-04-21 06:47 |
|
|
how to make a combined PDB file? by fenghc » Mon, 2013-04-01 06:27 |
3 |
14,794 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to make a resfile by dflaher » Fri, 2017-11-03 10:26 |
3 |
4,240 |
by smlewis Wed, 2017-11-08 12:08 |
|
|
how to make benchmark? by albumns » Wed, 2012-04-04 05:23 |
23 |
28,461 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
How to make Rosetta's sampling more aggresive ? by jiongzhang » Mon, 2012-03-12 11:04 |
1 |
2,161 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
How to minimize only a few key residues' orientation by Ronghai Cheng » Mon, 2018-11-05 18:37 |
2 |
2,320 |
by Ronghai Cheng Tue, 2018-11-13 21:56 |
|
|
How to model a protein that dimerizes to a small molecule? by pholland » Wed, 2011-05-25 07:29 |
3 |
5,157 |
by pholland Mon, 2014-04-21 06:47 |
|
|
How to modify disulfide bonds constrain in homology modeling by eunwook » Mon, 2013-05-13 04:56 |
1 |
2,764 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to obtain alignment file for comparative modeling under Rosetta 3.1? by lennylv » Tue, 2010-05-25 01:29 |
11 |
16,785 |
by sabine Mon, 2014-04-21 06:47 |
|
|
how to optimize the weights? by Lindsay » Tue, 2012-04-10 07:40 |
7 |
6,004 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
how to output a structure when scoring it? by tianbu » Tue, 2012-07-31 09:38 |
3 |
4,027 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
how to perform model quality assessment of rosetta generated models? by Danielsebas » Tue, 2019-09-24 05:03 |
0 |
891 |
by Danielsebas Tue, 2019-09-24 05:03 |
|
|
How to prepare the pdblist file for docking_ensmble in Rosetta3.4 by sunlufinal » Mon, 2015-06-01 19:27 |
1 |
2,633 |
by rmoretti Fri, 2015-07-03 12:58 |
|
|
How to prevent rotamers from being pruned from the interaction graph? by msun » Wed, 2013-04-17 14:19 |
2 |
2,738 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to provide multiple templates for Robetta with RosettaCM option? by lanselibai » Wed, 2021-06-23 14:06 |
1 |
908 |
by lanselibai Wed, 2021-06-23 14:53 |
|
|
How to put rdc data in refinement protocol? by zhisheng » Tue, 2012-11-20 03:55 |
13 |
11,345 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
How to read the output score file from rosetta? by Sunyp_IM » Sun, 2017-08-27 05:29 |
1 |
2,842 |
by rmoretti Mon, 2017-08-28 09:32 |
|
|
How to recover out files when run crashs by samuelrpita » Tue, 2015-07-28 12:54 |
2 |
2,895 |
by samuelrpita Thu, 2015-08-06 14:23 |
|
|
How to relax a protein model calling Rosetta functions from my C++ code by sncrivelli » Tue, 2011-10-25 00:16 |
1 |
2,965 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to relax only one domain of a protein and keep the rest of them fixed by tevang » Sun, 2011-04-10 03:16 |
14 |
13,846 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
how to relax structure constraining CA in Rosetta3.2? by albumns » Tue, 2011-02-15 06:15 |
2 |
2,528 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to remove clashes in peptide bonds and proline residue? by Anatol » Fri, 2012-08-31 09:26 |
2 |
2,987 |
by Anatol Mon, 2014-04-21 06:47 |
|
|
How to run docking in rosetta with small molecule by ajaniharesh » Tue, 2012-02-28 03:58 |
1 |
3,850 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to run Rosetta3 in parallel by lennylv » Mon, 2009-03-30 04:21 |
6 |
9,387 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
How to score the crystal structure? by vsjasion » Fri, 2011-11-18 15:49 |
