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assymetric dymer modelling with comparative and ab initio

Submitted by marcia on Mon, 2013-10-14 08:33

Hello,

I'm a newbie at Rosetta, and I need to figure out if i can do something.
I have an assymetric homo dimer PDB structure, but each monomer has about ~230 missing residues (with predicted high probability of being disordered). Each monomer has this organization (from amino to carboxyl):

[known structure domain][missing structure domain]

The protein-protein interactions of the asymm dimer are between the domains with known structure. I need to figure out how the missing structure domains interact with the structured ones, through the generation of thousands of models.

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Rosetta 3 - Applications

error with Boost when building PyRosetta

Submitted by skipper on Fri, 2013-10-11 23:10

OS info:
Linux 2.6.18-164.el5 #1 SMP Tue Aug 18 15:51:48 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux
Red Hat Enterprise Linux Server release 5.4 (Tikanga)

Python info:
Python 2.7.3 (default, Sep 26 2012, 11:26:26)
[GCC 4.1.2 20080704 (Red Hat 4.1.2-46)] on linux2

Rosetta version 3.4

I was trying to compile pyrosetta from source following the instructions in rosetta_source/src/python/bindings/building.txt.
I installed all the required software and library.
but compiling finished with failure.

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PyRosetta - Build/Install

Symmetry definition for coiled-coil dimer and trimer

Submitted by kszczepaniak on Fri, 2013-10-11 05:33

Hi,

I'm trying to define symmetry with Rosetta de novo symmetry definition script:
https://www.rosettacommons.org/manuals/archive/rosetta3.5_user_guide/d4/...

I would like to get a symmetry where two helix chains are antiparallel, how can I do it? I know how to get two parallel chains symmetry.

Also, I would like to get trimer symmetry where two chains are parallel and one is antiparallel. How can I make it?

best wishes,
Krzysiek

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Rosetta 3 - Applications

Full Protocol

Submitted by shekhar on Fri, 2013-10-04 01:07

Hello,

I am a newbie to RosettaDock, so this query might be a trivial one for some. I am trying to perform protein-protein docking with the "Full Protocol". What I understood from the manual, for using this protocol, no additional flag is required. I did the same but all I got was an error. This is what I used:
/path/rosetta_source/bin/docking_protocol.linuxgccrelease \
-database path/rosetta_database\
-s combined.pdb \
-nstruct 3000\
-ex1 -ex2aro \
-use_input_sc \
-partners Y_X \
-dock_pert 3 8 \
-mute core.util.prof \
-out:overwrite -out:file:fullatom \

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Rosetta 3 - Applications

Scoring after switching back to fullatom

Submitted by thorx020 on Thu, 2013-10-03 08:06

Hello,

I have a problem with scoring a pose after switching it back from centroid to fullatom representation. I did some troubleshooting and this is what happened:
1. Load PDB into PyRosetta
2. Score it with the 'standard' scorefunction (value ~ -43 REU)
3. Switch pose to centroid representation (do nothing else)
4. Switch pose back to fullatom representation.
5. Score pose again with same scorefunction in Step 2 (value ~35,0000 REU)

Why does switching back to fullatom representation destabilize the structure so drastically, even though I didn't perturb it in any way?

Thanks.

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PyRosetta - General

Problems with SmoothFragmentMover

Submitted by epalovcak on Wed, 2013-10-02 09:20

Hi, I'm new to Rosetta/PyRosetta and I'm having trouble getting the SmoothFragmentMover to work. According to the PyRosetta pdf I found at the Gray lab website, this should work:

movemap = Movemap()
movemap.set_bb(True)
fragset = ConstantLengthFragSet(3)
fragset.read_fragment_file(path_to_3mer_frags)
smoothmover = SmoothFragmentMover(fragset, movemap)

Instead of creating the mover, I get an error saying that it needs another argument, a 'FragmentCost' object:

ArgumentError: Python argument types in

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PyRosetta - General

Loop modelling before peptide docking

Submitted by wsgosal on Tue, 2013-10-01 07:24

Hi all!

I am using FlexPepDock to dock a peptide to a target. The target has a loop which has missing electron density for 6 residues, and I want to compare how filling in this loop will affect FlexPepDock poses - the loop is too close to the docking position of the peptide for me to be comfortable not dealing with this situation.

It is not clear to me how to proceed. I have the following questions:

1. The overall loop is ~21 amino acids. Presumably, I can just remodel the missing 6 residues. Is this assumption correct?

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Rosetta 3 - Applications

usage of score3

Submitted by Run on Sat, 2013-09-28 02:06

In the protocol of ClassicAbinito,stage4 finished Abinitio,why we needed a stage5 to really finish Abinitio?
And if I want to input a series of dihedral angles(or a pdb file),use Rosetta to calculate the score3,then output the score information of score3. How to write the code?I just know general usage of ClassicAbinitio ,but don't know how to let Rosetta(or object) use the input information.Is there any example code I can learn?

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Rosetta 3 - Applications

defining interface in interface analyzer

Submitted by aa20 on Fri, 2013-09-27 11:08

How does interface analyzer identify the residues at the interface and can it be restricted using resfile? I mean can I define the residues that make the interface. What would be an appropriate syntax for such a resfile?

For example, in a 6 chain (ABCDEF) PDB containing 174 aa, how do I define the interface as being between residues 8A and 8D and calculate the output results based on just these two residues.

Thanks

Abhishek

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