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

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Thank you!

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: 

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

Post Situation: 

Error in snugdock application

Category: 
Docking

 

 Hi all

 Recently  I;m involved in antibody related project

 While I'm running snugdock application with my antibody( H chain: Lchain) and antigen complex

 I got following error :

 Can't find residue type 'VRT' in type set of mode fa_standard

 In my PDB , only standard amino acid residues are there.

 and I think VRT means something like virtual related object.

 I don't know why this kind of error occur

 Attached file is my pdb file with this error

Post Situation: 

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