The problem hasn't been solved
Dear all,
I am trying to perform a comparative homology modelling with the following command line
rosetta_scripts.linuxgccdebug @flags -database ~/rosetta_2013wk36_bundle/main/database/ -nstruct 10
the rosetta scripts is:
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
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?
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?
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
Keywords:
SymmDock
Helical Symmetry
Dear RosettaCommons,
we're trying to model a protein complex in helical symmetry with SymmDock in Rosetta 3.5.
There is one problem occuring always, which we coundn't solve so far: In most of the resulting
models there are single residues displaced from the backbone of the protein. Often the whole structure
looks completely broken. Relating to this we made the observation that the master subunit is not affected
but the strength of the effect (number of displaced residues) increases with the number of jumps between the master
interface design is changing a terminal aminoacid in my complex and
I would like to mutate it back to wildtype using the MutateResidue
mover, but every time I try to do that for the N or C terminus I get
segmentation fault. This is system independant, I see this for every complex I work with.
Is there a way around it, without going back to the interface design ?
Thanks
Jarek
Hi,
I try to use Rosetta 3.4 to calculate the ddG of a protein.
The command I use is
$ROSETTA/rosetta_source/bin/ddg_monomer.linuxgccrelease -in:file:s test.pdb --ddg::weight_file ddg.wts -ddg::iterations 20 -ddg::dump_pdbs true -database $ROSETTA/rosetta_database/ -ddg::local_opt_only true -ddg::min_cst false -ddg::mean true -ddg::min false -ddg::sc_min_only true -in:file:fullatom -resfile test.resfile
Everything goes well but some proteins have problems.
For example core.pack.task.ResfileReader: On line 2, the pose does not have residue with chain=A, PDBnum=1
This is the result of abinitio.I found there are six kinds of scorefunction(score0,score1,score2,score3,score4,score5).I don't know the difference of them.Would you please tell me something about these six kinds of scorefunction?Thank you.
Stage 1
Folding with score0 for max of 2000
protocols.abinitio: Replaced extended chain after 15 cycles.
protocols.moves.MonteCarlo: ClassicFragmentM trials= 15; accepts= 0.9333; energy_drop/trial= 0.00000
protocols.abinitio: ------------------------------------------------------------
Scores Weight Raw Score Wghtd.Score
Hi all,
When the simulations protocol mentioned in "Large-scale characterization of peptide-MHC binding landscapes with structural simulations" will be released? The papers says the protocol will be available in next public release but I can't find it in Rosetta latest version 3.5.
Thanks
