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How can I automate mutations with PyRosetta or other Rosetta software?

Category: 
PyRosetta

I need to create mutant peptides with Rosetta to use in Virtual Screening, the mutations need to be kinda ''random'' (not chosen directly by me) and, if possible, following an evolutionary bias (genetic algorithm). I'm really new at protein modelling and I have only used AlphaFold. Rosetta has many ways to use, and I'm kinda lost, should I use Rosetta Scripts or PyRosetta? Can I do this with both? I haven't found any tutorial that explains how to create mutant peptides following a genetic algorithm with rosetta :(  I don't know where to start.

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Ab initio peptide design to use as ligands in docking

Category: 
PyRosetta

I need to create peptides to use them as flexible ligands in docking (DockThor platform). I'm new at pyRosetta so I've only seen 1 tutorial until now. I'm using the following code

import pyrosetta
from pyrosetta import *
from pyrosetta.toolbox import *
init()

peptide_sequence = 'insert peptide sequence'
pose = pose_from_sequence(peptide_sequence)

scorefxn = get_fa_scorefxn()

# define variavel score before relax
score_before_relax = scorefxn(pose)

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Different results FastRelax pyrosetta vs rosetta_scripts

Category: 
PyRosetta

Hi everyone,

I want to relax a designed disulfide bond with FastRelax, but when I try to do it in Pyrosetta it seems like it gets no optimization at all. However, when I try FastRelax in rosetta scripts I get a good geometry. Could you please help me identify what I am missing in my Pyrosetta code?

Thank you!

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Challenge with applying AntibodyCDRGrafter method and MinMover method

Category: 
PyRosetta

I've been trying to trial designing antibody CDRs. Thus far I haven't had much luck applying standard methods. I've converted my antibody to AHO scheme with PyIgClassify and applied the cleanATOM method, however, I am still running into the following error prompt. Any recommendations on how to resolve this, would be great.

I've applied the AntibodyInfo method and am able to print the antibody with the sequences of each CDR, so I don't think the first portion about start and end not being contained is correct.

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How to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å).

Category: 
PyRosetta

Hi

I am a beginner in pyroseta and now need to use pyrosetta to generate decoys of RNA with different RMSDs (e.g. 1Å, 5Å, 10Å), I checked the manual but it is still not clear, can you give me some guidance, thank you!

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Problem importing AlphaFold PDB

Category: 
PyRosetta

I have tried to import a PDB that came from an AlphaFold Docking run. I have repaired it using the PRAS server to add the OXT lines (file attached) but it still won't import. Here is the script for import followed by the first lines of the results with the error messge "discarding 4 atoms at position 1 in...".

 

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Installing PyRosetta on Jupyterlab notebook (i.e. not colab)

Category: 
PyRosetta

Hi Rosetta team.

I want to install PyRosetta on Jupyterlab notebook (i.e. not colab).

More specifically, the Jupyterlab notebook was spun up from a virtual machine (VM) on the Google Cloud Platform (GCP).

I tried to use ordinary installation commands from colab notebooks, that were

!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init()

but didn't work, giving 

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How to resolve the error about pyrosetta.distributed

Category: 
PyRosetta

Hello. I'm getting a lot of help from looking at the questions and answers here.

I'm learning it by running it one by one through pyrosetta notebook.

distributed_overview.ipynb

It says pyrosetta is not recognized when running in the conda environment with the above file, is there any way?

Also, the pyrosetta.distributed environment is not working well, so do you have a URL or guide to refer to?

Thank you in advance for your reply.

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%time results = list(xml_obj(pose_obj)) error

Category: 
PyRosetta

08.02-Ligand-Docking-pyrosetta.distributed.ipynb

When I ran the following syntax in this file, an error came out and it did not proceed.

if not os.getenv("DEBUG"):

    %time results = list(xml_obj(pose_obj))

I also set up Conda on Google Collabor
There is an error, do you know how to solve it?

The results of the implementation were as follows

 

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