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Energy and RG in the new rosetta3.4 ( like and )


I have a huge database of PDB files and I need to calculate their RG along with their energy(any relevant scoring).
Earlier version of Rosetta had and type of files which did this kind of job.

Is there something similar for Rosetta3.4 ?
Please advise

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symmetric Docking- TRIMER in Rosetta 3.4 ?

I need to do certain symmetric docking to generate its homodimer and homotrimer and I am using Rosetta 3.4 Symmetric docking to achieve it.

I used the following command to generate homodimers :

./bin/SymDock.linuxgccrelease -docking:dock_ppk -symmetry:symmetry_definition ./sym_def_dimer.dat -symmetry:initialize_rigid_
body_dofs -database ../rosetta_database/ -out:nstruct 2 -out:file:fullatom -s S_00000001.pdb

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how to optimize the weights?

I found that there are optimize_weights directory in the protocol directory in the rosetta 3.3 and 3.4. What's the function of this protocol and how to use it? I think this is for weights optimization. If I understand correct In this case, if I have 1 more energy term(suppose this term is totally new), how do I use ”optimize_weights“ to optimize the weights? Thank you very much!

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Single Strand DNA (ssDNA) 3D structure prediction

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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Best scoring function ofr Structure Prediction

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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Protein Structure Prediction

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.

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

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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