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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?

Hi,
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.
Thanks,
Nuria

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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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ddg_monomer problem

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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