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I can't find the workflow about modeling disordered regsion using rosetta?

I'm a new user of rosetta3.3
I have road the RosettaCon 2010 paper about modeling disordered regsion,
and I want to reproduce the first method result,
but I can't find the workflow of this paper.
I have got a decoy set using abinitio apps,I need the code of prediction of Disordered Segments at Termini.

Thanks a lot for your help!

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Problem with sending individual energy terms using PyMOL Mover

Hi All,
I'm having a problem sending individual energy terms to PyMOL. I'm using 2.011, and going directly from the tutorial:

py = PyMOL_Mover()
py.send_energy(p, "fa_sol")

This is the error that I get:
PyMolMover.send_energy(PyMOL_Mover, Pose, str)
did not match C++ signature:
send_energy(protocols::moves::PyMolMover {lvalue}, core::pose::Pose , core::scoring::ScoreType stype=rosetta.core.scoring.__scoring_all_at_once_.ScoreType.end_of_score_type_enumeration)

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Loop Modeling with fixed backbone


I wanted to model two tight turns in my protein keeping the backbone of the protein fixed. This was done to evaluate the change in the energy due to changes in loop sequence and also to look for low energy conformations. I wanted only some selected residues at those loop positions for which I made a resfile.

Here are the parameter for loop modeling :-

-loops:refine refine_kic
-loops:input_pdb 1gfl.pdb
-loops:loop_file loop_file.loop
-in:file:native 1gfl.pdb
-resfile : resfile

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How does one prevent Rosetta from connecting two separate chains?

I have a homodimer of two separate chains, each one 31 residues long. I am attempting to run a comparative modeling protocol. Every pdb output has the two chains connected, which screws up subsequent relaxation.

How do I change the input fasta file, align file, and/or flags file to indicate that there are two separate chains?


Current files:
fasta file:
> Tm7_37

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start pose and native pose don't match in lengh


I want to use a crystal structure with a shorter protein sequence as my native structure during loop re-modelling so the rmsd of generated structures will be aligned to it. But there is always an error:

ERROR: Start pose and native pose don't match in length
ERROR:: Exit from: src/protocols/loops/ line: 222

How to force to align the same region of the two structures?

Many thanks.

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How to generate score file for loop refinement or modelling?


I used rosetta3.3 to refine loops in my protein. And the command I used is

loop -loops::input_pdb protein.pdb -loops::loop_file protein.loop_file -loops::frag_sizes 9 3 1 -in::file::fullatom -loops::frag_files protein_aat000_09.200_R3.gz protein_aat000_03.200_R3.gz none -loops::random_loop -loops::refine refine_kic -abinitio::rerun 1 -abinitio::start_native -database $database -out:nstruct 100 -ex1 -ex2 >loops.log

But among the output files there is no scorefile (

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RMS determination using Rosetta 3.3

To give some context, I have a set of decoys that I've run cluster analysis on and now I'm trying to look at analyzing the clusters to see what similarities there are within the cluster. The long term goal is to analyze the 0th cluster, which contains the most structures, which is hypothesized to be the most likely place for where the true structure will be. That being all fine and dandy, I've isolated the poses that I need and was trying to determine the rms of each pose against the middle pose of the cluster.

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Pair potential

Does anyone know if the pair term has changed since it's introduction? Does it use the same pdb statistics and bins as described in:
Simons, K. T., Ruczinski, I., Kooperberg, C., Fox, B. A., Bystroff, C. & Baker,D. (1999) Proteins Struct. Funct. Genet. 34, 82–95.

It seems as though the term is the same for centroid and full-atom scoring. Is this true?

Post Situation: 


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