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Segmentation fault (core dumped) error when importing pyrosetta with Tensorflow

Category: 
PyRosetta

Hi my workflow involves importing pyrosetta and tensorflow together in a single python script. And whenever I import both modules and run the program, I'm keep getting segmentation fault (core dumped) error. Here is my code:

import tensorflow as tf
from pyrosetta import *

If I put them other way around

from pyrosetta import *
import tensorflow as tf

I get Floating point exception (core dumped)

 

Here is my system information:

OS type: Fedora Linux 38 (64 bit)

Post Situation: 

Serialization for Python 3.5

Category: 
PyRosetta

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:

Post Situation: 

Scoring function for disordered peptide ddG calculations?

Category: 
PyRosetta

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

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

Category: 
PyRosetta

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

Post Situation: 

Error about rifdocking step 15

Category: 
PyRosetta

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_

Post Situation: 

Installing pyrosetta for proteinmpnn use

Category: 
Design
PyRosetta

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.


 

Post Situation: 

NMR NOE based structure prediction

Category: 
PyRosetta

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.

Post Situation: 

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

Category: 
PyRosetta

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

Post Situation: 

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