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Structure prediction

clustering output file has few structures

Submitted by fabiotrovato on Mon, 2020-08-17 11:37
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 

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Forums: 
Rosetta 3 - Applications

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

Submitted by brspurri on Sun, 2020-08-16 16:16
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).

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Rosetta 3 - Applications

Modeling-Using RosettaCM

Submitted by jlawrie on Wed, 2020-08-12 08:46
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

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Forums: 
Rosetta 3 - Applications

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