1 |
2,337 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
How to set jump between ligands by Zehui Zhou » Wed, 2023-02-15 04:48 |
0 |
322 |
by Zehui Zhou Wed, 2023-02-15 07:12 |
|
|
How to set start coordinates for ligand when doing protein_ligand docking by Huanhuan » Wed, 2021-08-18 21:09 |
3 |
1,573 |
by matteoferla Fri, 2021-08-20 08:37 |
|
|
How to set the enviroment variable $ROSETTA3, $ $ROSETTA3_DB, $ROSETTA_TOOLS? by Sunyp_IM » Thu, 2017-07-27 01:07 |
1 |
4,204 |
by SenyorDrew Sat, 2017-07-29 09:59 |
|
|
how to set the output name for fixbb design by Lindsay » Mon, 2012-04-30 09:32 |
1 |
2,070 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to set up options in rosetta by alejandro » Wed, 2011-04-06 02:08 |
3 |
4,855 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to site the scoring application in rosetta3.1? by doranhen » Thu, 2012-07-05 10:07 |
1 |
2,375 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to specify a specific rotamer by Lior_UCSF » Wed, 2018-02-21 20:35 |
1 |
1,453 |
by rmoretti Thu, 2018-02-22 09:29 |
|
|
How to specify constraints during fold-and-dock? by sarah_b » Tue, 2020-05-12 01:55 |
3 |
2,262 |
by matteoferla Thu, 2020-05-14 07:01 |
|
|
How to specify residue numbers in a resfile for a batch of pdbs, while some of them have missing residue numbers? by johnnytam100 » Wed, 2019-05-08 02:30 |
2 |
2,350 |
by johnnytam100 Wed, 2019-05-15 18:45 |
|
|
how to transfer the rosetta score to physical unit? by Lindsay » Thu, 2012-06-28 09:33 |
7 |
7,716 |
by Lindsay Mon, 2014-04-21 06:47 |
|
|
How to transform a pose from symmetric into non-symmetric? by msardejani » Tue, 2016-10-04 16:55 |
2 |
2,455 |
by msardejani Wed, 2016-10-05 10:53 |
|
|
How to turn off output of POSE_ENERGIES_TABLE by lah435 » Tue, 2015-02-03 21:21 |
4 |
4,233 |
by jwillis Sat, 2015-02-07 20:40 |
|
|
how to use AbinitioRelax.mpi.linuxgccrelease? by albumns » Mon, 2012-03-26 22:50 |
5 |
6,398 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
how to use backrub in rosetta3.1 by lqzhang » Mon, 2010-01-11 14:43 |
3 |
3,224 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
How to use Rosetta 3.1 to model the structure of an antibody? by sylvia » Mon, 2009-10-26 14:06 |
2 |
3,297 |
by vanita Mon, 2014-04-21 06:47 |
|
|
How to use Rosetta Position constraint docking? by libai2098 » Mon, 2011-05-09 01:08 |
1 |
2,204 |
by libai2098 Mon, 2014-04-21 06:47 |
|
|
how to use rosettadesign to do mutations on protein structure by lqzhang » Thu, 2010-03-04 07:43 |
3 |
4,001 |
by vanita Mon, 2014-04-21 06:47 |
|
|
How to use RotamerDump to access one and two-body energy tables? by msun » Wed, 2013-01-16 12:26 |
3 |
3,135 |
by msun Mon, 2014-04-21 06:47 |
|
|
How to use the <CavityVolume> filter in the released version of Rosetta by BioPython » Sun, 2019-05-12 20:07 |
0 |
1,007 |
by BioPython Sun, 2019-05-12 20:07 |
|
|
Hydrogen bond detection and shape complementarity by sujigeorge1979 » Fri, 2019-06-14 02:39 |
3 |
2,269 |
by sujigeorge1979 Thu, 2019-06-27 01:30 |
|
|
hydrophobicity patch by Lindsay » Fri, 2012-05-04 08:24 |
7 |
8,783 |
by Lindsay Mon, 2014-04-21 06:47 |
|
|
hydroxyproline patching problem by aaj » Mon, 2016-02-22 07:33 |
2 |
2,840 |
by aaj Mon, 2016-02-29 04:45 |
|
|
I am a beginner in rosetta software and need help to build params file by nais » Fri, 2011-03-18 13:37 |
3 |
6,668 |
by rmoretti Mon, 2014-04-21 06:47 |
|
|
I can't find the workflow about modeling disordered regsion using rosetta? by lihowe » Thu, 2011-12-29 03:45 |
