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Using rosetta 3 to make a fragment library and then use it to model loop of a protein structure

Submitted by bharat_46010 on Sun, 2011-01-23 05:22

Hi,

I want to know how to generate a fragment library for rosetta ... The method given in the documentation is not the one I want as , I want to retreive fragments of 8 or above residues taken from pdb consisting the loop regions of various proteins not on the basis of any resembling sequence.. Also I want to know what's the structure of this file consisting the fragments (means what does the last 4 columns tell)

1bvy F 24 L E -111.045 104.882 178.947 0.947 12.265 16.922 3 0.000 P 1 F 1

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Rosetta 3 - General

ROsetta installation on windows

Submitted by bharat_46010 on Tue, 2011-01-18 20:40

Hi all,

I am new to rosetta and I tried installing rosetta on windows 7 ... First I installed scons using scons-2.0.1.win32.exe file downloaded from scons website... after that I tried using the command -> scons bin mode=release
in cygwin but its saying that the command not found ... I already added the location of scons to environment variables

Pls help

BHARAT

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Rosetta 3 - Build/Install

Executing the mc simulation of polyalanine fragment

Submitted by bharat_46010 on Mon, 2011-01-17 19:18

Hi,

I am trying to run the monte carlo simulation of a polyalanine fragment given in the tutorial .. After typing the whole script in notepad and saving with .py extension and after ruuning on xterm window I am getting the following error ...

In [41]: ipython mc.py
------------------------------------------------------------
File "", line 1
ipython mc.py
^
SyntaxError: invalid syntax

Can anybody let me know how do I have to run such scripts or how to execute that tutorial

----
BHARAT

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PyRosetta - General

Symmetric local protein docking

Submitted by efratmas on Mon, 2011-01-17 04:52

Hi.

I installed Rosetta2.3 and I'm trying to use it for local docking of protein complexes witn Cn symmetry.
For my first try, I'm trying to refine the solved trimer with PDB code 1QU9

I tryied to follow the instructions in http://www.rosettacommons.org/guide/Symmetrical%20Docking ,
and these were my steps:
1. I downloaded the file 1qu9.pdb
2. prepaking:
rosetta.release aa 1qu9 _ -dock -s 1qu9 -prepack_full -quiet -ex1 -ex2aro_only
3. symmetric local docking:

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Rosetta++ - General

De novo loop modeling using pyrosetta

Submitted by bharat_46010 on Sun, 2011-01-16 17:38

I want to model loop regions for an already solved structure of my protein. I want to replace the loop regions with new loop segments which are longer in size than the original ones present in the structure + the sequence of the loop should also be different. I want to know whether this can be achieved by using the pyrosetta suite and if so .. how can it be done..

Regards
-----------
Bharat

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PyRosetta - General

energy minimization of loop only

Submitted by jtmacd on Wed, 2011-01-12 07:09

Hi,

Is there a way of energy minimizing a loop while keeping the rest of the protein fixed using any of the Rosetta apps?

I don't want to do full scale CCD loop remodelling - just a simple energy gradient minimization or similar small scale relaxation of a loop conformation I already have. In the relax app there seems to be an option called -constrain_relax_segments but it doesn't seem to do what I want. I also don't think I want to do backrub moves either as I just want to find a local minimum.

thanks again for all the help!

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Rosetta 3 - General

'-norepack_disulf' flag NOT work in Ligand-protein docking ?

Submitted by darlintai on Tue, 2011-01-11 22:21

Dear All :

I met some problems when I try to dock a small molecule to a protein using the command "ligand_dock.linuxgccrelease"

What I want:

repack most of the sidechain of protein, but there are several disulfide bonds in the proteins, and I try to use the Flags '-fix_disulf' to
find the disulfide bonds and use '-norepack_disulf' to freeze the CYS involved in the disulfide bonds. the Flags file includes flowing lines :

-extra_res_fa BSP.params
-nstruct 2
-fix_disulf
-norepack_disulf
-out:file:renumber_pdb -no_optH
-ex1 -ex1aro
-randomize2
-uniform_trans 5

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Rosetta 3 - General

Symmetric local protein docking

Submitted by efratmas on Tue, 2011-01-11 03:00

Hi.
I installed Rosetta3.1 and I'm trying to use it for local docking of protein complexes witn Cn symmetry.
The program docking_protocol.linuxgccrelease is running and produces the results but it prints out a warning:
"core.scoring.SymmetricScoreFunction: Warning!!! Using a symmetric score function on a non-symmetric pose"

I'll be happy to know what am I doing wrong...

Here are my steps:
1) I have a model of a trimer that I want to refine.
I deleted one of the monomers and saved the remaining 2 monomers (chains A and B) in a pdb file.
2) I ran prepacking by:

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Rosetta 3 - General

error about 'std::bad_alloc' during running

Submitted by zhisheng on Mon, 2011-01-10 09:45

Hi,

I just installed rosetta and used a small peptide to see whether rosetta worked properly. But when I run runRosetta3.com in the 'rosetta' directory, it aborted at a 'Stage 4' sometime later. The following is the screen message,

Stage 4
Folding with score3 for 40000
terminate called after throwing an instance of 'std::bad_alloc'
what(): std::bad_alloc
Aborted

How to fix this problem?

Many thanks!

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Rosetta 3 - General

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