The problem hasn't been solved
Hello
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 RG_Energy.cc and RG_Energy_Fast.cc type of files which did this kind of job.
Is there something similar for Rosetta3.4 ?
Please advise
Hi,
I found that is dfire in rosetta3.4. I am curious that if I want to use this energy, what option should I use when run the rosetta design? Thank you!
I have about 100000 PDB files and I need to calculate their free energy and total energy.
Does Rosetta3.4 have any such tool to calculate it ?
Please advise.
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
Hi,
I saw the word "minirosetta" many many times, but I can not find any program related with minirosetta. What is the different between minirosetta and rostta3? And where can I download the minirosetta? Thank you very much!
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！
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.
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?
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
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
