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Compile C++ Rosetta to Pyrosetta ERROR

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Compile C++ Rosetta to Pyrosetta ERROR

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Compile C++ Rosetta to Pyrosetta

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Compile C++ Rosetta to Pyrosetta

Category: 
Structure prediction

Dear all,
        I am trying to compile a c++ version of Rosetta into a python version in my ubuntu system(Ubuntu 5.4.0-6ubuntu1~16.04.12) recently, because I modified some c++ files in C++ Rosetta to add a fragment library which has fragments with a variable length (And it can compile successfully in c++ version of Rosetta).

Post Situation: 

Fewer than expected structures in clustering output

Category: 
Structure prediction

Dear community,

I am running structure prediction of a protein whose tertiary structure is unknown. I use the standard abinitio protocol explained in the Rosetta tutorial(s). I have currently generated 3000 decoys, which I tried to cluster in order to have an idea of which structures were mostly populated.

Using the following command for clustering:

cluster.default.linuxgccrelease -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out -in:file:s *.pdb 

Post Situation: 

Successful RosettaCM?

Category: 
Structure prediction

Hello,

I recieve this message following my comaprative modeling for a single structure (as a test) as seen in the attahced screenshot. Was my run successful or is there something wrong with the generated PDB structure? Any information would be appreciated. I am just confused with the lines:

core.optimization.Minimizer: (0) [ WARNING ] LBFGS MAX CYCLES 200 EXCEEDED, BUT FUNC NOT CONVERGED!

protocols::checkpoint: (0) Deleting checkpoints of FastRelax

Post Situation: 

clustering output file has few structures

Category: 
Structure prediction

Dear community,

I am running structure prediction of a protein whose tertiary structure is unknown. I use the standard abinitio protocol explained in the Rosetta tutorial(s). I have currently generated 3000 decoys, which I tried to cluster in order to have an idea of which structures were mostly populated.

Using the following command for clustering:

cluster.default.linuxgccrelease -in:file:fullatom -cluster:radius 3 -nooutput -out:file:silent ./cluster.out -in:file:s *.pdb 

Post Situation: 

RosettaAntibody3 is failing with "Error: no input sequences were specified!"

Category: 
Structure prediction
Design

Hi all,

I am tryig to use RosettaAntibody3 to build a homology model for my antibody sequence. I am following the protocol workflow outlined in detail here: https://www.rosettacommons.org/docs/latest/application_documentation/antibody/antibody-protocol. The only difference is that I am modleing a VHH (heavy chain only antibody).

Post Situation: 

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