RosettaCommons - PyRosetta

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Post Situation:

Serialization for Python 3.5

Getmo — Fri, 31 May 2024 19:36:43 +0000

I am working with a GitHub repo (Link) that creates a pipeline for the Rocklin et al. 2017, Science metrics. The provided environment yml file specifies python 3.5 while the code imports pyrosetta.distributed libraries. I've looked through the archive release versions of PyRosetta but did not see a serialization/distributed build for Python 3.5. I've tried running the code with the available 3.5 build but get the following error code:

"CRITICAL:root:Exception while running score_designs.score_pdb_file: __cereal_getstate__ requires pyrosetta '--serialization' build."

Is there an internal or old version of PyRosetta that supports serialization for Python 3.5?

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Post Situation:

Scoring function for disordered peptide ddG calculations?

austin.weigle.usda — Tue, 28 May 2024 21:52:28 +0000

I am looking to do a ddG analysis on some peptide structures that I have developed through simulation. Previously, I have used pyrosetta for performing ddG analyses on membrane proteins. In that case, I was able to use the franklin_2019 weights as my scoring function.

Poking around, I have seen that there are a good number of weights files listed as:
/PATH/pyrosetta/lib/python3.9/site-packages/pyrosetta/database/scoring/weights/*.wts

I know from my experience that there is a function specific for membrane proteins, and that there is something like a default scoring function in REF2015 (https://www.rosettacommons.org/docs/latest/rosetta_basics/scoring/score-types). Is there any documentation to point out specific scoring functions for different applications, including disordered proteins or peptides?

Thanks,

Austin Weigle

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Post Situation:

Unable to get non-commercial license to get username/password

David123 — Fri, 17 May 2024 22:39:02 +0000

Hi team,

As noted in the steps to get non commercial license, there is a license form people can fill up to register for username/password to use Pyrosetta. Seems the form is unable to find.

Thanks for assistance.

david

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Post Situation:

Segmentation fault encountered using Interface

WenyuanW — Tue, 02 Apr 2024 20:41:58 +0000

Hi All,

I ran into repeated segmentation fault error when I tried to utilize the InterfaceAnalyzerMover to calcualte interaction energy between the two protein chains.

Here is my script:

import pyrosetta
from pyrosetta.rosetta.core.import_pose import pose_from_file
from pyrosetta.rosetta.protocols.analysis import InterfaceAnalyzerMover
import sys

def calculate_interface_energy(pdb_file, chain_target, chain_partners):
    """
    Calculates the interaction energy between one chain and a complex formed by other chains in a protein structure.
    
    Args:
        pdb_file (str): Path to the PDB file.
        chain_target (str): Identifier for the target chain.
        chain_partners (str): Identifiers for the partner chains concatenated.
        
    Returns:
        float: The interaction energy between the target chain and the partner chains.
    """

    # Load the PDB file into a Pose object
    pose = pose_from_file(pdb_file)

    # Define the complex as a combination of the target chain and partner chains
    complex_identifier = chain_target + "_" + chain_partners

    # Setup the InterfaceAnalyzerMover for the defined complex
    interface_analyzer = InterfaceAnalyzerMover()
    interface_analyzer.set_interface(complex_identifier)
    interface_analyzer.test_move(pose)  # Test the move to ensure the interface is correctly defined
    interface_analyzer.apply(pose)  # Apply the mover to the pose

    # Retrieve the computed interface energy
    interface_energy = interface_analyzer.get_interface_dG()

    return interface_energy


def main():
    # Specify your parameters
    pdb_file = sys.argv[1]
    chain_target = "A"     # The single chain you are focusing on
    chain_partners = "B"  # The other chains, treated as a combined entity

    # Initialize PyRosetta
    pyrosetta.init(extra_options="-mute all -load_PDB_components false -extra_res_fa GDP.params")

    # Calculate and print the interface energy
    interface_energy = calculate_interface_energy(pdb_file, chain_target, chain_partners)
    print(f"Interface energy between chain {chain_target} and chains {chain_partners}: {interface_energy} REU")

if __name__=="__main__":
    main()

The seg-fault error happens with either test_move, or apply (when I comment out test_move)

I can't figure out the problem because it seems to me that the error stems from the underlying C++ script.

Any suggestion is appreciated.

P.S. I cannot attach the test input I used because it is too big and this forum doesn't take the zipped version. If the error cannot be replicated with a different input, I will try to paste the PDB content as plain text in replies.

