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fragment-based loop modeling to get a helix at the loop site

Submitted by berk on Wed, 2013-05-29 06:00

Hi every body,

I am a new Rosetta user,
I want to model loops of my protein by preforming using fragment-based loop modelling of Rosetta,(De Novo protein-designing module).
I will use this command for modelling
in:file:fullatom
-loops:input_pdb
-loops:loop_file
-loops:frag_sizes
-loops:frag_files
-loops:remodel quick_ccd
-in:file:native
-loops:ccd_closure
-loops:random_loop
-out:prefix _
-out:file:scorefile out.sc
-mute core.io.database

But I don’t know how can I find my fragments file from database and which database,
would you please help me in this subject.

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Rosetta 3 - General

How to do ab initio with fixed part of protein

Submitted by eunwook on Tue, 2013-04-16 03:00

There is a amino sequence 1 to 156.

Some part of the residues which were definded by homology are between 100 and 156.

That means "I've already have a secondary structure for 100 to 156."

Finally, I want to fix between 100 and 156 residues during ab initio.

Please tell me what could I do for this work. Exactly what command do I use?

I used rosetta3.4

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Rosetta 3 - General

[TopologyBroker Exception]: BBTorsion at pos 468unitialized...unclaimed

Submitted by tevang on Wed, 2013-04-10 15:07

Greetings,

I am trying to run minirosetta to create ab initio the missing ends from a crystal structure (2JLO) as in rosetta_demos/homology_modeling_with_end_extension, but I get this strange error:

protocols.relax.FastRelax: ================== Using default script ==================
protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
protocols.general_abinitio: AbrelaxMover: S_0001
loops: Extended: (-0,+0) LOOP 1 9 0 0 0
loops: Extended: (-1,+0) LOOP 467 667 0 0 0
protocols.topo_broker: Enlarged loops:

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Rosetta 3 - Applications

Give diferent chain information for a single sequence (comparative modeling)

Submitted by Martin Floor on Tue, 2013-04-02 08:59

I am trying to obtain a comparative model for a fusion protein. The query sequence have two repeats of a single motif that form a monomeric structure. The template structures are, by the way, homodimeric proteins that have this motif in two separate chains. I would like to make the model giving the relative structural information that this two chains have in the homodimer. I do not know how to said this to rosetta in the alignment file:

Query sequence:

------XXXXXXXXXXXXXXXXXXX----------XXXXXXXXXXXXXXXX--------

Template (chain A)

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Rosetta 3 - General

membrane scoring function performance

Submitted by tevang on Wed, 2013-03-20 08:40

Dear forum,

I have used the minirosetta application with the membrane_highres_t1.wts scoring function to create 1817 models. Among them only 48 had negative score, which ranged between -948.737 and -633.723. In contrast the rest of the models had score between 37700.552 and 197471.510. How can this happen? Does it mean that the scoring function is not suitable for my transmembrane protein?

Below is my parameter file:

-database /home/thomas/Programs/Rosetta3.4/rosetta_database
-run:protocol threading

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