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Structure prediction

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: 

Modeling-Using RosettaCM

Category: 
Structure prediction

Hello,

I am new to Rosetta3 and was just suggested to use the RosettaCM protocol rather than minirosetta. I tried to carry out this protocol however, I keep coming to the same error (attached screenshot). I have included my input files as well. I prepared the template PDB as instructuded and inclded necessary target fasta file, and target tempalte alignment file (grishin format). To upload file names were changed to include .txt. Any insight would be helpful.

Justin

Post Situation: 

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