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PyRosetta - General

Post Situation:

Error about rifdocking step 15

ng98 — Mon, 22 Jan 2024 00:30:06 +0000

I am still working on the Cao protocol. And I ran into another problem. When I ran step 15: Motif extraction. I ran the following command:
/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py -in:file:silent /home/gaon/cao_protocol/protocol_test_E/input/rifdock_out/fd_output_splits/xaa.silent -ref_pdb /home/gaon/cao_protocol/protocol_test_E/input/output/rif_64_output_sca0.8_noKR.rif.gz_target_chainchanged.pdb -out_prefix mot_

It reported this error:
core.conformation.Conformation: Found disulfide between residues 117 145
length of the binder 65
basic.io.database: Database file opened: scoring/score_functions/elec_cp_reps.dat
core.scoring.elec.util: Read 40 countpair representative atoms
core.pack.dunbrack.RotamerLibrary: shapovalov_lib_fixes_enable option is true.
core.pack.dunbrack.RotamerLibrary: Binary rotamer library selected: /home/gaon/miniconda3/lib/python3.11/site-packages/pyrosetta/database/rotamer/beta_nov2016/Dunbrack10.lib.bin
core.pack.dunbrack.RotamerLibrary: Using Dunbrack library binary file '/home/gaon/miniconda3/lib/python3.11/site-packages/pyrosetta/database/rotamer/beta_nov2016/Dunbrack10.lib.bin'.
core.pack.dunbrack.RotamerLibrary: Dunbrack 2010 library took 0.169196 seconds to load from binary
total score of the complex: -442.187
Traceback (most recent call last):
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 302, in <module>
graph = get_my_interface_graph(pose)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/gaon/cao_protocol/cao_2021_protocol/motif_extraction.py", line 94, in get_my_interface_graph
edge = it.__mul__()
^^^^^^^^^^
AttributeError: 'pyrosetta.rosetta.utility.graph.EdgeListConstItera' object has no attribute '__mul__'. Did you mean: '__module__'?
Could anyone please help me solve this problem?

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Rosetta 3 - Applications

Post Situation:

Solved

Demo scripts for proteinmpnn in pyrosetta

lwhitm1 — Thu, 09 Nov 2023 01:57:57 +0000

Are there currently any demo scripts/usage examples for using proteinmpnn in pyrosetta? I've found the module documentation here:https://graylab.jhu.edu/PyRosetta.documentation/index.html

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Post Situation:

Installing pyrosetta for proteinmpnn use

lwhitm1 — Mon, 06 Nov 2023 12:38:02 +0000

What is the best way to install PyRosetta for use with Protein MPNN? I am installing it for myself on an hpc cluster (redhat linux 8) and haven't found much documentation outside of that for the general PyRosetta install.

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Design

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Post Situation:

NMR NOE based structure prediction

Pooja — Mon, 25 Sep 2023 06:39:29 +0000

Based on the NMR NOE data, I want to use PyRosetta for the structure prediction of my peptides having unnatural amino acids. I went through the manual but couldn't find much information for structure prediction based on NMR data. It would be of great help if you cite protocols, scripts or literature used to determine the structure using NMR data in PyRosetta.

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Post Situation:

Altered pLDDT scores after running FastRelax on AlphaFold Multimer output pdb files

franz72 — Sun, 17 Sep 2023 21:08:14 +0000

Hello,

I hope this message finds you well. I noticed after running FastRelax on output pdb files from AlphaFold Multimer that the pLDDT scores encoded in the B-factor fields have been altered. Is there a way to avoid this and maintain the original pLDDT scores? I have attached the code I am running below.

Thank you,

Franz

!pip install pyrosettacolabsetup
import pyrosettacolabsetup; pyrosettacolabsetup.install_pyrosetta()
import pyrosetta; pyrosetta.init('-ex1 -ex2 -use_input_sc -no_optH false -flip_HNQ -nstruct 1')
from pyrosetta import *
from pyrosetta.teaching import *
#input pdb file
pose = pose_from_pdb('unrelaxed_97.pdb')
#shorten name
fr = pyrosetta.rosetta.protocols.relax.FastRelax()
#get ref2015 scoring function
fr.set_scorefxn(get_score_function())
#flags from benchmark study Yin et al., 2022
fr.constrain_relax_to_start_coords(True)
fr.coord_constrain_sidechains(True)
fr.ramp_down_constraints(False)
#run FastRelax
fr.apply(pose)
#download relaxed structure
pose.dump_pdb('relaxed_97.pdb')

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