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Single Strand DNA (ssDNA) 3D structure prediction

Submitted by mkoohim on Fri, 2012-04-06 00:52

I have an ssDNA and want to predict its 3D structure. Can I use Rosetta?
The secondary structure of my sequence is attached. For RNA we can use Rosetta to predict 3D structure but unfortunately I could not find any tools that predict tertiary structure of ssDNA? Please guide me, can i simply change Ts to Us, and predict a 3D RNA structure using Rosetta etc and finally in 3D structure replace Us with Ts?

Thank you very much.

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Rosetta 3 - Applications

Best scoring function ofr Structure Prediction

Submitted by Nuria on Thu, 2012-04-05 13:52

Hi everybody!
Any tip of a good scoring function for structure prediction? I want to do a first low resolution structure prediction from a sequence, using the centroid mode, but I don`t know which could be the best terms and the weight for each of them. In order to do it more complicated, the protein is a intrinsically unstructure protein, with some alpha helix content. Any tip?

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PyRosetta - Applications

Protein Structure Prediction

Submitted by Nuria on Thu, 2012-04-05 12:36

Hi everybody,
I am trying to use pyrosetta to make a prediction of the structure of a protein. I am new with python and pyrosetta and I am having difficulties. Anyone could tell me the best way of doing it? Which scripts should I use first,..? My idea was using an script to make a first structure calculation in centroid mode, and afterwards doing a refinement, loop modeling, side-chain packling and so on.
Anyone has a simple scrits to do the first taks? the protein folding? I ahve found one but it uses a pdb, I just have a sequence.
Thanks,
Nuria

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PyRosetta - Scripts

Individual residue repacking causes segmentation fault or "ERROR: seqpos >= 1 ERROR:: Exit from: src/core/conformation/Confo..."

Submitted by msellers on Wed, 2012-04-04 12:27

PyRosetta 47983.64bit Linux

When selectively repacking a pose containing disulfide bonds, choosing to temporarily repack residues that do not include all CYDs results in a segfault or ERROR.

example pose: 1-HIS, 2-CYD, 3-PHE, 4-MET, 5-GLY, 6-VAL, 7-CYD, 8-ILE

For the procedure:

1. load pose
2. pt = standard_packer_task(pose)
3. pt.restrict_to_repacking()
4. pt.temporarily_fix_everything()
5. pt.temporarily_set_pack_residue(3,True)
6. pm = PackRotamersMover(scorefxn,pt)
7. pm.apply(pose)

I get:

ERROR: seqpos >= 1

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PyRosetta - General

ddg_monomer problem

Submitted by deltag on Wed, 2012-04-04 07:53

Dear Rosetta users,

I am running ddg_monomer for a mutant following the instructions (renumbering the residues, pre-relax the structure, and build up a mutant file). The calculation for the wt runs okay. But when it reaches to the mutant. I got errors. Here are some information. I attached the flag file, cst file as well as the pre-relaxed pdb file. I appreciate your help.

Lei

Error messages:

ERROR: pose.residue(resnum).name1() == wt
ERROR:: Exit from: src/apps/public/ddg/ddg_monomer.cc line: 169

Command to run:

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Rosetta 3 - Applications

Problems installing Rosetta in linux 32 bits

Submitted by Nuria on Mon, 2012-04-02 13:29

Hi,
I am trying to install PyRosetta v2.0 (beta) in Ubuntu Linux 32 bits. I installed python 2.5 and manage to put it as default (2.7 was default in Ubuntu). But, when I tried to import PyRosetta ("from rosetta import" * or "import rosetta") I got the following answer:

Traceback (most recent call last):
File "", line 1, in
File "rosetta/_init_.py", line 11, in
import utility
File "rosetta/utility/_init_.py", line 1, in
from _utility_all_at_once import *
ImportError: libpython2.6.so.1.0: cannot open shared object file: No such file or directory

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PyRosetta - Build/Install

Energy of individual loop/region

Submitted by jadolfbr on Mon, 2012-04-02 13:15

Hi All,

I have an experiment that I did loop modeling on for 6 loops in each PDB. Energy vs. to_native_RMSD of the lowest energies are awful, so I now need the individual energies for each loop.

What I am trying to get is basically the total residue energy and the 2 body contributions of each of the loop residues' neighbors. Having trouble in a few different areas.
First, using score.eval_ci_2b and observing the non-zero energies gives the same scoretypes, with different energies as eval_cd_2b. This makes no sense...VDW, fa_pair, hack_elec are all ci_2b energies...

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PyRosetta - General

How can i introduce hydrogen bond as constraint?

Submitted by sp1020 on Mon, 2012-04-02 05:12

Hi everyone,

i need you help~

i am trying to introduce hydrogen bond constraints.

something like this:

Let O on residue 1 and N on residue 10 form hydrogen bond.
Let N on residue 1 and O on residue 20 form hydrogen bond.
etc.

i had tried to place the two hydrogen bond atoms close as distance constraint.

but mostly the distance constraint is not enough

so i want to calculate hydrogen bond as a constraint.

i had tried to use hbonds.HBondSet().

but i can only display hydrogen bond state uwing hbonds.HBondSet().show()

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PyRosetta - General

General Protein Folding Question

Submitted by twopint23oz on Sun, 2012-04-01 22:57

Hello. I have a few questions about abinitio structure prediction.

1) Can abinitio predict secondary structure as well, or does it just take secondary structure as a given based on inputs for fragment picker?

2) Is it worth using Rosetta to fold an 800 AA long protein? Are there some tips/tricks needed to run predictions for such a large protein?

Thanks.

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Rosetta 3 - General

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