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When posting build/install question please specify the following information about your system and PyRosetta version, this will allow us to answer your questions more accurate and faster:

- OS type,
- OS version
- OS arch (32 or 64bit)
for example: Ubuntu Linux 10.04 32Bit or Mac OS X 10.6

- Python version
- Python arch (32 or 64bit) if different from OS

- Version of PyRosetta including SVN revision number.

Thank you!

Post Situation: 

FARFAR2 error: no edge found that contains seqpos!

Category: 
Nucleic Acids

Hi,

I am running MPI version of rna_denovo using command below using PDB, sequence, and secondary structure as inputs :

rna_denovo.mpi.linuxgccrelease -fasta rna_sequence.fasta -secstruct_general_file rna.secstruct -native 2CKY_1.pdb -align_pdb 2CKY_1.pdb -rmsd_screen 4.0 -cycles 20000 -minimize_rna true -nstruct 100 -out:file:silent FARFAR2_native_2CKY_1.out -use_legacy_job_distributor

However, this job is failed with no edge error as mentioned in ROSETTA_CRASH.log:

###################################

Post Situation: 

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: 

Error concerning PhenixInterface upon running rosetta.run_tests

Category: 
Compilation

I have successully compiled rosetta 2019.47.61047_bundle using 'rosetta.build_phenix_interface' command on a fedora 40 pc with gcc-12.3.0.

When I run 'rosetta.run_tests' I get the following error that apparently concerns PhenixInterface.

The same error occurs even with the most recent rosetta version on the website.

Any hint?

 

##############################################################################################################
#
# Rosetta crash log. 
#

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: 

Abnormal output of ScoreCutoffFilter

Category: 
Scoring

Hi everyone!

The output of `ScoreCuoffFilter` looks like this:
ResResE Res1 Res2 fa_atr fa_rep fa_sol fa_intra_r fa_intra_s lk_ball_wt fa_elec pro_close hbond_sr_b hbond_lr_b hbond_bb_s hbond_sc dslf_fa13 omega fa_dun p_aa_pp yhh_planar ref rama_prepr total
ResResE 83_6531 72_6532 -1.663 0.129 1.501 0.000 0.000 -0.424 0.258 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.198
....

Post Situation: 

Error about using BuildDeNovoBackboneMover

Category: 
Design

Hi! I am sorry for asking about the segementation fault problems because this be caused by many things. It is the first time I wrote a Rosetta scripts and I really stuck on the script.

I tried to use BuildDeNovoBackboneMover to generate backbones based on the antibody structure I got, I wrote the xml file but it shows:

[FILE]: SIGSEGV
[LINE]: 11
[START_MESSAGE]

Segmentation Fault

[END_MESSAGE]
[END_CRASH_REPORT]

This is my XML file:

Post Situation: 

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