2 |
2,988 |
by wangyr Mon, 2014-04-21 06:47 |
|
|
I generated a table of images & info of the premade NCAA params in the database by matteoferla » Sun, 2020-02-16 06:27 |
4 |
2,737 |
by matteoferla Sat, 2020-03-21 09:14 |
|
|
I got so many atoms in one residue by ylwang » Tue, 2020-03-24 04:40 |
3 |
1,924 |
by ylwang Tue, 2020-03-24 19:35 |
|
|
I got the message "bad format in first line of silent file". How do I resolve this? by monos_morpheus » Thu, 2011-02-03 21:09 |
1 |
2,286 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
I got the message "ERROR: Residue names must be unique!". by monos_morpheus » Sun, 2011-02-06 03:55 |
2 |
3,550 |
by monos_morpheus Mon, 2014-04-21 06:47 |
|
|
I have a .tab file. How do I extract information from it? by monos_morpheus » Tue, 2011-02-08 09:30 |
4 |
5,060 |
by monos_morpheus Mon, 2014-04-21 06:47 |
|
|
I made a params file generation webpage by matteoferla » Wed, 2020-07-22 03:08 |
0 |
834 |
by matteoferla Wed, 2020-07-22 03:08 |
|
|
I made a RDKit Chem.Mol to params converter — feedback welcome! by matteoferla » Sun, 2020-05-03 10:14 |
1 |
1,635 |
by jadolfbr Sun, 2020-05-03 19:38 |
|
|
I Need Help on Validation for a Ligand Docking Experiment. by tbelec » Sat, 2021-03-20 13:27 |
1 |
1,394 |
by matteoferla Mon, 2021-03-22 08:29 |
|
|
I used mpirun/mpiexec and it runs same job 32times by leygkn » Mon, 2020-09-21 00:53 |
6 |
3,846 |
by jadolfbr Thu, 2020-09-24 10:04 |
|
|
I'm a total beginner to Rosetta 3.2 and there are no tutorials for me to follow. Can someone help.? =) by monos_morpheus » Wed, 2011-02-02 08:11 |
12 |
10,602 |
by monos_morpheus Mon, 2014-04-21 06:47 |
|
|
I've got two doubts by jrcf » Sun, 2016-01-10 07:45 |
1 |
1,898 |
by smlewis Sun, 2016-01-10 10:02 |
|
|
Icouldnot find DDMI protocol for design protein by ladimafakher » Mon, 2018-02-12 09:22 |
1 |
1,587 |
by rmoretti Mon, 2018-02-12 09:39 |
|
|
idealization error by albumns » Mon, 2011-02-07 01:28 |
1 |
2,062 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
Identical decoys by aroop » Tue, 2012-09-25 12:50 |
4 |
4,494 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
ignore loops on threading by fred » Tue, 2014-11-11 11:33 |
5 |
4,994 |
by rmoretti Tue, 2014-11-18 10:01 |
|
|
incomparable ddG values by ela » Fri, 2018-08-31 02:53 |
0 |
1,122 |
by ela Fri, 2018-08-31 02:53 |
|
|
Inconsistent scoring by "aa_composition" term by chenna » Thu, 2022-02-24 03:00 |
1 |
764 |
by vmulligan Thu, 2022-03-03 18:48 |
|
|
industrial example of ROSETTA modeled protein by banshee » Sat, 2016-04-23 23:40 |
5 |
4,948 |
by banshee Tue, 2016-04-26 00:47 |
|
|
Ineffective Constraints by Sandy » Tue, 2017-09-05 19:36 |
2 |
2,205 |
by CameronJA Wed, 2022-01-19 20:50 |
|
|
Information about “membrane_highres_Menv_smooth.wts” by Groros » Sun, 2011-10-02 03:59 |
3 |
3,712 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
input secondary structure prediction to AbinitioRelax by biofisikx » Mon, 2010-08-09 12:36 |
2 |
2,533 |
by biofisikx Mon, 2014-04-21 06:47 |
|
|
input_score_filter not taken by program cluster ? by Anonymous » Mon, 2012-06-11 09:14 |
9 |
8,675 |
by attesor Fri, 2014-10-31 04:49 |
|
|
Installing on windows using MinGW by abdullah_ahmed » Wed, 2010-09-15 08:45 |
1 |
1,929 |
by smlewis Mon, 2014-04-21 06:47 |
|
|
Installing rosetta 3.0 by dalemu » Thu, 2009-09-24 13:28 |
1 |
2,675 |
by smlewis Mon, 2014-04-21 06:47 |
Log in to post new content in the forum.
