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Changing constraints code and compiling

Submitted by Ashafix on Sat, 2013-07-06 05:13

Dear Rosetta community,

after reading a lot of helpful posts I managed to compile Rosetta 3.4 on Ubuntu 11.04 in a virtual machine on Windows 7. It runs without any problems and abinitio folding actually works.
I wanted to add a new constraint function (just to test some weird idea, don't ask), unfortunately I neither speak C++, nor understand how the inner organs of Rosetta work.

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Rosetta 3 - Build/Install

trouble in floppytail modelling

Submitted by ytao on Thu, 2013-06-27 13:15

Hi,

I'm using floppytail app (rosetta 3.5) to model my protein complex. The first chain in pdb file is a 353 residue protein and the second chain is a 138 residue protein. The "floppytail" region is N-terminal residues 1-37 in the second chain.

In the generated structures I noticed that the N-term residue of second chain (beginning of "floppytail") is not moving in space. All generated structures overlap in first chain(residue 1-353), and the first residue of second chain(residue 354 in pdb). I think the first chain is not supposed to move but I wanted N-term of second chain to move.

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Rosetta 3 - Applications

strange effect in: SymDock.linuxgccrelease

Submitted by ast on Tue, 2013-06-11 11:05

Hi,

I have a strange problem regarding SymDock:
I did symmetry Rosetta previously using RosettaScrips 3.4. And it worked fine so far. Since I want to do docking on that symmetric molecule and - at least to my understanding - the Docking is not ported to Scripts for symmetry mode, I choose to use SymDock.
When I try to run it with exactly the same .pdb .sym and .params as in Scrips (which worked fine!) I get "
"...
protocols.simple_moves_symmetry.SymDockingInitialPerturbation: initialize_rigid_body_dofs: true

ERROR: unrecognized atom_type_name COO

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Rosetta 3 - Applications

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

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